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Sample records for metagenomics terrestrial ecology

  1. Towards tera terra: Terabase sequencing of terrestrial metagenomics

    SciTech Connect (OSTI)

    Jansson, J.

    2011-06-15

    Microbial ecologists are taking a metagenomics approach to analyze complex and diverse soil microbial communities.

  2. Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics

    SciTech Connect (OSTI)

    Hua, Zheng-Shuang; Han, Yu-Jiao; Chen, Lin-Xing; Liu, Jun; Hu, Min; Li, Sheng-Jin; Kuang, Jia-Liang; Chain, Patrick SG; Huang, Li-Nan; Shu, Wen-Sheng

    2014-11-07

    Here we report that high-throughput sequencing is expanding our knowledge of microbial diversity in the environment. Still, understanding the metabolic potentials and ecological roles of rare and uncultured microbes in natural communities remains a major challenge. To this end, we applied a ‘divide and conquer’ strategy that partitioned a massive metagenomic data set (>100 Gbp) into subsets based on K-mer frequency in sequence assembly to a low-diversity acid mine drainage (AMD) microbial community and, by integrating with an additional metatranscriptomic assembly, successfully obtained 11 draft genomes most of which represent yet uncultured and/or rare taxa (relative abundance <1%). We report the first genome of a naturally occurring Ferrovum population (relative abundance >90%) and its metabolic potentials and gene expression profile, providing initial molecular insights into the ecological role of these lesser known, but potentially important, microorganisms in the AMD environment. Gene transcriptional analysis of the active taxa revealed major metabolic capabilities executed in situ, including carbon- and nitrogen-related metabolisms associated with syntrophic interactions, iron and sulfur oxidation, which are key in energy conservation and AMD generation, and the mechanisms of adaptation and response to the environmental stresses (heavy metals, low pH and oxidative stress). Remarkably, nitrogen fixation and sulfur oxidation were performed by the rare taxa, indicating their critical roles in the overall functioning and assembly of the AMD community. Finally, our study demonstrates the potential of the ‘divide and conquer’ strategy in high-throughput sequencing data assembly for genome reconstruction and functional partitioning analysis of both dominant and rare species in natural microbial assemblages.

  3. Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Hua, Zheng-Shuang; Han, Yu-Jiao; Chen, Lin-Xing; Liu, Jun; Hu, Min; Li, Sheng-Jin; Kuang, Jia-Liang; Chain, Patrick SG; Huang, Li-Nan; Shu, Wen-Sheng

    2014-11-07

    Here we report that high-throughput sequencing is expanding our knowledge of microbial diversity in the environment. Still, understanding the metabolic potentials and ecological roles of rare and uncultured microbes in natural communities remains a major challenge. To this end, we applied a ‘divide and conquer’ strategy that partitioned a massive metagenomic data set (>100 Gbp) into subsets based on K-mer frequency in sequence assembly to a low-diversity acid mine drainage (AMD) microbial community and, by integrating with an additional metatranscriptomic assembly, successfully obtained 11 draft genomes most of which represent yet uncultured and/or rare taxa (relative abundance <1%). We reportmore » the first genome of a naturally occurring Ferrovum population (relative abundance >90%) and its metabolic potentials and gene expression profile, providing initial molecular insights into the ecological role of these lesser known, but potentially important, microorganisms in the AMD environment. Gene transcriptional analysis of the active taxa revealed major metabolic capabilities executed in situ, including carbon- and nitrogen-related metabolisms associated with syntrophic interactions, iron and sulfur oxidation, which are key in energy conservation and AMD generation, and the mechanisms of adaptation and response to the environmental stresses (heavy metals, low pH and oxidative stress). Remarkably, nitrogen fixation and sulfur oxidation were performed by the rare taxa, indicating their critical roles in the overall functioning and assembly of the AMD community. Finally, our study demonstrates the potential of the ‘divide and conquer’ strategy in high-throughput sequencing data assembly for genome reconstruction and functional partitioning analysis of both dominant and rare species in natural microbial assemblages.« less

  4. Metagenomic Insights into Evolution of a Heavy Metal-Contaminated...

    Office of Scientific and Technical Information (OSTI)

    exposure to high concentrations of heavy metals, nitric acid and organic solvents (;;50 ... metagenomics; microbial ecology; bioremediation Word Cloud More Like This Full Text ...

  5. Livermore Metagenomics Analysis Toolkit

    Energy Science and Technology Software Center (OSTI)

    2012-10-01

    LMAT is designed to take as input a collection of raw metagenomic sequencer reads, and search each read against a reference genome database and assign a taxonomic label and confidence value to each read and report a summary of the predicted taxonomic contents of the metagenomic sample.

  6. Ecological

    Office of Legacy Management (LM)

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  7. Evaluate and characterize mechanisms controlling transport, fate, and effects of army smokes in the aerosol wind tunnel: Transport, transformations, fate, and terrestrial ecological effects of hexachloroethane obscurant smokes

    SciTech Connect (OSTI)

    Cataldo, D.A.; Ligotke, M.W.; Bolton, H. Jr.; Fellows, R.J.; Van Voris, P.; McVeety, B.D.; Li, Shu-mei W.; McFadden, K.M.

    1989-09-01

    The terrestrial transport, chemical fate, and ecological effects of hexachloroethane (HC) smoke were evaluated under controlled wind tunnel conditions. The primary objectives of this research program are to characterize and assess the impacts of smoke and obscurants on: (1) natural vegetation characteristic of US Army training sites in the United States; (2) physical and chemical properties of soils representative of these training sites; and (3) soil microbiological and invertebrate communities. Impacts and dose/responses were evaluated based on exposure scenarios, including exposure duration, exposure rate, and sequential cumulative dosing. Key to understanding the environmental impacts of HC smoke/obscurants is establishing the importance of environmental parameters such as relative humidity and wind speed on airborne aerosol characteristics and deposition to receptor surfaces. Direct and indirect biotic effects were evaluated using five plant species and two soil types. HC aerosols were generated in a controlled atmosphere wind tunnel by combustion of hexachloroethane mixtures prepared to simulate normal pot burn rates and conditions. The aerosol was characterized and used to expose plant, soil, and other test systems. Particle sizes of airborne HC ranged from 1.3 to 2.1 {mu}m mass median aerodynamic diameter (MMAD), and particle size was affected by relative humidity over a range of 20% to 85%. Air concentrations employed ranged from 130 to 680 mg/m{sup 3}, depending on exposure scenario. Chlorocarbon concentrations within smokes, deposition rates for plant and soil surfaces, and persistence were determined. The fate of principal inorganic species (Zn, Al, and Cl) in a range of soils was assessed.

  8. Recovering complete and draft population genomes from metagenome datasets

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Sangwan, Naseer; Xia, Fangfang; Gilbert, Jack A.

    2016-03-08

    Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture microorganisms. Here, we provide a synthesis of available methods to bin metagenomic contigs into species-level groups and highlight how genetic diversity, sequencing depth, and coverage influence binning success. Despite the computational cost on application to deeply sequenced complex metagenomes (e.g., soil), covarying patterns of contig coverage across multiple datasets significantly improves the binning process. We also discuss and compare current genome validation methods and reveal how these methods tackle the problem ofmore » chimeric genome bins i.e., sequences from multiple species. Finally, we explore how population genome assembly can be used to uncover biogeographic trends and to characterize the effect of in situ functional constraints on the genome-wide evolution.« less

  9. High-resolution metagenomics targets major functional types in complex microbial communities

    SciTech Connect (OSTI)

    Kalyuzhnaya, Marina G.; Lapidus, Alla; Ivanova, Natalia; Copeland, Alex C.; McHardy, Alice C.; Szeto, Ernest; Salamov, Asaf; Grigoriev, Igor V.; Suciu, Dominic; Levine, Samuel R.; Markowitz, Victor M.; Rigoutsos, Isidore; Tringe, Susannah G.; Bruce, David C.; Richardson, Paul M.; Lidstrom, Mary E.; Chistoserdova, Ludmila

    2009-08-01

    Most microbes in the biosphere remain uncultured and unknown. Whole genome shotgun (WGS) sequencing of environmental DNA (metagenomics) allows glimpses into genetic and metabolic potentials of natural microbial communities. However, in communities of high complexity metagenomics fail to link specific microbes to specific ecological functions. To overcome this limitation, we selectively targeted populations involved in oxidizing single-carbon (C{sub 1}) compounds in Lake Washington (Seattle, USA) by labeling their DNA via stable isotope probing (SIP), followed by WGS sequencing. Metagenome analysis demonstrated specific sequence enrichments in response to different C{sub 1} substrates, highlighting ecological roles of individual phylotypes. We further demonstrated the utility of our approach by extracting a nearly complete genome of a novel methylotroph Methylotenera mobilis, reconstructing its metabolism and conducting genome-wide analyses. This approach allowing high-resolution genomic analysis of ecologically relevant species has the potential to be applied to a wide variety of ecosystems.

  10. de novo Metagenomic Assembly (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Koren, Sergey [University of Maryland

    2013-01-22

    University of Maryland's Sergey Koren on "denovo Metagenomic Assembly" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  11. Challenges and opportunities in understanding microbial communities with metagenome assembly (accompanied by IPython Notebook tutorial)

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Howe, Adina; Chain, Patrick S. G.

    2015-07-09

    Metagenomic investigations hold great promise for informing the genetics, physiology, and ecology of environmental microorganisms. Current challenges for metagenomic analysis are related to our ability to connect the dots between sequencing reads, their population of origin, and their encoding functions. Assembly-based methods reduce dataset size by extending overlapping reads into larger contiguous sequences (contigs), providing contextual information for genetic sequences that does not rely on existing references. These methods, however, tend to be computationally intensive and are again challenged by sequencing errors as well as by genomic repeats. While numerous tools have been developed based on these methodological concepts, theymore » present confounding choices and training requirements to metagenomic investigators. To help with accessibility to assembly tools, this review also includes an IPython Notebook metagenomic assembly tutorial. This tutorial has instructions for execution any operating system using Amazon Elastic Cloud Compute and guides users through downloading, assembly, and mapping reads to contigs of a mock microbiome metagenome. Despite its challenges, metagenomic analysis has already revealed novel insights into many environments on Earth. As software, training, and data continue to emerge, metagenomic data access and its discoveries will to grow.« less

  12. Challenges and opportunities in understanding microbial communities with metagenome assembly (accompanied by IPython Notebook tutorial)

    SciTech Connect (OSTI)

    Howe, Adina; Chain, Patrick S. G.

    2015-07-09

    Metagenomic investigations hold great promise for informing the genetics, physiology, and ecology of environmental microorganisms. Current challenges for metagenomic analysis are related to our ability to connect the dots between sequencing reads, their population of origin, and their encoding functions. Assembly-based methods reduce dataset size by extending overlapping reads into larger contiguous sequences (contigs), providing contextual information for genetic sequences that does not rely on existing references. These methods, however, tend to be computationally intensive and are again challenged by sequencing errors as well as by genomic repeats. While numerous tools have been developed based on these methodological concepts, they present confounding choices and training requirements to metagenomic investigators. To help with accessibility to assembly tools, this review also includes an IPython Notebook metagenomic assembly tutorial. This tutorial has instructions for execution any operating system using Amazon Elastic Cloud Compute and guides users through downloading, assembly, and mapping reads to contigs of a mock microbiome metagenome. Despite its challenges, metagenomic analysis has already revealed novel insights into many environments on Earth. As software, training, and data continue to emerge, metagenomic data access and its discoveries will to grow.

  13. Terrestrial sequestration

    ScienceCinema (OSTI)

    Charlie Byrer

    2010-01-08

    Terrestrial sequestration is the enhancement of CO2 uptake by plants that grow on land and in freshwater and, importantly, the enhancement of carbon storage in soils where it may remain more permanently stored. Terrestrial sequestration provides an opportunity for low-cost CO2 emissions offsets.

  14. Terrestrial sequestration

    SciTech Connect (OSTI)

    Charlie Byrer

    2008-03-10

    Terrestrial sequestration is the enhancement of CO2 uptake by plants that grow on land and in freshwater and, importantly, the enhancement of carbon storage in soils where it may remain more permanently stored. Terrestrial sequestration provides an opportunity for low-cost CO2 emissions offsets.

  15. Evaluate and characterize mechanisms controlling transport, fate and effects of army smokes in an aerosol wind tunnel: Transport, transformations, fate and terrestrial ecological effects of fog oil obscurant smokes: Final report

    SciTech Connect (OSTI)

    Cataldo, D.A.; Van Voris, P.; Ligotke, M.W.; Fellows, R.J.; McVeety, B.D.; Li, Shu-mei W.; Bolton, H. Jr.; Fredrickson, J.K.

    1989-01-01

    The terrestrial transport, chemical fate, and ecological effects of fog oil (FO) smoke obscurants were evaluated under controlled wind tunnel conditions. The primary objectives of this research program are to characterize and assess the impacts of smoke and obscurants on: (1) natural vegetation characteristic of US Army training sites in the United States; (2) physical and chemical properties of soils representative of these training sites; and (3) soil microbiological and invertebrate communities. Impacts and dose/responses were evaluated based on an exposure scenario, including exposure duration, exposure rate, and sequential cumulative dosing. Key to understanding the environmental impacts of fog oil smoke/obscurants is establishing the importance of environmental parameters, such as relative humidity and wind speed on airborne aerosol characteristics and deposition to receptor surfaces. Direct and indirect biotic effects were evaluated using five plant species and three soil types. 29 refs., 35 figs., 32 tabs.

  16. Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes

    SciTech Connect (OSTI)

    Aziz, Ramy K.; Dwivedi, Bhakti; Akhter, Sajia; Breitbart, Mya; Edwards, Robert A.

    2015-05-08

    Phages are the most abundant biological entities on Earth and play major ecological roles, yet the current sequenced phage genomes do not adequately represent their diversity, and little is known about the abundance and distribution of these sequenced genomes in nature. Although the study of phage ecology has benefited tremendously from the emergence of metagenomic sequencing, a systematic survey of phage genes and genomes in various ecosystems is still lacking, and fundamental questions about phage biology, lifestyle, and ecology remain unanswered. To address these questions and improve comparative analysis of phages in different metagenomes, we screened a core set of publicly available metagenomic samples for sequences related to completely sequenced phages using the web tool, Phage Eco-Locator. We then adopted and deployed an array of mathematical and statistical metrics for a multidimensional estimation of the abundance and distribution of phage genes and genomes in various ecosystems. Experiments using those metrics individually showed their usefulness in emphasizing the pervasive, yet uneven, distribution of known phage sequences in environmental metagenomes. Using these metrics in combination allowed us to resolve phage genomes into clusters that correlated with their genotypes and taxonomic classes as well as their ecological properties. By adding this set of metrics to current metaviromic analysis pipelines, where they can provide insight regarding phage mosaicism, habitat specificity, and evolution.

  17. Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Aziz, Ramy K.; Dwivedi, Bhakti; Akhter, Sajia; Breitbart, Mya; Edwards, Robert A.

    2015-05-08

    Phages are the most abundant biological entities on Earth and play major ecological roles, yet the current sequenced phage genomes do not adequately represent their diversity, and little is known about the abundance and distribution of these sequenced genomes in nature. Although the study of phage ecology has benefited tremendously from the emergence of metagenomic sequencing, a systematic survey of phage genes and genomes in various ecosystems is still lacking, and fundamental questions about phage biology, lifestyle, and ecology remain unanswered. To address these questions and improve comparative analysis of phages in different metagenomes, we screened a core set ofmore » publicly available metagenomic samples for sequences related to completely sequenced phages using the web tool, Phage Eco-Locator. We then adopted and deployed an array of mathematical and statistical metrics for a multidimensional estimation of the abundance and distribution of phage genes and genomes in various ecosystems. Experiments using those metrics individually showed their usefulness in emphasizing the pervasive, yet uneven, distribution of known phage sequences in environmental metagenomes. Using these metrics in combination allowed us to resolve phage genomes into clusters that correlated with their genotypes and taxonomic classes as well as their ecological properties. By adding this set of metrics to current metaviromic analysis pipelines, where they can provide insight regarding phage mosaicism, habitat specificity, and evolution.« less

  18. Comparative Metagenomics of Freshwater Microbial Communities

    SciTech Connect (OSTI)

    Hemme, Chris; Deng, Ye; Tu, Qichao; Fields, Matthew; Gentry, Terry; Wu, Liyou; Tringe, Susannah; Watson, David; He, Zhili; Hazen, Terry; Tiedje, James; Rubin, Eddy; Zhou, Jizhong

    2010-05-17

    Previous analyses of a microbial metagenome from uranium and nitric-acid contaminated groundwater (FW106) showed significant environmental effects resulting from the rapid introduction of multiple contaminants. Effects include a massive loss of species and strain biodiversity, accumulation of toxin resistant genes in the metagenome and lateral transfer of toxin resistance genes between community members. To better understand these results in an ecological context, a second metagenome from a pristine groundwater system located along the same geological strike was sequenced and analyzed (FW301). It is hypothesized that FW301 approximates the ancestral FW106 community based on phylogenetic profiles and common geological parameters; however, even if is not the case, the datasets still permit comparisons between healthy and stressed groundwater ecosystems. Complex carbohydrate metabolism has been almost entirely lost in the stressed ecosystem. In contrast, the pristine system encodes a wide diversity of complex carbohydrate metabolism systems, suggesting that carbon turnover is very rapid and less leaky in the healthy groundwater system. FW301 encodes many (~;;160+) carbon monoxide dehydrogenase genes while FW106 encodes none. This result suggests that the community is frequently exposed to oxygen from aerated rainwater percolating into the subsurface, with a resulting high rate of carbon metabolism and CO production. When oxygen levels fall, the CO then serves as a major carbon source for the community. FW301 appears to be capable of CO2 fixation via the reductive carboxylase (reverse TCA) cycle and possibly acetogenesis, activities; these activities are lacking in the heterotrophic FW106 system which relies exclusively on respiration of nitrate and/or oxygen for energy production. FW301 encodes a complete set of B12 biosynthesis pathway at high abundance suggesting the use of sodium gradients for energy production in the healthy groundwater community. Overall

  19. Research | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Research Gene Odum forest sampling marked tortoise geochemical sampling quantifying radionuclide absorption collcting microbes microsatellite development R E S E A R C H A R E A S * Aquatic and terrestrial ecology * Biogeochemistry & soil science * Environmental microbiology * Herpetology * Hydrology * Molecular genetics * Physiological ecology * Conservation biology * Radiation ecology * Ecotoxicology and risk assessment * Remediation and restoration SREL scientists pursue a wide variety of

  20. Metagenome Assembly at the DOE JGI (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Chain, Patrick [DOE JGI at LANL

    2013-01-22

    Patrick Chain of DOE JGI at LANL, Co-Chair of the Metagenome-specific Assembly session, on "Metagenome Assembly at the DOE JGI" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  1. Metagenomes from Argonne's MG-RAST Metagenomics Analysis Server

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    MG-RAST has a large number of datasets that researchers have deposited for public use. As of July, 2014, the number of metagenomes represented by MG-RAST numbered more than 18,500, and the number of available sequences was more than 75 million! The public can browse the collection several different ways, and researchers can login to deposit new data. Researchers have the choice of keeping a dataset private so that it is viewable only by them when logged in, or they can choose to make a dataset public at any time with a simple click of a link. MG-RAST was launched in 2007 by the Mathematics and Computer Science Division at Argonne National Laboratory (ANL). It is part of the toolkit available to the Terragenomics project, which seeks to do a comprehensive metagenomics study of U.S. soil. The Terragenomics project page is located at http://www.mcs.anl.gov/research/projects/terragenomics/.

  2. Under-detection of endospore-forming Firmicutes in metagenomic...

    Office of Scientific and Technical Information (OSTI)

    Under-detection of endospore-forming Firmicutes in metagenomic data Prev Next Title: Under-detection of endospore-forming Firmicutes in metagenomic data Microbial diversity ...

  3. Metagenomics, metatranscriptomics and single cell genomics reveal...

    Office of Scientific and Technical Information (OSTI)

    and single cell genomics reveal functional response of active Oceanospirillales to Gulf oil spill Citation Details In-Document Search Title: Metagenomics, metatranscriptomics and...

  4. Ocean Viral Metagenomics (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Rohwer, Forest

    2011-04-26

    Forest Rohwer from San Diego State University talks about "Ocean Viral Metagenomics" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

  5. Ecology, Microbial

    SciTech Connect (OSTI)

    Konopka, Allan

    2009-05-15

    Microbial ecology is a relatively young discipline within the field of microbiology. Its modern history spans just the past 60 years, and the field is defined by its emphasis on understanding the interactions of microbes with their environment, rather than their behavior under artificial laboratory conditions. Because microbes are ubiquitous, microbial ecologists study a broad diversity of habitats that range from aquatic to terrestrial to plant- or animal-associated. This has made it a challenge to identify unifying principles within the field. One approach is to recognize that although the activity of microbes in nature have effects at the macroscale, they interact with their physical, chemical and biological milieu at a scale of micrometers. At this scale, several different microbial ecosystems can be defined, based upon association with particles, the presence of environmental gradients and the continuous availability of water. Principles applicable to microbial ecology reflect not only their population ecology and physiological ecology, but also their broad versatility and quantitative importance in the biosphere as biogeochemical catalysts and capacity for rapid physiological and evolutionary responses.

  6. Ecology, Microbial

    SciTech Connect (OSTI)

    Konopka, Allan

    2009-03-19

    Microbial ecology is a relatively young discipline within the field of microbiology. Its modern history spans just the past 60 years, and the field is defined by its emphasis on understanding the interactions of microbes with their environment, rather than their behavior under artificial laboratory conditions. Because microbes are ubiquitous, microbial ecologists study a broad diversity of habitats that range from aquatic to terrestrial to plant- or animal-associated. This has made it a challenge to identify unifying principles within the field. One approach is to recognize that although the activity of microbes in nature have effects at the macroscale, they interact with their physical, chemical and biological milieu at a scale of micrometers. At this scale, several different microbial ecosystems can be defined, based upon association with particles, the presence of environmental gradients and the continuous availability of water. Principles applicable to microbial ecology reflect not only their population ecology and physiological ecology, but also their broad versatility and quantitative importance in the biosphere as biogeochemical catalysts and capacity for rapid physiological and evolutionary responses.

  7. Assembling the Marine Metagenome, One Cell at a Time

    SciTech Connect (OSTI)

    Woyke, Tanja; Xie, Gary; Copeland, Alex; Gonzalez, Jose M.; Han, Cliff; Kiss, Hajnalka; Saw, Jimmy H.; Senin, Pavel; Yang, Chi; Chatterji, Sourav; Cheng, Jan-Fang; Eisen, Jonathan A.; Sieracki, Michael E.; Stepanauskas, Ramunas

    2010-06-24

    The difficulty associated with the cultivation of most microorganisms and the complexity of natural microbial assemblages, such as marine plankton or human microbiome, hinder genome reconstruction of representative taxa using cultivation or metagenomic approaches. Here we used an alternative, single cell sequencing approach to obtain high-quality genome assemblies of two uncultured, numerically significant marine microorganisms. We employed fluorescence-activated cell sorting and multiple displacement amplification to obtain hundreds of micrograms of genomic DNA from individual, uncultured cells of two marine flavobacteria from the Gulf of Maine that were phylogenetically distant from existing cultured strains. Shotgun sequencing and genome finishing yielded 1.9 Mbp in 17 contigs and 1.5 Mbp in 21 contigs for the two flavobacteria, with estimated genome recoveries of about 91percent and 78percent, respectively. Only 0.24percent of the assembling sequences were contaminants and were removed from further analysis using rigorous quality control. In contrast to all cultured strains of marine flavobacteria, the two single cell genomes were excellent Global Ocean Sampling (GOS) metagenome fragment recruiters, demonstrating their numerical significance in the ocean. The geographic distribution of GOS recruits along the Northwest Atlantic coast coincided with ocean surface currents. Metabolic reconstruction indicated diverse potential energy sources, including biopolymer degradation, proteorhodopsin photometabolism, and hydrogen oxidation. Compared to cultured relatives, the two uncultured flavobacteria have small genome sizes, few non-coding nucleotides, and few paralogous genes, suggesting adaptations to narrow ecological niches. These features may have contributed to the abundance of the two taxa in specific regions of the ocean, and may have hindered their cultivation. We demonstrate the power of single cell DNA sequencing to generate reference genomes of uncultured

  8. Assembling The Marine Metagenome, One Cell At A Time

    SciTech Connect (OSTI)

    Xie, Gang; Han, Shunsheng; Kiss, Hajnalka; Saw, Jimmy; Senin, Pavel; Woyke, Tanja; Copeland, Alex; Gonzalez, Jose; Chatterji, Sourav; Cheng, Jan - Fang; Eisen, Jonathan A; Sieracki, Michael E; Stepanauskas, Ramunas

    2008-01-01

    The difficulty associated with the cultivation of most microorganisms and the complexity of natural microbial assemblages, such as marine plankton or human microbiome, hinder genome reconstruction of representative taxa using cultivation or metagenomic approaches. Here we used an alternative, single cell sequencing approach to obtain high-quality genome assemblies of two uncultured, numerically significant marine microorganisms. We employed fluorescence-activated cell sorting and multiple displacement amplification to obtain hundreds of micrograms of genomic DNA from individual, uncultured cells of two marine flavobacteria from the Gulf of Maine that were phylogenetically distant from existing cultured strains. Shotgun sequencing and genome finishing yielded 1.9 Mbp in 17 contigs and 1.5 Mbp in 21 contigs for the two flavobacteria, with estimated genome recoveries of about 91% and 78%, respectively. Only 0.24% of the assembling sequences were contaminants and were removed from further analysis using rigorous quality control. In contrast to all cultured strains of marine flavobacteria, the two single cell genomes were excellent Global Ocean Sampling (GOS) metagenome fragment recruiters, demonstrating their numerical significance in the ocean. The geographic distribution of GOS recruits along the Northwest Atlantic coast coincided with ocean surface currents. Metabolic reconstruction indicated diverse potential energy sources, including biopolymer degradation, proteorhodopsin photometabolism, and hydrogen oxidation. Compared to cultured relatives, the two uncultured flavobacteria have small genome sizes, few non-coding nucleotides, and few paralogous genes, suggesting adaptations to narrow ecological niches. These features may have contributed to the abundance of the two taxa in specific regions of the ocean, and may have hindered their cultivation. We demonstrate the power of single cell DNA sequencing to generate reference genomes of uncultured taxa from a complex

  9. The JGI Metagenome Program (2009 JGI User Meeting)

    ScienceCinema (OSTI)

    Tringe, Susannah Green

    2011-04-25

    Susannah Tringe discussed the DOE JGI Metagenomic Program on March 25, 2009 at the 4th Annual User Meeting.

  10. The JGI Metagenome Program (2009 JGI User Meeting)

    SciTech Connect (OSTI)

    Tringe, Susannah Green

    2009-03-25

    Susannah Tringe discussed the DOE JGI Metagenomic Program on March 25, 2009 at the 4th Annual User Meeting.

  11. A Collaborative Ecosystem Model for Metagenomics Data Preservation (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    SciTech Connect (OSTI)

    Cochrane, Guy

    2011-10-12

    EMBL-EBI's Guy Cochrane on "A Collaborative Ecosystem Model for Metagenomics Data Preservation" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  12. Marriage or Civil Unions for Single Cells and Metagenomics (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Rusch, Doug [J. Craig Venter Institute

    2013-01-22

    JCVI's Doug Rusch on "Marriage or Civil Unions for Single Cells and Metagenomes" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  13. A Collaborative Ecosystem Model for Metagenomics Data Preservation (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Cochrane, Guy [EMBL-EBI

    2013-01-22

    EMBL-EBI's Guy Cochrane on "A Collaborative Ecosystem Model for Metagenomics Data Preservation" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  14. Meta-IDBA: A de novo Assembler for Metagenomic Data (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Chin, Francis [University of Hong Kong

    2013-01-22

    University of Hong Kong's Francis Chin on "Meta-­IDBA: A de novo Assembler for Metagenomic Data" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  15. Metagenome Data Integration, Data Storage, and Retrieval (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    White, Owen [University of Maryland

    2013-01-22

    University of Maryland's Owen White on "Metagenome Data Integration, Data Storage and Retrieval" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  16. Terrestrial Climate Change and Ecosystem Response Recorded in Lake

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Sediments and Related Deposits terrestrial climate change Terrestrial Climate Change and Ecosystem Response Recorded in Lake Sediments and Related Deposits Reconstruction of past terrestrial climate and ecosystem response relies on archives that incorporate and preserve information about changes in temperature, precipitation, nutrients, vegetation, fire history, etc. The resolution and length of such paleoclimate/ecological records is dependent on the type of archive. Although much

  17. Metazen – metadata capture for metagenomes

    SciTech Connect (OSTI)

    Bischof, Jared; Harrison, Travis; Paczian, Tobias; Glass, Elizabeth; Wilke, Andreas; Meyer, Folker

    2014-12-08

    Background: As the impact and prevalence of large-scale metagenomic surveys grow, so does the acute need for more complete and standards compliant metadata. Metadata (data describing data) provides an essential complement to experimental data, helping to answer questions about its source, mode of collection, and reliability. Metadata collection and interpretation have become vital to the genomics and metagenomics communities, but considerable challenges remain, including exchange, curation, and distribution. Currently, tools are available for capturing basic field metadata during sampling, and for storing, updating and viewing it. These tools are not specifically designed for metagenomic surveys; in particular, they lack the appropriate metadata collection templates, a centralized storage repository, and a unique ID linking system that can be used to easily port complete and compatible metagenomic metadata into widely used assembly and sequence analysis tools. Results: Metazen was developed as a comprehensive framework designed to enable metadata capture for metagenomic sequencing projects. Specifically, Metazen provides a rapid, easy-to-use portal to encourage early deposition of project and sample metadata. Conclusion: Metazen is an interactive tool that aids users in recording their metadata in a complete and valid format. A defined set of mandatory fields captures vital information, while the option to add fields provides flexibility.

  18. Metazen – metadata capture for metagenomes

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Bischof, Jared; Harrison, Travis; Paczian, Tobias; Glass, Elizabeth; Wilke, Andreas; Meyer, Folker

    2014-12-08

    Background: As the impact and prevalence of large-scale metagenomic surveys grow, so does the acute need for more complete and standards compliant metadata. Metadata (data describing data) provides an essential complement to experimental data, helping to answer questions about its source, mode of collection, and reliability. Metadata collection and interpretation have become vital to the genomics and metagenomics communities, but considerable challenges remain, including exchange, curation, and distribution. Currently, tools are available for capturing basic field metadata during sampling, and for storing, updating and viewing it. These tools are not specifically designed for metagenomic surveys; in particular, they lack themore » appropriate metadata collection templates, a centralized storage repository, and a unique ID linking system that can be used to easily port complete and compatible metagenomic metadata into widely used assembly and sequence analysis tools. Results: Metazen was developed as a comprehensive framework designed to enable metadata capture for metagenomic sequencing projects. Specifically, Metazen provides a rapid, easy-to-use portal to encourage early deposition of project and sample metadata. Conclusion: Metazen is an interactive tool that aids users in recording their metadata in a complete and valid format. A defined set of mandatory fields captures vital information, while the option to add fields provides flexibility.« less

  19. Metagenomics, metatranscriptomics and single cell genomics reveal functional response of active Oceanospirillales to Gulf oil spill

    SciTech Connect (OSTI)

    Mason, Olivia U.; Hazen, Terry C.; Borglin, Sharon; Chain, Patrick S. G.; Dubinsky, Eric A.; Fortney, Julian L.; Han, James; Holman, Hoi-Ying N.; Hultman, Jenni; Lamendella, Regina; Mackelprang, Rachel; Malfatti, Stephanie; Tom, Lauren M.; Tringe, Susannah G.; Woyke, Tanja; Zhou, Jizhong; Rubin, Edward M.; Jansson, Janet K.

    2012-06-12

    The Deepwater Horizon oil spill in the Gulf of Mexico resulted in a deep-sea hydrocarbon plume that caused a shift in the indigenous microbial community composition with unknown ecological consequences. Early in the spill history, a bloom of uncultured, thus uncharacterized, members of the Oceanospirillales was previously detected, but their role in oil disposition was unknown. Here our aim was to determine the functional role of the Oceanospirillales and other active members of the indigenous microbial community using deep sequencing of community DNA and RNA, as well as single-cell genomics. Shotgun metagenomic and metatranscriptomic sequencing revealed that genes for motility, chemotaxis and aliphatic hydrocarbon degradation were significantly enriched and expressed in the hydrocarbon plume samples compared with uncontaminated seawater collected from plume depth. In contrast, although genes coding for degradation of more recalcitrant compounds, such as benzene, toluene, ethylbenzene, total xylenes and polycyclic aromatic hydrocarbons, were identified in the metagenomes, they were expressed at low levels, or not at all based on analysis of the metatranscriptomes. Isolation and sequencing of two Oceanospirillales single cells revealed that both cells possessed genes coding for n-alkane and cycloalkane degradation. Specifically, the near-complete pathway for cyclohexane oxidation in the Oceanospirillales single cells was elucidated and supported by both metagenome and metatranscriptome data. The draft genome also included genes for chemotaxis, motility and nutrient acquisition strategies that were also identified in the metagenomes and metatranscriptomes. These data point towards a rapid response of members of the Oceanospirillales to aliphatic hydrocarbons in the deep sea.

  20. Platform-Independent Method for Detecting Errors in Metagenomic...

    Office of Scientific and Technical Information (OSTI)

    Title: Platform-Independent Method for Detecting Errors in Metagenomic Sequencing Data: DRISEE Authors: Keegan, K. P. ; Trimble, W. L. ; Wilkening, J. ; Wilke, A. ; Harrison, T. ; ...

  1. An Experimental Metagenome Data Management and AnalysisSystem

    SciTech Connect (OSTI)

    Markowitz, Victor M.; Korzeniewski, Frank; Palaniappan, Krishna; Szeto, Ernest; Ivanova, Natalia N.; Kyrpides, Nikos C.; Hugenholtz, Philip

    2006-03-01

    The application of shotgun sequencing to environmental samples has revealed a new universe of microbial community genomes (metagenomes) involving previously uncultured organisms. Metagenome analysis, which is expected to provide a comprehensive picture of the gene functions and metabolic capacity of microbial community, needs to be conducted in the context of a comprehensive data management and analysis system. We present in this paper IMG/M, an experimental metagenome data management and analysis system that is based on the Integrated Microbial Genomes (IMG) system. IMG/M provides tools and viewers for analyzing both metagenomes and isolate genomes individually or in a comparative context.

  2. METAGENOMICS-ENABLED UNDERSTANDING OF THE FUNCTIONS AND ACTIVITIES...

    Office of Scientific and Technical Information (OSTI)

    Technical Report: METAGENOMICS-ENABLED UNDERSTANDING OF THE FUNCTIONS AND ACTIVITIES OF MICROBIAL COMMUNITIES AT ERSP FIELD RESEARCH Citation Details In-Document Search Title: ...

  3. Global metagenomic survey reveals a new bacterial candidate phylum...

    Office of Scientific and Technical Information (OSTI)

    This lineage had remained hidden as a taxonomic 'blind spot' because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic ...

  4. FOAM (Functional Ontology Assignments for Metagenomes): A Hidden...

    Office of Scientific and Technical Information (OSTI)

    Ontology Assignments for Metagenomes): A Hidden Markov Model (HMM) database with environmental focus Citation Details In-Document Search Title: FOAM (Functional Ontology...

  5. High-throughput metagenomic technologies for complex microbial...

    Office of Scientific and Technical Information (OSTI)

    formats Prev Next Title: High-throughput metagenomic technologies for complex microbial community analysis. Open and closed formats You are accessing a document from...

  6. Exploiting HPC Platforms for Metagenomics: Challenges and Opportunities (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Canon, Shane [LBNL

    2013-01-22

    DOE JGI's Zhong Wang, chair of the High-performance Computing session, gives a brief introduction before Berkeley Lab's Shane Canon talks about "Exploiting HPC Platforms for Metagenomics: Challenges and Opportunities" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  7. SRS ECOLOGY ENVIRONMENTAL INFORMATION DOCUMENT

    SciTech Connect (OSTI)

    Wike, L; Doug Martin, D; Eric Nelson, E; Nancy Halverson, N; John Mayer, J; Michael Paller, M; Rodney Riley, R; Michael Serrato, M

    2006-03-01

    The SRS Ecology Environmental Information Document (EEID) provides a source of information on the ecology of Savannah River Site (SRS). The SRS is a U.S. Department of Energy (DOE)--owned property on the upper Atlantic Coastal Plain of South Carolina, centered approximately 40 kilometers (25 miles) southeast of Augusta, Georgia. The entire site was designated a National Environmental Research Park in 1972 by the Atomic Energy Commission, the predecessor of DOE. This document summarizes and synthesizes ecological research and monitoring conducted on the three main types of ecosystems found at SRS: terrestrial, wetland and aquatic. It also summarizes the available information on the threatened and endangered species found on the Savannah River Site. SRS is located along the Savannah River and encompasses an area of 80,267 hectares (310 square miles) in three South Carolina counties. It contains diverse habitats, flora, and fauna. Habitats include upland terrestrial areas, wetlands, streams, reservoirs, and the adjacent Savannah River. These diverse habitats support a variety of plants and animals, including many commercially or recreationally valuable species and several rare, threatened, or endangered species. Soils are the basic terrestrial resource, influencing the development of terrestrial biological communities. Many different soils exist on the SRS, from hydric to well-drained, and from sand to clay. In general, SRS soils are predominantly well-drained loamy sands.

  8. MetaVelvet: An Extension of Velvet Assembler to de novo Metagenome Assembly from Short Sequence Reads (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Sakakibara, Yasumbumi [Keio University

    2013-01-22

    Keio University's Yasumbumi Sakakibara on "MetaVelvet: An Extension of Velvet Assembler to de novo Metagenome Assembly from Short Sequence Reads" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  9. Evaluation of the Cow Rumen Metagenome; Assembly by Single Copy Gene Analysis and Single Cell Genome Assemblies(Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Sczyrba, Alex [DOE JGI

    2013-01-22

    DOE JGI's Alex Sczyrba on "Evaluation of the Cow Rumen Metagenome" and "Assembly by Single Copy Gene Analysis and Single Cell Genome Assemblies" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  10. Effective Analysis of NGS Metagenomic Data with Ultra-Fast Clustering Algorithms (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Li, Weizhong [San Diego Supercomputer Center

    2013-01-22

    San Diego Supercomputer Center's Weizhong Li on "Effective Analysis of NGS Metagenomic Data with Ultra-fast Clustering Algorithms" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  11. Using Soir Lucene for Large-Scale Metagenomics Data Retrieval and Analysis (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Goll, Johannes [JCVI

    2013-01-22

    JCVI's Johannes Goll on "Using Solr/Lucene for Large-Scale Metagenomics Data Retrieval and Analysis" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  12. Fizzy. Feature subset selection for metagenomics

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Ditzler, Gregory; Morrison, J. Calvin; Lan, Yemin; Rosen, Gail L.

    2015-11-04

    Background: Some of the current software tools for comparative metagenomics provide ecologists with the ability to investigate and explore bacterial communities using α– & β–diversity. Feature subset selection – a sub-field of machine learning – can also provide a unique insight into the differences between metagenomic or 16S phenotypes. In particular, feature subset selection methods can obtain the operational taxonomic units (OTUs), or functional features, that have a high-level of influence on the condition being studied. For example, in a previous study we have used information-theoretic feature selection to understand the differences between protein family abundances that best discriminate betweenmore » age groups in the human gut microbiome. Results: We have developed a new Python command line tool, which is compatible with the widely adopted BIOM format, for microbial ecologists that implements information-theoretic subset selection methods for biological data formats. We demonstrate the software tools capabilities on publicly available datasets. Conclusions: We have made the software implementation of Fizzy available to the public under the GNU GPL license. The standalone implementation can be found at http://github.com/EESI/Fizzy.« less

  13. Fizzy. Feature subset selection for metagenomics

    SciTech Connect (OSTI)

    Ditzler, Gregory; Morrison, J. Calvin; Lan, Yemin; Rosen, Gail L.

    2015-11-04

    Background: Some of the current software tools for comparative metagenomics provide ecologists with the ability to investigate and explore bacterial communities using α– & β–diversity. Feature subset selection – a sub-field of machine learning – can also provide a unique insight into the differences between metagenomic or 16S phenotypes. In particular, feature subset selection methods can obtain the operational taxonomic units (OTUs), or functional features, that have a high-level of influence on the condition being studied. For example, in a previous study we have used information-theoretic feature selection to understand the differences between protein family abundances that best discriminate between age groups in the human gut microbiome. Results: We have developed a new Python command line tool, which is compatible with the widely adopted BIOM format, for microbial ecologists that implements information-theoretic subset selection methods for biological data formats. We demonstrate the software tools capabilities on publicly available datasets. Conclusions: We have made the software implementation of Fizzy available to the public under the GNU GPL license. The standalone implementation can be found at http://github.com/EESI/Fizzy.

  14. J Vaun McArthur | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    McArthur Faculty & Scientists SREL Home J Vaun McArthur Savannah River Ecology Laboratory P O Drawer E, Aiken, SC 29802 (803) 725-5317 office (803) 725-3309 fax mcarthur(at)srel.uga.edu My research interests focus on aquatic microbial ecology; ecological genetics of microbes; interactions between terrestrial and aquatic ecosystems; stream community metabolism; and macroinvertebrate ecology. Current research projects include: Indirect selection for antibiotic resistance in coastal oceans

  15. What is microbial community ecology?

    SciTech Connect (OSTI)

    Konopka, Allan

    2009-11-11

    The activities of complex communities of microbes affect biogeochemical transformations in natural, managed and engineered ecosystems. Meaningfully defining what constitutes a community of interacting microbial populations is not trivial, but is important for rigorous progress in the field. Important elements of research in microbial community ecology include the analysis of functional pathways for nutrient resource and energy flows, mechanistic understanding of interactions between microbial populations and their environment, and the emergent properties of the complex community. Some emergent properties mirror those analyzed by community ecologists who study plants and animals: biological diversity, functional redundancy and system stability. However, because microbes possess mechanisms for the horizontal transfer of genetic information, the metagenome may also be considered a community property.

  16. Single Cell and Metagenomic Assemblies: Biology Drives Technical Choices and Goals (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Stepanauskas, Ramunas [Bigelow Laboratory

    2013-01-22

    DOE JGI's Tanja Woyke, chair of the Single Cells and Metagenomes session, delivers an introduction, followed by Bigelow Laboratory's Ramunas Stepanauskas on "Single Cell and Metagenomic Assemblies: Biology Drives Technical Choices and Goals" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  17. Genome-wide Selective Sweeps in Natural Bacterial Populations Revealed by Time-series Metagenomics

    SciTech Connect (OSTI)

    Chan, Leong-Keat; Bendall, Matthew L.; Malfatti, Stephanie; Schwientek, Patrick; Tremblay, Julien; Schackwitz, Wendy; Martin, Joel; Pati, Amrita; Bushnell, Brian; Foster, Brian; Kang, Dongwan; Tringe, Susannah G.; Bertilsson, Stefan; Moran, Mary Ann; Shade, Ashley; Newton, Ryan J.; Stevens, Sarah; McMcahon, Katherine D.; Mamlstrom, Rex R.

    2014-05-12

    Multiple evolutionary models have been proposed to explain the formation of genetically and ecologically distinct bacterial groups. Time-series metagenomics enables direct observation of evolutionary processes in natural populations, and if applied over a sufficiently long time frame, this approach could capture events such as gene-specific or genome-wide selective sweeps. Direct observations of either process could help resolve how distinct groups form in natural microbial assemblages. Here, from a three-year metagenomic study of a freshwater lake, we explore changes in single nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in populations of Chlorobiaceae and Methylophilaceae. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied considerably among closely related, co-occurring Methylophilaceae populations. SNP allele frequencies, as well as the relative abundance of certain genes, changed dramatically over time in each population. Interestingly, SNP diversity was purged at nearly every genome position in one of the Chlorobiaceae populations over the course of three years, while at the same time multiple genes either swept through or were swept from this population. These patterns were consistent with a genome-wide selective sweep, a process predicted by the ecotype model? of diversification, but not previously observed in natural populations.

  18. Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens

    SciTech Connect (OSTI)

    Aylward, Frank O.; Burnum, Kristin E.; Scott, Jarrod J.; Suen, Garret; Tringe, Susannah G.; Adams, Sandra M.; Barry, Kerrie W.; Nicora, Carrie D.; Piehowski, Paul D.; Purvine, Samuel O.; Starrett, Gabriel J.; Goodwin, Lynne A.; Smith, Richard D.; Lipton, Mary S.; Currie, Cameron R.

    2012-09-01

    Herbivores gain access to nutrients stored in plant biomass largely by harnessing the metabolic activities of microbes. Leaf-cutter ants of the genus Atta are a hallmark example; these dominant Neotropical herbivores cultivate symbiotic fungus gardens on massive quantities of fresh plant forage. As the external digestive system of the ants, fungus gardens facilitate the production and sustenance of millions of workers in mature Atta colonies. Here we use metagenomic, and metaproteomic techniques to characterize the bacterial diversity and overall physiological potential of fungus gardens from two species of Atta. Our analysis of over 1.2 Gbp of community metagenomic sequence and three 16S pyrotag libraries reveals that, in addition to harboring the dominant fungal crop, these ecosystems contain abundant populations of Enterobacteriaceae, including the genera Enterobacter, Pantoea, Klebsiella, Citrobacter, and Escherichia. We show that these bacterial communities possess genes commonly associated with lignocellulose degradation, and likely participate in the processing of plant biomass. Additionally, we demonstrate that bacteria in these environments encode a diverse suite of biosynthetic pathways, and that they may enrich the nitrogen-poor forage of the ants with B-vitamins, amino acids, and proteins. These results are consistent with the hypothesis that fungus gardens are highly-specialized fungus-bacteria communities that efficiently convert plant material into usable energy for their ant hosts. Together with recent investigations into the microbial symbionts of vertebrates, our work underscores the importance of microbial communities to the ecology and evolution of herbivorous metazoans.

  19. Metagenomic and functional analysis of hindgut microbiota of...

    Office of Scientific and Technical Information (OSTI)

    of hindgut microbiota of a wood-feeding higher termite Citation Details In-Document Search Title: Metagenomic and functional analysis of hindgut microbiota of a wood-feeding ...

  20. An experience report : Porting the MG-RAST Rapid Metagenomics...

    Office of Scientific and Technical Information (OSTI)

    An experience report : Porting the MG-RAST Rapid Metagenomics Analysis Pipeline to the Cloud Citation Details In-Document Search Title: An experience report : Porting the MG-RAST ...

  1. Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California

    SciTech Connect (OSTI)

    Hawley, Erik R.; Piao, Hailan; Scott, Nicole M.; Malfatti, Stephanie; Pagani, Ioanna; Huntemann, Marcel; Chen, Amy; del Rio, Tijana G.; Foster, Brian; Copeland, A.; Jansson, Janet K.; Pati, Amrita; Gilbert, Jack A.; Tringe, Susannah G.; Lorenson, Thomas D.; Hess, Matthias

    2014-01-02

    Crude oils can be major contaminants of the marine ecosystem and microorganisms play a significant role in the degradation of the main constituents of crude oil. To increase our understanding of the microbial hydrocarbon degradation process in the marine ecosystem, we collected crude oil from an active seep area located in the Santa Barbara Channel (SBC) and generated a total of about 52 Gb of raw metagenomic sequence data. The assembled data comprised ~500 Mb, representing ~1.1 million genes derived primarily from chemolithoautotrophic bacteria. Members of Oceanospirillales, a bacterial order belonging to the Deltaproteobacteria, recruited less than 2% of the assembled genes within the SBC metagenome. In contrast, the microbial community associated with the oil plume that developed in the aftermath of the Deepwater Horizon (DWH) blowout in 2010, was dominated by Oceanospirillales, which comprised more than 60% of the metagenomic data generated from the DWH oil plume. This suggests that Oceanospirillales might play a less significant role in the microbially mediated hydrocarbon conversion within the SBC seep oil compared to the DWH plume oil. We hypothesize that this difference results from the SBC oil seep being mostly anaerobic, while the DWH oil plume is aerobic. Within the Archaea, the phylum Euryarchaeota, recruited more than 95% of the assembled archaeal sequences from the SBC oil seep metagenome, with more than 50% of the sequences assigned to members of the orders Methanomicrobiales and Methanosarcinales. These orders contain organisms capable of anaerobic methanogenesis and methane oxidation (AOM) and we hypothesize that these orders and their metabolic capabilities may be fundamental to the ecology of the SBC oil seep.

  2. Exploration of Metagenome Assemblies with an Interactive Visualization Tool

    SciTech Connect (OSTI)

    Cantor, Michael; Nordberg, Henrik; Smirnova, Tatyana; Andersen, Evan; Tringe, Susannah; Hess, Matthias; Dubchak, Inna

    2014-07-09

    Metagenomics, one of the fastest growing areas of modern genomic science, is the genetic profiling of the entire community of microbial organisms present in an environmental sample. Elviz is a web-based tool for the interactive exploration of metagenome assemblies. Elviz can be used with publicly available data sets from the Joint Genome Institute or with custom user-loaded assemblies. Elviz is available at genome.jgi.doe.gov/viz

  3. Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

    SciTech Connect (OSTI)

    Morgan, Jenna L.; Darling, Aaron E.; Eisen, Jonathan A.

    2009-12-01

    Background: Microbial life dominates the earth, but many species are difficult or even impossible to study under laboratory conditions. Sequencing DNA directly from the environment, a technique commonly referred to as metagenomics, is an important tool for cataloging microbial life. This culture-independent approach involves collecting samples that include microbes in them, extracting DNA from the samples, and sequencing the DNA. A sample may contain many different microorganisms, macroorganisms, and even free-floating environmental DNA. A fundamental challenge in metagenomics has been estimating the abundance of organisms in a sample based on the frequency with which the organism's DNA was observed in reads generated via DNA sequencing. Methodology/Principal Findings: We created mixtures of ten microbial species for which genome sequences are known. Each mixture contained an equal number of cells of each species. We then extracted DNA from the mixtures, sequenced the DNA, and measured the frequency with which genomic regions from each organism was observed in the sequenced DNA. We found that the observed frequency of reads mapping to each organism did not reflect the equal numbers of cells that were known to be included in each mixture. The relative organism abundances varied significantly depending on the DNA extraction and sequencing protocol utilized. Conclusions/Significance: We describe a new data resource for measuring the accuracy of metagenomic binning methods, created by in vitro-simulation of a metagenomic community. Our in vitro simulation can be used to complement previous in silico benchmark studies. In constructing a synthetic community and sequencing its metagenome, we encountered several sources of observation bias that likely affect most metagenomic experiments to date and present challenges for comparative metagenomic studies. DNA preparation methods have a particularly profound effect in our study, implying that samples prepared with different

  4. Los Alamos creates bioinformatics tool for metagenome analysis

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Bioinformatics tool for metagenome analysis Los Alamos creates bioinformatics tool for metagenome analysis Scientists have developed a new method for DNA analysis of microbial communities such as those found in the ocean, the soil, and our own guts. March 18, 2015 Many molecular biology studies begin with purified DNA and RNA extracted from the soil and other complex environments such as the human gut. Scientists at Los Alamos National Laboratory have developed a new method for DNA analysis of

  5. Supporting biosLos Alamos creates bioinformatics tool for metagenome

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    analysisurveillance via the web creates bioinformatics tool for metagenome analysis Alumni Link: Opportunities, News and Resources for Former Employees Latest Issue:September 2015 all issues All Issues » submit Los Alamos creates bioinformatics tool for metagenome analysis Scientists have developed a new method for DNA analysis of microbial communities such as those found in the ocean, the soil, and our own guts. May 1, 2015 Many molecular biology studies begin with purified DNA and RNA

  6. Metagenomics, metaMicrobesOnline and Kbase Data Integration (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Dehal, Paramvir [LBNL

    2013-01-22

    Berkeley Lab's Paramvir Dehal on "Managing and Storing large Datasets in MicrobesOnline, metaMicrobesOnline and the DOE Knowledgebase" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  7. Introduction to Metagenomics at DOE JGI (Opening Remarks for the Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Kyrpides, Nikos [DOE JGI

    2013-01-22

    After a quick introduction by DOE JGI Director Eddy Rubin, DOE JGI's Nikos Kyrpides delivers the opening remarks at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011

  8. Kurt Buhlmann | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Buhlmann Curriculum Vitae Faculty & Scientists SREL Home SREL Herpetology Kurt A. Buhlmann Savannah River Ecology Laboratory P O Drawer E, Aiken, SC 29802 (803) 725-5293 office (803) 725-3309 fax buhlmann(at)uga.edu Research interests: A major focus of my research has been the life history and evolutionary ecology of amphibians and reptiles, primarily chelonians, with application to conservation and habitat management. Past research has included evaluation of terrestrial habitat requirements

  9. EXTRACT: Interactive extraction of environment metadata and term suggestion for metagenomic sample annotation

    SciTech Connect (OSTI)

    Pafilis, Evangelos; Buttigieg, Pier Luigi; Ferrell, Barbra; Pereira, Emiliano; Schnetzer, Julia; Arvanitidis, Christos; Jensen, Lars Juhl

    2016-01-01

    The microbial and molecular ecology research communities have made substantial progress on developing standards for annotating samples with environment metadata. However, sample manual annotation is a highly labor intensive process and requires familiarity with the terminologies used. We have therefore developed an interactive annotation tool, EXTRACT, which helps curators identify and extract standard-compliant terms for annotation of metagenomic records and other samples. Behind its web-based user interface, the system combines published methods for named entity recognition of environment, organism, tissue and disease terms. The evaluators in the BioCreative V Interactive Annotation Task found the system to be intuitive, useful, well documented and sufficiently accurate to be helpful in spotting relevant text passages and extracting organism and environment terms. Here the comparison of fully manual and text-mining-assisted curation revealed that EXTRACT speeds up annotation by 15–25% and helps curators to detect terms that would otherwise have been missed.

  10. Metagenomic analysis of permafrost microbial community response to thaw

    SciTech Connect (OSTI)

    Mackelprang, R.; Waldrop, M.P.; DeAngelis, K.M.; David, M.M.; Chavarria, K.L.; Blazewicz, S.J.; Rubin, E.M.; Jansson, J.K.

    2011-07-01

    We employed deep metagenomic sequencing to determine the impact of thaw on microbial phylogenetic and functional genes and related this data to measurements of methane emissions. Metagenomics, the direct sequencing of DNA from the environment, allows for the examination of whole biochemical pathways and associated processes, as opposed to individual pieces of the metabolic puzzle. Our metagenome analyses revealed that during transition from a frozen to a thawed state there were rapid shifts in many microbial, phylogenetic and functional gene abundances and pathways. After one week of incubation at 5°C, permafrost metagenomes converged to be more similar to each other than while they were frozen. We found that multiple genes involved in cycling of C and nitrogen shifted rapidly during thaw. We also constructed the first draft genome from a complex soil metagenome, which corresponded to a novel methanogen. Methane previously accumulated in permafrost was released during thaw and subsequently consumed by methanotrophic bacteria. Together these data point towards the importance of rapid cycling of methane and nitrogen in thawing permafrost.

  11. Terrestrial Carbon Cycle

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    cycle Terrestrial Carbon Cycle "Only about half of the CO2 released into the atmosphere by human activities currently resides in the atmosphere, the rest absorbed on land and in the oceans. The period over which the carbon will be sequestered is unclear, and the efficiency of future sinks is unknown." US Carbon Cycle Research Plan "We" desire to be able to predict the future spatial and temporal distribution of sources and sinks of atmospheric CO2 and their interaction

  12. Metagenomic gene annotation by a homology-independent approach

    SciTech Connect (OSTI)

    Froula, Jeff; Zhang, Tao; Salmeen, Annette; Hess, Matthias; Kerfeld, Cheryl A.; Wang, Zhong; Du, Changbin

    2011-06-02

    Fully understanding the genetic potential of a microbial community requires functional annotation of all the genes it encodes. The recently developed deep metagenome sequencing approach has enabled rapid identification of millions of genes from a complex microbial community without cultivation. Current homology-based gene annotation fails to detect distantly-related or structural homologs. Furthermore, homology searches with millions of genes are very computational intensive. To overcome these limitations, we developed rhModeller, a homology-independent software pipeline to efficiently annotate genes from metagenomic sequencing projects. Using cellulases and carbonic anhydrases as two independent test cases, we demonstrated that rhModeller is much faster than HMMER but with comparable accuracy, at 94.5percent and 99.9percent accuracy, respectively. More importantly, rhModeller has the ability to detect novel proteins that do not share significant homology to any known protein families. As {approx}50percent of the 2 million genes derived from the cow rumen metagenome failed to be annotated based on sequence homology, we tested whether rhModeller could be used to annotate these genes. Preliminary results suggest that rhModeller is robust in the presence of missense and frameshift mutations, two common errors in metagenomic genes. Applying the pipeline to the cow rumen genes identified 4,990 novel cellulases candidates and 8,196 novel carbonic anhydrase candidates.In summary, we expect rhModeller to dramatically increase the speed and quality of metagnomic gene annotation.

  13. MetaGenomic Assembly by Merging (MeGAMerge)

    SciTech Connect (OSTI)

    Scholz Chien-Chi Lo, Matthew B.

    2015-08-03

    "MetaGenomic Assembly by Merging" (MeGAMerge)Is a novel method of merging of multiple genomic assembly or long read data sources for assembly by use of internal trimming/filtering of data, followed by use of two 3rd party tools to merge data by overlap based assembly.

  14. Ecological Risk Assessments

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Ecological Risk Assessments Ecological Risk Assessments Ecological risk assessment is the appraisal of potential adverse effects of exposure to contaminants on plants and animals....

  15. DOE JGI Quality Metrics; Approaches to Scaling and Improving Metagenome Assembly (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Copeland, Alex [DOE JGI]; Brown, C Titus [Michigan State University

    2013-01-22

    DOE JGI's Alex Copeland on "DOE JGI Quality Metrics" and Michigan State University's C. Titus Brown on "Approaches to Scaling and Improving Metagenome Assembly" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  16. Computational Challenges for Microbial Genome and Metagenome Analysis (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Mavrommatis, Kostas

    2011-06-08

    Kostas Mavrommatis of the DOE JGI gives a presentation on "Computational Challenges for Microbial Genome & Metagenome Analysis" at the JGI/Argonne HPC Workshop on January 26, 2010.

  17. Overview of IMG Challenges (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Markowitz, Victor [JGI

    2013-01-22

    DOE JGI's Victor Markowitz gives an overview of IMG challenges at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  18. Gene and translation initiation site prediction in metagenomic sequences

    SciTech Connect (OSTI)

    Hyatt, Philip Douglas; LoCascio, Philip F; Hauser, Loren John; Uberbacher, Edward C

    2012-01-01

    Gene prediction in metagenomic sequences remains a difficult problem. Current sequencing technologies do not achieve sufficient coverage to assemble the individual genomes in a typical sample; consequently, sequencing runs produce a large number of short sequences whose exact origin is unknown. Since these sequences are usually smaller than the average length of a gene, algorithms must make predictions based on very little data. We present MetaProdigal, a metagenomic version of the gene prediction program Prodigal, that can identify genes in short, anonymous coding sequences with a high degree of accuracy. The novel value of the method consists of enhanced translation initiation site identification, ability to identify sequences that use alternate genetic codes and confidence values for each gene call. We compare the results of MetaProdigal with other methods and conclude with a discussion of future improvements.

  19. Metagenome of a Versatile Chemolithoautotroph from Expanding Oceanic Dead Zones

    SciTech Connect (OSTI)

    Walsh, David A.; Zaikova, Elena; Howes, Charles L.; Song, Young; Wright, Jody; Tringe, Susannah G.; Tortell, Philippe D.; Hallam, Steven J.

    2009-07-15

    Oxygen minimum zones (OMZs), also known as oceanic"dead zones", are widespread oceanographic features currently expanding due to global warming and coastal eutrophication. Although inhospitable to metazoan life, OMZs support a thriving but cryptic microbiota whose combined metabolic activity is intimately connected to nutrient and trace gas cycling within the global ocean. Here we report time-resolved metagenomic analyses of a ubiquitous and abundant but uncultivated OMZ microbe (SUP05) closely related to chemoautotrophic gill symbionts of deep-sea clams and mussels. The SUP05 metagenome harbors a versatile repertoire of genes mediating autotrophic carbon assimilation, sulfur-oxidation and nitrate respiration responsive to a wide range of water column redox states. Thus, SUP05 plays integral roles in shaping nutrient and energy flow within oxygen-deficient oceanic waters via carbon sequestration, sulfide detoxification and biological nitrogen loss with important implications for marine productivity and atmospheric greenhouse control.

  20. The MG-RAST Metagenomics Database and Portal in 2015

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Wilke, Andreas; Bischof, Jared; Gerlach, Wolfgang; Glass, Elizabeth; Harrison, Travis; Keegan, Kevin; Paczian, Tobias; Trimble, William L.; Bagchi, Saurabh; Grama, Ananth; et al

    2015-12-09

    MG-RAST (http://metagenomics.anl.gov) is an opensubmission data portal for processing, analyzing, sharing and disseminating metagenomic datasets. Currently, the system hosts over 200 000 datasets and is continuously updated. The volume of submissions has increased 4-fold over the past 24 months, now averaging 4 terabasepairs per month. In addition to several new features, we report changes to the analysis workflow and the technologies used to scale the pipeline up to the required throughput levels. Lastly, to show possible uses for the data from MG-RAST, we present several examples integrating data and analyses from MG-RAST into popular third-party analysis tools or sequence alignmentmore » tools.« less

  1. IMG/M: A data management and analysis system for metagenomes

    SciTech Connect (OSTI)

    Markowitz, Victor M.; Ivanova, Natalia N.; Szeto, Ernest; Palaniappan, Krishna; Chu, Ken; Dalevi, Daniel; Chen, I-Min A.; Grechkin,Yuri; Dubchak,Inna; Anderson, Iain; Lykidis, Athanasios; Mavromatis,Konstantinos; Hug enholtz, Phil; Kyrpides, Nikos C.

    2007-08-01

    IMG/M is a data management and analysis system for microbial community genomes (metagenomes) hosted at the Joint Genome Institute (JGI). IMG/M consists of metagenome data integrated with isolate microbial genomes from the Integrated Microbial Genomes (IMG) system. IMG/M provides IMG's comparative data analysis tools extended to handle metagenome data, together with metagenome-specific analysis tools. IMG/M is available at http://img.jgi.doe.gov/m. Studies of the collective genomes (also known as metagenomes) of environmental microbial communities (also known as microbiomes) are expected to lead to advances in environmental cleanup, agriculture, industrial processes, alternative energy production, and human health (1). Metagenomes of specific microbiome samples are sequenced by organizations worldwide, such as the Department of Energy's (DOE) Joint Genome Institute (JGI), the Venter Institute and the Washington University in St. Louis using different sequencing strategies, technology platforms, and annotation procedures. According to the Genomes OnLine Database, about 28 metagenome studies have been published to date, with over 60 other projects ongoing and more in the process of being launched (2). The Department of Energy's (DOE) Joint Genome Institute (JGI) is one of the major contributors of metagenome sequence data, currently sequencing more than 50% of the reported metagenome projects worldwide. Due to the higher complexity, inherent incompleteness, and lower quality of metagenome sequence data, traditional assembly, gene prediction, and annotation methods do not perform on these datasets as well as they do on isolate microbial genome sequences (3, 4). In spite of these limitations, metagenome data are amenable to a variety of analyses, as illustrated by several recent studies (5-10). Metagenome data analysis is usually set up in the context of reference isolate genomes and considers the questions of composition and functional or metabolic potential of

  2. Metagenomic insights into evolution of heavy metal-contaminated groundwater microbial community

    SciTech Connect (OSTI)

    Hemme, C.L.; Deng, Y.; Gentry, T.J.; Fields, M.W.; Wu, L.; Barua, S.; Barry, K.; Green-Tringe, S.; Watson, D.B.; He, Z.; Hazen, T.C.; Tiedje, J.M.; Rubin, E.M.; Zhou, J.

    2010-07-01

    Understanding adaptation of biological communities to environmental change is a central issue in ecology and evolution. Metagenomic analysis of a stressed groundwater microbial community reveals that prolonged exposure to high concentrations of heavy metals, nitric acid and organic solvents ({approx}50 years) has resulted in a massive decrease in species and allelic diversity as well as a significant loss of metabolic diversity. Although the surviving microbial community possesses all metabolic pathways necessary for survival and growth in such an extreme environment, its structure is very simple, primarily composed of clonal denitrifying {gamma}- and {beta}-proteobacterial populations. The resulting community is overabundant in key genes conferring resistance to specific stresses including nitrate, heavy metals and acetone. Evolutionary analysis indicates that lateral gene transfer could have a key function in rapid response and adaptation to environmental contamination. The results presented in this study have important implications in understanding, assessing and predicting the impacts of human-induced activities on microbial communities ranging from human health to agriculture to environmental management, and their responses to environmental changes.

  3. EXTRACT: Interactive extraction of environment metadata and term suggestion for metagenomic sample annotation

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Pafilis, Evangelos; Buttigieg, Pier Luigi; Ferrell, Barbra; Pereira, Emiliano; Schnetzer, Julia; Arvanitidis, Christos; Jensen, Lars Juhl

    2016-01-01

    The microbial and molecular ecology research communities have made substantial progress on developing standards for annotating samples with environment metadata. However, sample manual annotation is a highly labor intensive process and requires familiarity with the terminologies used. We have therefore developed an interactive annotation tool, EXTRACT, which helps curators identify and extract standard-compliant terms for annotation of metagenomic records and other samples. Behind its web-based user interface, the system combines published methods for named entity recognition of environment, organism, tissue and disease terms. The evaluators in the BioCreative V Interactive Annotation Task found the system to be intuitive, useful, wellmore » documented and sufficiently accurate to be helpful in spotting relevant text passages and extracting organism and environment terms. Here the comparison of fully manual and text-mining-assisted curation revealed that EXTRACT speeds up annotation by 15–25% and helps curators to detect terms that would otherwise have been missed.« less

  4. Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community

    SciTech Connect (OSTI)

    Hemme, Christopher; Deng, Ye; Gentry, Terry; Fields, Matthew Wayne; Wu, Liyou; Barua, Soumitra; Barry, Kerry; Green-Tringe, Susannah; Watson, David B; He, Zhili; Hazen, Terry; Tiedje, James M.; Rubin, Edward M.; Zhou, Jizhong

    2010-02-01

    Understanding adaptation of biological communities to environmental change is a central issue in ecology and evolution. Metagenomic analysis of a stressed groundwater microbial community reveals that prolonged exposure to high concentrations of heavy metals, nitric acid and organic solvents (~50 years) has resulted in a massive decrease in species and allelic diversity as well as a significant loss of metabolic diversity. Although the surviving microbial community possesses all metabolic pathways necessary for survival and growth in such an extreme environment, its structure is very simple, primarily composed of clonal denitrifying - and -proteobacterial populations. The resulting community is overabundant in key genes conferring resistance to specific stresses including nitrate, heavy metals and acetone. Evolutionary analysis indicates that lateral gene transfer could have a key function in rapid response and adaptation to environmental contamination. The results presented in this study have important implications in understanding, assessing and predicting the impacts of human-induced activities on microbial communities ranging from human health to agriculture to environmental management, and their responses to environmental changes.

  5. FAMeS: Fidelity of Analysis of Metagenomic Samples

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Metagenomics is a rapidly emerging field of research for studying microbial communities. To evaluate methods currently used to process metagenomic sequences, simulated datasets of varying complexity were constructed by combining sequencing reads randomly selected from 113 isolate genomes. These datasets were designed to model real metagenomes in terms of complexity and phylogenetic composition. Assembly, gene prediction and binning, employing methods commonly used for the analysis of metagenomic datasets at the DOE JGI, were performed. This site provides access to the simulated datasets, and aims to facilitate standardized benchmarking of tools for metagenomic analysis. FAMeS now hosts data coming from a comprehensive study of methodologies used to create OTUs from 16S rRNA targeted studies of microbial communities. Studies of phylogenetic markers at the molecular level have revealed a vast biodiversity of microorganisms living in the sea, land, and even within the human body. Microbial diversity studies of uncharacterized environments typically seek to estimate the richness and diversity of endemic microflora using a 16S rRNA gene sequencing approach. When most of the species in an environment are unknown and cannot be classified through a database search, researchers cluster 16S sequences into operational taxonomic units (OTUs) or phylotypes, thereby providing an estimate of population structure. Using real 16S sequence data, we have performed a critical analysis of OTU clustering methodologies to assess the potential variability in OTU quality. FAMeS provides the sequence data, taxonomic information, multiple sequence alignments, and distance matrices used and described in the core paper, as well as compiled results of more than 700 unique OTU methods. [The above was copied from the FAMeS home page at http://fames.jgi-psf.org/] The core paper behind FAMeS is: Konstantinos Mavromatis, Natalia Ivanova, Kerrie Barry, Harris Shapiro, Eugene Goltsman, Alice C Mc

  6. Introduction to Metagenomics at DOE JGI: Program Overview and Program Informatics (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Tringe, Susannah [DOE JGI

    2013-01-22

    Susannah Tringe of the DOE Joint Genome Institute talks about the Program Overview and Program Informatics at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011

  7. Pacific Northwest Laboratory annual report for 1984 to the DOE Office of Energy Research. Part 2. Ecological sciences

    SciTech Connect (OSTI)

    Novich, C.M.

    1985-02-01

    Research progress is reported in the following areas: (1) the terrestrial ecology of semi-arid sites; (2) marine sciences; (3) radionuclide fate and effects; (4) waste mobilization, fate and effects; and (5) theoretical research on environmental sampling. (ACR)

  8. Within- and among-population level differences in response to chronic copper exposure in southern toads, Anaxyrus terrestris

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Within- and among-population level differences in response to chronic copper exposure in southern toads, Anaxyrus terrestris Stacey L. Lance * , R. Wesley Flynn, Matthew R. Erickson 1 , David E. Scott Savannah River Ecology Laboratory, University of Georgia, P.O. Drawer E, Aiken, SC 29802, USA a r t i c l e i n f o Article history: Received 5 September 2012 Received in revised form 29 January 2013 Accepted 5 February 2013 Keywords: Anaxyrus (Bufo) terrestris Amphibian Copper Ecotoxicology Metal

  9. Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River

    SciTech Connect (OSTI)

    Brown, Bonnie L.; LePrell, Rebecca V.; Franklin, Rima B.; Rivera, Maria C.; Cabral, Francine M.; Eaves, Hugh L.; Gardiakos, Vicki; Keegan, Kevin P.; King, Timothy L.

    2015-09-19

    Knowledge of the diversity and ecological function of the microbial consortia of James River in Virginia, USA, is essential to developing a more complete understanding of the ecology of this model river system. Metagenomic analysis of James River's planktonic microbial community was performed for the first time using an unamplified genomic library and a 16S rDNA amplicon library prepared and sequenced by Ion PGM and MiSeq, respectively. From the 0.46-Gb WGS library (GenBank:SRR1146621; MG-RAST:4532156.3), 4 x 106 reads revealed >3 x 106 genes, 240 families of prokaryotes, and 155 families of eukaryotes. From the 0.68-Gb 16S library (GenBank:SRR2124995; MG-RAST:4631271.3; EMB:2184), 4 x 106 reads revealed 259 families of eubacteria. Results of the WGS and 16S analyses were highly consistent and indicated that more than half of the bacterial sequences were Proteobacteria, predominantly Comamonadaceae. The most numerous genera in this group were Acidovorax (including iron oxidizers, nitrotolulene degraders, and plant pathogens), which accounted for 10 % of assigned bacterial reads. Polaromonas were another 6 % of all bacterial reads, with many assignments to groups capable of degrading polycyclic aromatic hydrocarbons. Albidiferax (iron reducers) and Variovorax (biodegraders of a variety of natural biogenic compounds as well as anthropogenic contaminants such as polycyclic aromatic hydrocarbons and endocrine disruptors) each accounted for an additional 3% of bacterial reads. Comparison of these data to other publically-available aquatic metagenomes revealed that this stretch of James River is highly similar to the upper Mississippi River, and that these river systems are more similar to aquaculture and sludge ecosystems than they are to lakes or to a pristine section of the upper Amazon River. Altogether, these analyses exposed previously unknown aspects of microbial biodiversity, documented

  10. Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Brown, Bonnie L.; LePrell, Rebecca V.; Franklin, Rima B.; Rivera, Maria C.; Cabral, Francine M.; Eaves, Hugh L.; Gardiakos, Vicki; Keegan, Kevin P.; King, Timothy L.

    2015-09-19

    Knowledge of the diversity and ecological function of the microbial consortia of James River in Virginia, USA, is essential to developing a more complete understanding of the ecology of this model river system. Metagenomic analysis of James River's planktonic microbial community was performed for the first time using an unamplified genomic library and a 16S rDNA amplicon library prepared and sequenced by Ion PGM and MiSeq, respectively. From the 0.46-Gb WGS library (GenBank:SRR1146621; MG-RAST:4532156.3), 4 x 106 reads revealed >3 x 106 genes, 240 families of prokaryotes, and 155 families of eukaryotes. From the 0.68-Gb 16S library (GenBank:SRR2124995; MG-RAST:4631271.3; EMB:2184),more » 4 x 106 reads revealed 259 families of eubacteria. Results of the WGS and 16S analyses were highly consistent and indicated that more than half of the bacterial sequences were Proteobacteria, predominantly Comamonadaceae. The most numerous genera in this group were Acidovorax (including iron oxidizers, nitrotolulene degraders, and plant pathogens), which accounted for 10 % of assigned bacterial reads. Polaromonas were another 6 % of all bacterial reads, with many assignments to groups capable of degrading polycyclic aromatic hydrocarbons. Albidiferax (iron reducers) and Variovorax (biodegraders of a variety of natural biogenic compounds as well as anthropogenic contaminants such as polycyclic aromatic hydrocarbons and endocrine disruptors) each accounted for an additional 3% of bacterial reads. Comparison of these data to other publically-available aquatic metagenomes revealed that this stretch of James River is highly similar to the upper Mississippi River, and that these river systems are more similar to aquaculture and sludge ecosystems than they are to lakes or to a pristine section of the upper Amazon River. Altogether, these analyses exposed previously unknown aspects of microbial biodiversity, documented the ecological responses of microbes to urban effects, and revealed

  11. Adaptation policies to increase terrestrial ecosystem resilience. Potential utility of a multicriteria approach

    SciTech Connect (OSTI)

    de Bremond, Ariane; Engle, Nathan L.

    2014-01-30

    Climate change is rapidly undermining terrestrial ecosystem resilience and capacity to continue providing their services to the benefit of humanity and nature. Because of the importance of terrestrial ecosystems to human well-being and supporting services, decision makers throughout the world are busy creating policy responses that secure multiple development and conservation objectives- including that of supporting terrestrial ecosystem resilience in the context of climate change. This article aims to advance analyses on climate policy evaluation and planning in the area of terrestrial ecosystem resilience by discussing adaptation policy options within the ecology-economy-social nexus. The paper evaluates these decisions in the realm of terrestrial ecosystem resilience and evaluates the utility of a set of criteria, indicators, and assessment methods, proposed by a new conceptual multi-criteria framework for pro-development climate policy and planning developed by the United Nations Environment Programme. Potential applications of a multicriteria approach to climate policy vis-A -vis terrestrial ecosystems are then explored through two hypothetical case study examples. The paper closes with a brief discussion of the utility of the multi-criteria approach in the context of other climate policy evaluation approaches, considers lessons learned as a result efforts to evaluate climate policy in the realm of terrestrial ecosystems, and reiterates the role of ecosystem resilience in creating sound policies and actions that support the integration of climate change and development goals.

  12. Panasonic Ecology Systems formerly Matsushita Ecology Systems...

    Open Energy Info (EERE)

    Ecology Systems Co) Place: Kasugai, Aichi, Japan Zip: 468-8522 Sector: Solar, Wind energy Product: Japanese manufacturer of energy efficient residential and commercial...

  13. Casting a Wider Net: Distributed Resources for Metagenomics (2010 JGI/ANL HPC Workshop)

    SciTech Connect (OSTI)

    Meyer, Folker [ANL] [ANL

    2010-01-26

    Folker Meyer from Argonne National Lab gives a presentation on "Casting a Wider Net: Distributed Resources for Metagenomics" at the JGI/Argonne HPC Workshop on January 26, 2010.

  14. Metagenomic assembly: Challenges, Successes and Validation ( 7th Annual SFAF Meeting, 2012)

    ScienceCinema (OSTI)

    Scholz, Matthew [Los Alamos National Laboratory

    2013-02-11

    Matthew Scholz on "Metagenomic assembly: Challenges, Successes and Validation" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  15. Metagenomics for Etiologic Agent Discovery (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema (OSTI)

    Ross, Matthew [Baylor College of Medicine

    2013-02-11

    Matthew Ross on "Metagenomics for etiological agent discovery" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  16. Casting a Wider Net: Distributed Resources for Metagenomics (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Meyer, Folker [ANL

    2011-06-08

    Folker Meyer from Argonne National Lab gives a presentation on "Casting a Wider Net: Distributed Resources for Metagenomics" at the JGI/Argonne HPC Workshop on January 26, 2010.

  17. Discovery of Genes and Genomes through Deep Metagenomic Sequencing of Cow Rumen (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Rubin, Eddy

    2011-04-25

    Director Eddy Rubin on "Discovery of Genes and Genomes through Deep Metagenomic Sequencing of Cow Rumen" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

  18. Signature Peptide-Enabled Metagenomics (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema (OSTI)

    McMahon, Ben [LANL

    2013-01-25

    Ben McMahon of Los Alamos National Laboratory (LANL) presents "Signature Peptide-Enabled Metagenomics" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  19. Road ecology in environmental impact assessment

    SciTech Connect (OSTI)

    Karlson, Mårten Mörtberg, Ulla Balfors, Berit

    2014-09-15

    Transport infrastructure has a wide array of effects on terrestrial and aquatic ecosystems, and road and railway networks are increasingly being associated with a loss of biodiversity worldwide. Environmental Impact Assessment (EIA) and Strategic Environmental Assessment (SEA) are two legal frameworks that concern physical planning, with the potential to identify, predict, mitigate and/or compensate transport infrastructure effects with negative impacts on biodiversity. The aim of this study was to review the treatment of ecological impacts in environmental assessment of transport infrastructure plans and projects. A literature review on the topic of EIA, SEA, biodiversity and transport infrastructure was conducted, and 17 problem categories on the treatment of biodiversity were formulated by means of a content analysis. A review of environmental impact statements and environmental reports (EIS/ER) produced between 2005 and 2013 in Sweden and the UK was then conducted using the list of problems as a checklist. The results show that the treatment of ecological impacts has improved substantially over the years, but that some impacts remain problematic; the treatment of fragmentation, the absence of quantitative analysis and that the impact assessment study area was in general delimited without consideration for the scales of ecological processes. Actions to improve the treatment of ecological impacts could include improved guidelines for spatial and temporal delimitation, and the establishment of a quantitative framework including tools, methods and threshold values. Additionally, capacity building and further method development of EIA and SEA friendly spatial ecological models can aid in clarifying the costs as well as the benefits in development/biodiversity tradeoffs. - Highlights: • The treatment of ecological impacts in EIA and SEA has improved. • Quantitative methods for ecological impact assessment were rarely used • Fragmentation effects were recognized

  20. New Ecology | Open Energy Information

    Open Energy Info (EERE)

    New Ecology Jump to: navigation, search Name: New Ecology Place: Boston, MA Website: www.newecology.com References: New Ecology1 Information About Partnership with NREL...

  1. Metagenomic Analysis of Microbial Symbionts in a Gutless Worm

    SciTech Connect (OSTI)

    Woyke, Tanja; Teeling, Hanno; Ivanova, Natalia N.; Hunteman, Marcel; Richter, Michael; Gloeckner, Frank Oliver; Boeffelli, Dario; Barry, Kerrie W.; Shapiro, Harris J.; Anderson, Iain J.; Szeto, Ernest; Kyrpides, Nikos C.; Mussmann, Marc; Amann, Rudolf; Bergin, Claudia; Ruehland, Caroline; Rubin, Edward M.; Dubilier, Nicole

    2006-05-01

    Symbioses between bacteria and eukaryotes are ubiquitous, yet our understanding of the interactions driving these associations is hampered by our inability to cultivate most host-associated microbes. Here we use a metagenomic approach to describe four co-occurring symbionts from the marine oligochaete Olavius algarvensis, a worm lacking a mouth, gut and nephridia. Shotgun sequencing and metabolic pathway reconstruction revealed that the symbionts are sulphur-oxidizing and sulphate-reducing bacteria, all of which are capable of carbon fixation, thus providing the host with multiple sources of nutrition. Molecular evidence for the uptake and recycling of worm waste products by the symbionts suggests how the worm could eliminate its excretory system, an adaptation unique among annelid worms. We propose a model that describes how the versatile metabolism within this symbiotic consortium provides the host with an optimal energy supply as it shuttles between the upper oxic and lower anoxic coastal sediments that it inhabits.

  2. Climate Perspectives: Change in the Terrestrial Arctic

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Perspectives: Change in the Terrestrial Arctic Climate Perspectives An interactive exploration of Arctic climate science through prisms of the visual arts, literary arts, info-vis, ...

  3. Microsoft PowerPoint - Microbial Genome and Metagenome Analysis Case Study (NERSC Workshop - May 7-8, 2009).ppt [Compatibility

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Microbial Genome & Metagenome Analysis: Computational Challenges Natalia N. Ivanova * Nikos C. Kyrpides * Victor M. Markowitz ** * Genome Biology Program, Joint Genome Institute ** Lawrence Berkeley National Lab Microbial genome & metagenome analysis General aims Understand microbial life Apply to agriculture, bioremediation, biofuels, human health Specific aims include Specific aims include Predict biochemistry & physiology of organisms based on genome sequence Explain known

  4. Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Assessment of Radionuclide Monitoring in the CSRA Savannah River NERP Research ... Upcoming Seminars The Savannah River Ecology Laboratory is a research unit of the ...

  5. Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance

    SciTech Connect (OSTI)

    Ahn, Tae-Hyuk; Crosskey, JJ; Pan, Chongle

    2015-01-01

    Motivation: Metagenomic sequencing of clinical samples provides a promising technique for direct pathogen detection and characterization in biosurveillance. Taxonomic analysis at the strain level can be used to resolve serotypes of a pathogen in biosurveillance. Sigma was developed for strain-level identification and quantification of pathogens using their reference genomes based on metagenomic analysis. Results: Sigma provides not only accurate strain-level inferences, but also three unique capabilities: (i) Sigma quantifies the statistical uncertainty of its inferences, which includes hypothesis testing of identified genomes and confidence interval estimation of their relative abundances; (ii) Sigma enables strain variant calling by assigning metagenomic reads to their most likely reference genomes; and (iii) Sigma supports parallel computing for fast analysis of large datasets. The algorithm performance was evaluated using simulated mock communities and fecal samples with spike-in pathogen strains. Availability and Implementation: Sigma was implemented in C++ with source codes and binaries freely available at http://sigma.omicsbio.org.

  6. SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Silva, Genivaldo Gueiros Z.; Green, Kevin T.; Dutilh, Bas E.; Edwards, Robert A.

    2015-10-09

    Analyzing the functional profile of a microbial community from unannotated shotgun sequencing reads is one of the important goals in metagenomics. Functional profiling has valuable applications in biological research because it identifies the abundances of the functional genes of the organisms present in the original sample, answering the question what they can do. Currently, available tools do not scale well with increasing data volumes, which is important because both the number and lengths of the reads produced by sequencing platforms keep increasing. Here, we introduce SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reducedmore » reference database to report the subsystems present in metagenomic datasets and profile their abundances. We tested SUPER-FOCUS with over 70 real metagenomes, the results showing that it accurately predicts the subsystems present in the profiled microbial communities, and is up to 1000 times faster than other tools.« less

  7. Terrestrial Climate Change and Ecosystem Response Recorded in...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Terrestrial Climate Change and Ecosystem Response Recorded in Lake Sediments and Related Deposits Reconstruction of past terrestrial climate and ecosystem response relies on ...

  8. Webinar-Terrestrial Solar Spectral Modeling for Renewable Energy...

    Open Energy Info (EERE)

    Webinar-Terrestrial Solar Spectral Modeling for Renewable Energy: SMARTS Model Jump to: navigation, search Tool Summary Name: Webinar-Terrestrial Solar Spectral Modeling for...

  9. Are GRACE-era Terrestrial Water Trends Driven by Anthropogenic...

    Office of Scientific and Technical Information (OSTI)

    Are GRACE-era Terrestrial Water Trends Driven by Anthropogenic Climate Change? Citation Details In-Document Search Title: Are GRACE-era Terrestrial Water Trends Driven by ...

  10. Thermoelectrics: From Space Power Systems to Terrestrial Waste...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Thermoelectrics: From Space Power Systems to Terrestrial Waste Heat Recovery Applications Thermoelectrics: From Space Power Systems to Terrestrial Waste Heat Recovery Applications ...

  11. Ecology Fact Sheets | Savannah River Ecology Laboratory Environmental...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Ecology Fact Sheets General Ecology: Mammals and Birds: An Amphibian's Eye View of Wetlands BioBarrierTm Carnivorous Plants Carolina Bays (HTML) Carolina Bays Deepwater Swamps PIT...

  12. Ecologic Institute | Open Energy Information

    Open Energy Info (EERE)

    Institute Name: Ecologic Institute Address: Pfalzburger Strasse 4344 Place: Berlin, Germany Year Founded: 1995 Phone Number: +49 (30) 86880-0 Website: ecologic.eu...

  13. DOE Manual Studies Terrestrial Carbon Sequestration

    Broader source: Energy.gov [DOE]

    There is considerable opportunity and growing technical sophistication to make terrestrial carbon sequestration both practical and effective, according to the latest carbon capture and storage "best practices" manual issued by the U.S. Department of Energy.

  14. Metagenome sequencing of a coastal marine microbial community from Monterey Bay, California

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Mueller, R. S.; Bryson, S.; Keift, B.; Li, Zhou; Pett-Ridge, J.; Chavex, F.; Robert Hettich; Pan, Chongle; Mayali, X.

    2015-04-30

    Heterotrophic microbes are critical components of aquatic food webs. Linkages between populations and the substrates they utilize are not well defined. We present the metagenome of microbial communities from the coastal Pacific Ocean exposed to various nutrient additions in order to better understand substrate utilization and partitioning in this environment.

  15. Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Eloe-Fadrosh, Emiley A.; Paez-Espino, David; Jarett, Jessica; Dunfield, Peter F.; Hedlund, Brian P.; Dekas, Anne E.; Grasby, Stephen E.; Brady, Allyson L.; Dong, Hailiang; Briggs, Brandon R.; et al

    2016-01-27

    We analyse the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum (‘Candidatus Kryptonia’) found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic ‘blind spot’ because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle withmore » conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery.« less

  16. (International meetings on ecology)

    SciTech Connect (OSTI)

    DeAngelis, D.L.; Garten, C.T. Jr.; Turner, M.G.

    1990-09-25

    the travelers attended the Fifth International Congress of Ecology (INTECOL) in Yokohama, Japan, and two presented invited papers and chaired symposia. One traveler also attended the OJI International Seminar in Gifu, Japan and the Fukuoka Symposium on Theoretical Ecology in Fukuoka, Japan and presented invited papers. At these scientific gatherings, a large number of symposia and specific presentations were relevant to current research at Oak Ridge National Laboratory (ORNL), especially in the areas of landscape dynamics, plant physiology, and aquatic ecosystems.

  17. Under-detection of endospore-forming Firmicutes in metagenomic data

    SciTech Connect (OSTI)

    Filippidou, Sevasti; Junier, Thomas; Wunderlin, Tina; Lo, Chien -Chi; Li, Po -E; Chain, Patrick S.; Junier, Pilar

    2015-04-25

    Microbial diversity studies based on metagenomic sequencing have greatly enhanced our knowledge of the microbial world. However, one caveat is the fact that not all microorganisms are equally well detected, questioning the universality of this approach. Firmicutes are known to be a dominant bacterial group. Several Firmicutes species are endospore formers and this property makes them hardy in potentially harsh conditions, and thus likely to be present in a wide variety of environments, even as residents and not functional players. While metagenomic libraries can be expected to contain endospore formers, endospores are known to be resilient to many traditional methods of DNA isolation and thus potentially undetectable. In this study we evaluated the representation of endospore-forming Firmicutes in 73 published metagenomic datasets using two molecular markers unique to this bacterial group (spo0A and gpr). Both markers were notably absent in well-known habitats of Firmicutes such as soil, with spo0A found only in three mammalian gut microbiomes. A tailored DNA extraction method resulted in the detection of a large diversity of endospore-formers in amplicon sequencing of the 16S rRNA and spo0A genes. However, shotgun classification was still poor with only a minor fraction of the community assigned to Firmicutes. Thus, removing a specific bias in a molecular workflow improves detection in amplicon sequencing, but it was insufficient to overcome the limitations for detecting endospore-forming Firmicutes in whole-genome metagenomics. In conclusion, this study highlights the importance of understanding the specific methodological biases that can contribute to improve the universality of metagenomic approaches.

  18. Under-detection of endospore-forming Firmicutes in metagenomic data

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Filippidou, Sevasti; Junier, Thomas; Wunderlin, Tina; Lo, Chien -Chi; Li, Po -E; Chain, Patrick S.; Junier, Pilar

    2015-04-25

    Microbial diversity studies based on metagenomic sequencing have greatly enhanced our knowledge of the microbial world. However, one caveat is the fact that not all microorganisms are equally well detected, questioning the universality of this approach. Firmicutes are known to be a dominant bacterial group. Several Firmicutes species are endospore formers and this property makes them hardy in potentially harsh conditions, and thus likely to be present in a wide variety of environments, even as residents and not functional players. While metagenomic libraries can be expected to contain endospore formers, endospores are known to be resilient to many traditional methodsmore » of DNA isolation and thus potentially undetectable. In this study we evaluated the representation of endospore-forming Firmicutes in 73 published metagenomic datasets using two molecular markers unique to this bacterial group (spo0A and gpr). Both markers were notably absent in well-known habitats of Firmicutes such as soil, with spo0A found only in three mammalian gut microbiomes. A tailored DNA extraction method resulted in the detection of a large diversity of endospore-formers in amplicon sequencing of the 16S rRNA and spo0A genes. However, shotgun classification was still poor with only a minor fraction of the community assigned to Firmicutes. Thus, removing a specific bias in a molecular workflow improves detection in amplicon sequencing, but it was insufficient to overcome the limitations for detecting endospore-forming Firmicutes in whole-genome metagenomics. In conclusion, this study highlights the importance of understanding the specific methodological biases that can contribute to improve the universality of metagenomic approaches.« less

  19. Assembly of large metagenome data sets using a Convey HC-1 hybrid core computer (7th Annual SFAF Meeting, 2012)

    ScienceCinema (OSTI)

    Copeland, Alex [DOE JGI

    2013-02-11

    Alex Copeland on "Assembly of large metagenome data sets using a Convey HC-1 hybrid core computer" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  20. Scalability of Comparative Analysis, Novel Algorithms and Tools (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Mavrommatis, Kostas [JGI

    2013-01-22

    DOE JGI's Kostas Mavrommatis, chair of the Scalability of Comparative Analysis, Novel Algorithms and Tools panel, at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  1. Genome Assembly Forensics: Metrics for Assessing Assembly Correctness (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Pop, Mihai [University of Maryland

    2013-01-22

    University of Maryland's Mihai Pop on "Genome Assembly Forensics: Metrics for Assessing Assembly Correctness" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  2. Scaling MG-RAST to Terabases (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Desai, Narayan [ANL

    2013-01-22

    Argonne National Lab's Narayan Desai on "Scaling MG-RAST to Terabases" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  3. Sequencing Single Cell Microbial Genomes with Microfluidic Amplifications Tools (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Quake, Steve [University of Stanford

    2013-01-22

    Stanford University's Steve Quake on "Sequencing Single Cell Microbial Genomes with Microfluidic Amplification Tools" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  4. Endosymbiont hunting in the metagenome of Asian citrus psyllid (Diaphorina citri) (7th Annual SFAF Meeting, 2012)

    ScienceCinema (OSTI)

    Saha, Surya [Cornell University

    2013-02-12

    Surya Saha on "Endosymbiont hunting in the metagenome of Asian citrus psyllid (Diaphorina citri)" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  5. Memory Efficient Sequence Analysis Using Compressed Data Structures (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Simpson, Jared [Wellcome Trust Sanger Institute

    2013-01-22

    Wellcome Trust Sanger Institute's Jared Simpson on "Memory efficient sequence analysis using compressed data structures" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011

  6. Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Mixed Swamp Forest This Set-Aside is one of the original ten SREL habitat reserve areas selected in 1968 to represent a diversity of bottomland hardwood/floodplain forest communities of a southern river swamp system. The majority of this Set-Aside is confined to the floodplain and, for the most part, these communities are relatively undisturbed, older growth mixtures of bottomland hardwood and swamp forests. Represented are aquatic, semi-aquatic, and terrestrial habitats associated with

  7. Ecological Communities by Design

    SciTech Connect (OSTI)

    Fredrickson, Jim K.

    2015-06-25

    In synthetic ecology, a nascent offshoot of synthetic biology, scientists aim to design and construct microbial communities with desirable properties. Such mixed populations of microorganisms can simultaneously perform otherwise incompatible functions. Compared with individual organisms, they can also better resist losses in function as a result of environmental perturbation or invasion by other species. Synthetic ecology may thus be a promising approach for developing robust, stable biotechnological processes, such as the conversion of cellulosic biomass to biofuels. However, achieving this will require detailed knowledge of the principles that guide the structure and function of microbial communities.

  8. The ecological highrise

    SciTech Connect (OSTI)

    Harnik, P.

    1982-09-01

    Suggestions are presented for ecological apartment living. These include 1) improvements made in living spaces such as polyethylene storm windows, window-box solar collectors, 2) roof-top technology of solar panels, windmills, or gardens and 3) share projects in which tenants organize to recycle or to share in purchase and upkeep of occasional-use equipment.

  9. The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. I. Microbial Diversity Based on 16S rRNA Gene Amplicons and Metagenomic Sequencing

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Thiel, Vera; Wood, Jason M.; Olsen, Millie T.; Tank, Marcus; Klatt, Christian G.; Ward, David M.; Bryant, Donald A.

    2016-06-17

    Microbial-mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin at Yellowstone National Park have been studied for nearly 50 years. The emphasis has mostly focused on the chlorophototrophic bacterial organisms of the phyla Cyanobacteria and Chloroflexi. In contrast, the diversity and metabolic functions of the heterotrophic community in the microoxic/anoxic region of the mat are not well understood. In this study we analyzed the orange-colored undermat of the microbial community of Mushroom Spring using metagenomic and rRNA-amplicon (iTag) analyses. Our analyses disclosed a highly diverse community exhibiting a high degree of unevenness, stronglymore » dominated by a single taxon, the filamentous anoxygenic phototroph, Roseiflexus spp. The second most abundant organisms belonged to the Thermotogae, which have been hypothesized to be a major source of H-2 from fermentation that could enable photomixotrophic metabolism by Chloroflexus and Roseiflexus spp. Other abundant organisms include two members of the Armatimonadetes (OP10); Thermocrinis sp.; and phototrophic and heterotrophic members of the Chloroflexi. Further, an Atribacteria (OP9/JS1) member; a sulfate-reducing Therrnodesulfovibrio sp.; a Planctomycetes member; a member of the EM3 group tentatively affiliated with the Thermotogae, as well as a putative member of the Arrninicenantes (OP8) represented ≥ 1% of the reads. Archaea were not abundant in the iTag analysis, and no metagenomic bin representing an archaeon was identified. A high microdiversity of 16S rRNA gene sequences was identified for the dominant taxon, Roseiflexus spp. Previous studies demonstrated that highly similar Synechococcus variants in the upper layer of the mats represent ecological species populations with specific ecological adaptations. In conclusion, this study suggests that similar putative ecotypes specifically adapted to different niches occur within the undermat community

  10. GenomePeek—an online tool for prokaryotic genome and metagenome analysis

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    McNair, Katelyn; Edwards, Robert A.

    2015-06-16

    As increases in prokaryotic sequencing take place, a method to quickly and accurately analyze this data is needed. Previous tools are mainly designed for metagenomic analysis and have limitations; such as long runtimes and significant false positive error rates. The online tool GenomePeek (edwards.sdsu.edu/GenomePeek) was developed to analyze both single genome and metagenome sequencing files, quickly and with low error rates. GenomePeek uses a sequence assembly approach where reads to a set of conserved genes are extracted, assembled and then aligned against the highly specific reference database. GenomePeek was found to be faster than traditional approaches while still keeping errormore » rates low, as well as offering unique data visualization options.« less

  11. FOAM (Functional Ontology Assignments for Metagenomes): A Hidden Markov Model (HMM) database with environmental focus

    SciTech Connect (OSTI)

    Prestat, Emmanuel; David, Maude M.; Hultman, Jenni; Ta , Neslihan; Lamendella, Regina; Dvornik, Jill; Mackelprang, Rachel; Myrold, David D.; Jumpponen, Ari; Tringe, Susannah G.; Holman, Elizabeth; Mavromatis, Konstantinos; Jansson, Janet K.

    2014-09-26

    A new functional gene database, FOAM (Functional Ontology Assignments for Metagenomes), was developed to screen environmental metagenomic sequence datasets. FOAM provides a new functional ontology dedicated to classify gene functions relevant to environmental microorganisms based on Hidden Markov Models (HMMs). Sets of aligned protein sequences (i.e. ‘profiles’) were tailored to a large group of target KEGG Orthologs (KOs) from which HMMs were trained. The alignments were checked and curated to make them specific to the targeted KO. Within this process, sequence profiles were enriched with the most abundant sequences available to maximize the yield of accurate classifier models. An associated functional ontology was built to describe the functional groups and hierarchy. FOAM allows the user to select the target search space before HMM-based comparison steps and to easily organize the results into different functional categories and subcategories. FOAM is publicly available at http://portal.nersc.gov/project/m1317/FOAM/.

  12. GenomePeek—an online tool for prokaryotic genome and metagenome analysis

    SciTech Connect (OSTI)

    McNair, Katelyn; Edwards, Robert A.

    2015-06-16

    As increases in prokaryotic sequencing take place, a method to quickly and accurately analyze this data is needed. Previous tools are mainly designed for metagenomic analysis and have limitations; such as long runtimes and significant false positive error rates. The online tool GenomePeek (edwards.sdsu.edu/GenomePeek) was developed to analyze both single genome and metagenome sequencing files, quickly and with low error rates. GenomePeek uses a sequence assembly approach where reads to a set of conserved genes are extracted, assembled and then aligned against the highly specific reference database. GenomePeek was found to be faster than traditional approaches while still keeping error rates low, as well as offering unique data visualization options.

  13. Omega: an Overlap-graph de novo Assembler for Meta-genomics

    SciTech Connect (OSTI)

    Haider, Bahlul; Ahn, Tae-Hyuk; Bushnell, Brian; Chai, JJ; Copeland, Alex; Pan, Chongle

    2014-01-01

    Motivation: Metagenomic sequencing allows reconstruction of mi-crobial genomes directly from environmental samples. Omega (overlap-graph metagenome assembler) was developed here for assembling and scaffolding Illumina sequencing data of microbial communities. Results: Omega found overlaps between reads using a prefix/suffix hash table. The overlap graph of reads was simplified by removing transitive edges and trimming small branches. Unitigs were generat-ed based on minimum cost flow analysis of the overlap graph. Obtained unitigs were merged to contigs and scaffolds using mate-pair information. Omega was compared with two de Bruijn graph assemblers, SOAPdenovo and IDBA-UD, using a publically-available Illumina sequencing dataset of a 64-genome mock com-munity. The assembly results were verified by their alignment with reference genomes. The overall performances of the three assem-blers were comparable and each assembler provided best results for a subset of genomes.

  14. Ecology Action: Small Market Advanced Retrofit Transformation...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Ecology Action: Small Market Advanced Retrofit Transformation Program (SMART) Ecology Action: Small Market Advanced Retrofit Transformation Program (SMART) Ecology Action: Small ...

  15. Valuation of ecological resources

    SciTech Connect (OSTI)

    Scott, M.J.; Bilyard, G.R.; Link, S.O.; Ricci, P.F.; Seely, H.E.; Ulibarri, C.A.; Westerdahl, H.E.

    1995-04-01

    Ecological resources are resources that have functional value to ecosystems. Frequently, these functions are overlooked in terms of the value they provide to humans. Environmental economics is in search of an appropriate analysis framework for such resources. In such a framework, it is essential to distinguish between two related subsets of information: (1) ecological processes that have intrinsic value to natural ecosystems; and (2) ecological functions that are values by humans. The present study addresses these concerns by identifying a habitat that is being displaced by development, and by measuring the human and ecological values associated with the ecological resources in that habitat. It is also essential to determine which functions are mutually exclusive and which are, in effect, complementary or products of joint production. The authors apply several resource valuation tools, including contingent valuation methodology (CVM), travel cost methodology (TCM), and hedonic damage-pricing (HDP). One way to derive upper-limit values for more difficult-to-value functions is through the use of human analogs, because human-engineered systems are relatively inefficient at supplying the desired services when compared with natural systems. Where data on the relative efficiencies of natural systems and human analogs exist, it is possible to adjust the costs of providing the human analog by the relative efficiency of the natural system to obtain a more realistic value of the function under consideration. The authors demonstrate this approach in an environmental economic case study of the environmental services rendered by shrub-steppe habitats of Benton County, Washington State.

  16. Development of Microarrays-Based Metagenomics Technology for Monitoring Sulfate-Reducing Bacteria in Subsurface Environments

    SciTech Connect (OSTI)

    Cindy, Shi

    2015-07-17

    At the contaminated DOE sites, sulfate-reducing bacteria (SRB) are a significant population and play an important role in the microbial community during biostimulation for metal reduction. However, the diversity, structure and dynamics of SRB communities are poorly understood. Therefore, this project aims to use high throughput sequencing-based metagenomics technologies for characterizing the diversity, structure, functions, and activities of SRB communities by developing genomic and bioinformatics tools to link the SRB biodiversity with ecosystem functioning.

  17. Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Ahn, Tae-Hyuk; Chai, Juanjuan; Pan, Chongle

    2014-09-29

    Motivation: Metagenomic sequencing of clinical samples provides a promising technique for direct pathogen detection and characterization in biosurveillance. Taxonomic analysis at the strain level can be used to resolve serotypes of a pathogen in biosurveillance. Sigma was developed for strain-level identification and quantification of pathogens using their reference genomes based on metagenomic analysis. Results: Sigma provides not only accurate strain-level inferences, but also three unique capabilities: (i) Sigma quantifies the statistical uncertainty of its inferences, which includes hypothesis testing of identified genomes and confidence interval estimation of their relative abundances; (ii) Sigma enables strain variant calling by assigning metagenomic readsmore » to their most likely reference genomes; and (iii) Sigma supports parallel computing for fast analysis of large datasets. In conclusion, the algorithm performance was evaluated using simulated mock communities and fecal samples with spike-in pathogen strains. Availability and Implementation: Sigma was implemented in C++ with source codes and binaries freely available at http://sigma.omicsbio.org.« less

  18. USING ANT COMMUNITIES FOR RAPID ASSESSMENT OF TERRESTRIAL ECOSYSTEM HEALTH

    SciTech Connect (OSTI)

    Wike, L; Doug Martin, D; Michael Paller, M; Eric Nelson, E

    2007-01-12

    Ecosystem health with its near infinite number of variables is difficult to measure, and there are many opinions as to which variables are most important, most easily measured, and most robust, Bioassessment avoids the controversy of choosing which physical and chemical parameters to measure because it uses responses of a community of organisms that integrate all aspects of the system in question. A variety of bioassessment methods have been successfully applied to aquatic ecosystems using fish and macroinvertebrate communities. Terrestrial biotic index methods are less developed than those for aquatic systems and we are seeking to address this problem here. This study had as its objective to examine the baseline differences in ant communities at different seral stages from clear cut back to mature pine plantation as a precursor to developing a bioassessment protocol. Comparative sampling was conducted at four seral stages; clearcut, 5 year, 15 year and mature pine plantation stands. Soil and vegetation data were collected at each site. All ants collected were preserved in 70% ethyl alcohol and identified to genus. Analysis of the ant data indicates that ants respond strongly to the habitat changes that accompany ecological succession in managed pine forests and that individual genera as well as ant community structure can be used as an indicator of successional change. Ants exhibited relatively high diversity in both early and mature seral stages. High ant diversity in the mature seral stages was likely related to conditions on the forest floor which favored litter dwelling and cool climate specialists.

  19. Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Mature Hardwood Forest The Mature Hardwood Forest Set-Aside is an excellent example of a relatively undisturbed, maturing hardwood forest containing both seasonally flooded bottomland and transitional upland habitats associated with a stream floodplain. This Set-Aside contains some of the best examples of stands of maturing hardwoods which represent the range of ecological variation in hardwood forest types on the SRS. While the vegetation on the xeric and mesic slopes of this Set-Aside is

  20. Environmental resources of selected areas of Hawaii: Ecological resources

    SciTech Connect (OSTI)

    Trettin, C.C.; Tolbert, V.R.; Jones, A.T.; Smith, C.R.; Kalmijn, A.J.

    1995-03-01

    This report has been prepared to make available and archive the background scientific data and related information collected on ecological resources during the preparation of the environmental impact statement (EIS) for Phases 3 and 4 of the Hawaii Geothermal Project (HGP) as defined by the state of Hawaii in its April 1989 proposal to Congress. Since the state of Hawaii is no longer pursuing or planning to pursue the HGP, DOE considers the project to be terminated. The background scientific data and related information presented in this report focus on several areas of Hawaii County. In this report, reference is made to these areas as study areas rather than as areas where proposed or alternative facilities of the HGP would be located. The resource areas addressed herein include terrestrial ecology, aquatic ecology, and marine ecology. The scientific background data and related information that were obtained from review of the (1) scientific literature, (2) government and private sector reports, (3) studies done under DOE interagency agreements with the US Fish and Wildlife Service (FWS) and with the US Army Corps of Engineers (COE), and (4) observations made during site visits are being made available for future research in these areas.

  1. Environmental Resources of Selected Areas of Hawaii: Ecological Resources (DRAFT)

    SciTech Connect (OSTI)

    Trettin, C.C.; Tolbert, V.R.; Jones, A.T.; Smith, C.R.; Kalmijn, A.J.

    1994-06-01

    This report has been prepared to make available and archive the background scientific data and related information collected on ecological resources during the preparation of the environmental impact statement (EIS) for Phases 3 and 4 of the Hawaii Geothermal Project (HGP) as defined by the state of Hawaii in its April 1989 proposal to Congress. The U.S. Department of Energy (COE) published a notice in the Federal Register on May 17, 1994 (Fed. Regist. 5925638) withdrawing its Notice of Intent (Fed. Regst. 575433) of February 14, 1992, to prepare the HGP-EIS. Since the state of Hawaii is no longer pursuing or planning to pursue the HGP, DOE considers the project to be terminated. The background scientific data and related information presented in this report focus on several areas of Hawaii County, including the southeastern coast, a potential development corridor along the Saddle Road between Hilo and the North Kohala District on the northwestern coast, and on the southeastern coast of Maui. In this report, reference is made to these areas as study areas rather than as areas where proposed or alternative facilities of the HGP would be located. The resource areas addressed herein include terrestrial ecology, aquatic ecology, and marine ecology. The scientific background data and related information is being made available for future research in these areas. This report describes the environmental resources present in the areas studied (i.e., the affected environment) and does not represent an assessment of environmental impacts.

  2. The Airborne Metagenome in an Indoor Urban Environment

    SciTech Connect (OSTI)

    Tringe, Susannah; Zhang, Tao; Liu, Xuguo; Yu, Yiting; Lee, Wah Heng; Yap, Jennifer; Yao, Fei; Suan, Sim Tiow; Ing, Seah Keng; Haynes, Matthew; Rohwer, Forest; Wei, Chia Lin; Tan, Patrick; Bristow, James; Rubin, Edward M.; Ruan, Yijun

    2008-02-12

    The indoor atmosphere is an ecological unit that impacts on public health. To investigate the composition of organisms in this space, we applied culture-independent approaches to microbes harvested from the air of two densely populated urban buildings, from which we analyzed 80 megabases genomic DNA sequence and 6000 16S rDNA clones. The air microbiota is primarily bacteria, including potential opportunistic pathogens commonly isolated from human-inhabited environments such as hospitals, but none of the data contain matches to virulent pathogens or bioterror agents. Comparison of air samples with each other and nearby environments suggested that the indoor air microbes are not random transients from surrounding outdoor environments, but rather originate from indoor niches. Sequence annotation by gene function revealed specific adaptive capabilities enriched in the air environment, including genes potentially involved in resistance to desiccation and oxidative damage. This baseline index of air microbiota will be valuable for improving designs of surveillance for natural or man-made release of virulent pathogens.

  3. Method for identifying anomalous terrestrial heat flows

    DOE Patents [OSTI]

    Del Grande, Nancy Kerr

    1977-01-25

    A method for locating and mapping the magnitude and extent of terrestrial heat-flow anomalies from 5 to 50 times average with a tenfold improved sensitivity over orthodox applications of aerial temperature-sensing surveys as used for geothermal reconnaissance. The method remotely senses surface temperature anomalies such as occur from geothermal resources or oxidizing ore bodies by: measuring the spectral, spatial, statistical, thermal, and temporal features characterizing infrared radiation emitted by natural terrestrial surfaces; deriving from these measurements the true surface temperature with uncertainties as small as 0.05 to 0.5 K; removing effects related to natural temperature variations of topographic, hydrologic, or meteoric origin, the surface composition, detector noise, and atmospheric conditions; factoring out the ambient normal-surface temperature for non-thermally enhanced areas surveyed under otherwise identical environmental conditions; distinguishing significant residual temperature enhancements characteristic of anomalous heat flows and mapping the extent and magnitude of anomalous heat flows where they occur.

  4. Long-period solar-terrestrial variability

    SciTech Connect (OSTI)

    Sonett, C.P. )

    1991-01-01

    Studies aimed at extending the record of solar-terrestrial variability to longer periods are discussed in a critical review of US research from the period 1987--1990. Sections are devoted to the sunspot index, radioactive carbon studies, a potential climate connection between radiocarbon changes and the solar irradiance cycle, Be-10 studies, geological laminae, solar neutrino counts, and the construction of data sets. Also included is a selective bibliography. 66 refs.

  5. Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    12 / Ellenton Bay Ellenton Bay Field 3-412 The Field 3-412/Ellenton Bay Set-Aside Area was one of the areas on the SRS selected for ecological studies in the early 1950's by scientists from the University of Georgia. This Area became well-known as a result of E. P. Odum's research on old-field succession and other studies of energy flow through ecosystems. Field 3-412 was one of the original ten SREL habitat reserve areas that were established on the SRS in the 1960's. This Area originally was

  6. Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Whipple/OHER Study Site This Set-Aside Area is 183.6 acres (74.3 ha) and is found within a fourth order reach segment of Upper Three Runs Creek (UTRC). This Set-Aside represents one of seven long-term vegetation study areas on the SRS. The site was named for its use in the Whipple-Good vegetation studies of the early 1980s, and in SREL's stream ecology studies for the DOE-HQ-Ofiice of Health, Environment, and Research (OHER). This site is representative of black gum-red bay (Nyssa

  7. Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    University of Georgia Old Laboratory Site This 113.1-acre (45.8 ha) Set-Aside Area, adjacent to the former location of the Savannah River Ecology Laboratory, is one of the original ten SREL habitat reserves and was selected to complement the old-field habitat/plant succession studies at Field 3-412 (Area #1) and Field 3-409 (Area #28). This relatively disturbed Set-Aside provided field study sites where manipulative research could be carried out on old-fields and radioecology experiments could

  8. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata

    SciTech Connect (OSTI)

    Liolios, Konstantinos; Chen, Amy; Mavromatis, Konstantinos; Tavernarakis, Nektarios; Hugenholtz, Phil; Markowitz, Victor; Kyrpides, Nikos C.

    2009-09-01

    The Genomes On Line Database (GOLD) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables and a search page. As of September 2009, GOLD contains information for more than 5800 sequencing projects, of which 1100 have been completed and their sequence data deposited in a public repository. GOLD continues to expand, moving toward the goal of providing the most comprehensive repository of metadata information related to the projects and their organisms/environments in accordance with the Minimum Information about a (Meta)Genome Sequence (MIGS/MIMS) specification.

  9. Fermilab | Sustainability | Nature/Ecology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Fermilab at Work Search Search Go Skip over navigation to main content Sustainability Nature and Ecology Sustainability Tips Electronics Stewardship Energy and Water Conservation...

  10. Employment | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Employment Openings are posted on the UGA Human Resources website. To search for employment opportunities at SREL, select Department #267 (Savannah River Ecology Laboratory). UGA HR

  11. SRS ecology: Environmental information document

    SciTech Connect (OSTI)

    Wike, L.D.; Shipley, R.W.; Bowers, J.A.

    1993-09-01

    The purpose of this Document is to provide a source of ecological information based on the exiting knowledge gained from research conducted at the Savannah River Site. This document provides a summary and synthesis of ecological research in the three main ecosystem types found at SRS and information on the threatened and endangered species residing there.

  12. Advanced Stirling conversion systems for terrestrial applications

    SciTech Connect (OSTI)

    Shaltens, R.K.

    1987-01-01

    Sandia National Laboratories (SNLA) is developing heat engines for terrestrial Solar distributed Heat Receivers. SNLA has identified the Stirling to be one of the most promising candidates for the terrestrial applications. The free-piston Stirling engine (FPSE) has the potential to meet the DOE goals for both performance and cost. Free-piston Stirling activities which are directed toward a dynamic power source for the space application are being conducted. Space power system requirements include high efficiency, very long life, high reliability and low vibration. The FPSE has the potential for future high power space conversion systems, either solar or nuclear powered. Generic free-piston technology is currently being developed for use with a residential heat pump under an Interagency Agreement. Also, an overview is presented of proposed conceptual designs for the Advanced Stirling Conversion System (ASCS) using a free-piston Stirling engine and a liquid metal heat pipe receiver. Power extraction includes both a linear alternator and hydraulic output capable of delivering approximately 25 kW of electrical power to the electric utility grid. Target cost of the engine/alternator is 300 dollars per kilowatt at a manufacturing rate of 10,000 units per year. The design life of the ASCS is 60,000 h (30 y) with an engine overhaul at 40,000 h (20 y). Also discussed are the key features and characteristics of the ASCS conceptual designs.

  13. Identification and resolution of microdiversity through metagenomic sequencing of parallel consortia

    SciTech Connect (OSTI)

    Nelson, William C.; Maezato, Yukari; Wu, Yu-Wei; Romine, Margaret F.; Lindemann, Stephen R.

    2016-01-01

    To gain a predictive understanding of the interspecies interactions within microbial communities that govern community function, the genomic complement of every member population must be determined. Although metagenomic sequencing has enabled the de novo reconstruction of some microbial genomes from environmental communities, microdiversity confounds current genome reconstruction techniques. To overcome this issue, we performed short-read metagenomic sequencing on parallel consortia, defined as consortia cultivated under the same conditions from the same natural community with overlapping species composition. The differences in species abundance between the two consortia allowed reconstruction of near-complete (est. >85% of gene complement) genome sequences for 17 of the 20 detected member species and revealed two Halomonas spp. and two Rhodobacteraceae sp. variants indistinguishable by amplicon analysis. Genomic comparison of these representative instances of inter- and intraspecies microdiversity suggest different mechanisms may result in expression of distinct roles in the community. In addition, isolation and complete genome sequence determination of six member species allowed an investigation into the sensitivity and specificity of genome reconstruction processes, demonstrating robustness across a wide range of sequence coverage (9x – 2700x).

  14. Using populations of human and microbial genomes for organism detection in metagenomes

    SciTech Connect (OSTI)

    Ames, Sasha K.; Gardner, Shea N.; Marti, Jose Manuel; Slezak, Tom R.; Gokhale, Maya B.; Allen, Jonathan E.

    2015-04-29

    Identifying causative disease agents in human patients from shotgun metagenomic sequencing (SMS) presents a powerful tool to apply when other targeted diagnostics fail. Numerous technical challenges remain, however, before SMS can move beyond the role of research tool. Accurately separating the known and unknown organism content remains difficult, particularly when SMS is applied as a last resort. The true amount of human DNA that remains in a sample after screening against the human reference genome and filtering nonbiological components left from library preparation has previously been underreported. In this study, we create the most comprehensive collection of microbial and reference-free human genetic variation available in a database optimized for efficient metagenomic search by extracting sequences from GenBank and the 1000 Genomes Project. The results reveal new human sequences found in individual Human Microbiome Project (HMP) samples. Individual samples contain up to 95% human sequence, and 4% of the individual HMP samples contain 10% or more human reads. In conclusion, left unidentified, human reads can complicate and slow down further analysis and lead to inaccurately labeled microbial taxa and ultimately lead to privacy concerns as more human genome data is collected.

  15. FOAM (Functional Ontology Assignments for Metagenomes): A Hidden Markov Model (HMM) database with environmental focus

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Prestat, Emmanuel; David, Maude M.; Hultman, Jenni; Ta , Neslihan; Lamendella, Regina; Dvornik, Jill; Mackelprang, Rachel; Myrold, David D.; Jumpponen, Ari; Tringe, Susannah G.; et al

    2014-09-26

    A new functional gene database, FOAM (Functional Ontology Assignments for Metagenomes), was developed to screen environmental metagenomic sequence datasets. FOAM provides a new functional ontology dedicated to classify gene functions relevant to environmental microorganisms based on Hidden Markov Models (HMMs). Sets of aligned protein sequences (i.e. ‘profiles’) were tailored to a large group of target KEGG Orthologs (KOs) from which HMMs were trained. The alignments were checked and curated to make them specific to the targeted KO. Within this process, sequence profiles were enriched with the most abundant sequences available to maximize the yield of accurate classifier models. An associatedmore » functional ontology was built to describe the functional groups and hierarchy. FOAM allows the user to select the target search space before HMM-based comparison steps and to easily organize the results into different functional categories and subcategories. FOAM is publicly available at http://portal.nersc.gov/project/m1317/FOAM/.« less

  16. Using populations of human and microbial genomes for organism detection in metagenomes

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Ames, Sasha K.; Gardner, Shea N.; Marti, Jose Manuel; Slezak, Tom R.; Gokhale, Maya B.; Allen, Jonathan E.

    2015-04-29

    Identifying causative disease agents in human patients from shotgun metagenomic sequencing (SMS) presents a powerful tool to apply when other targeted diagnostics fail. Numerous technical challenges remain, however, before SMS can move beyond the role of research tool. Accurately separating the known and unknown organism content remains difficult, particularly when SMS is applied as a last resort. The true amount of human DNA that remains in a sample after screening against the human reference genome and filtering nonbiological components left from library preparation has previously been underreported. In this study, we create the most comprehensive collection of microbial and reference-freemore » human genetic variation available in a database optimized for efficient metagenomic search by extracting sequences from GenBank and the 1000 Genomes Project. The results reveal new human sequences found in individual Human Microbiome Project (HMP) samples. Individual samples contain up to 95% human sequence, and 4% of the individual HMP samples contain 10% or more human reads. In conclusion, left unidentified, human reads can complicate and slow down further analysis and lead to inaccurately labeled microbial taxa and ultimately lead to privacy concerns as more human genome data is collected.« less

  17. Plutonium Isotopes in the Terrestrial Environment at the Savannah...

    Office of Scientific and Technical Information (OSTI)

    Plutonium Isotopes in the Terrestrial Environment at the Savannah River Site, USA. A Long-Term Study Citation Details In-Document Search Title: Plutonium Isotopes in the ...

  18. Improved assemblies using a source-agnostic pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of contigs

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Scholz, Matthew; Lo, Chien -Chi; Chain, Patrick S. G.

    2014-10-01

    Assembly of metagenomic samples is a very complex process, with algorithms designed to address sequencing platform-specific issues, (read length, data volume, and/or community complexity), while also faced with genomes that differ greatly in nucleotide compositional biases and in abundance. To address these issues, we have developed a post-assembly process: MetaGenomic Assembly by Merging (MeGAMerge). We compare this process to the performance of several assemblers, using both real, and in-silico generated samples of different community composition and complexity. MeGAMerge consistently outperforms individual assembly methods, producing larger contigs with an increased number of predicted genes, without replication of data. MeGAMerge contigs aremore » supported by read mapping and contig alignment data, when using synthetically-derived and real metagenomic data, as well as by gene prediction analyses and similarity searches. Ultimately, MeGAMerge is a flexible method that generates improved metagenome assemblies, with the ability to accommodate upcoming sequencing platforms, as well as present and future assembly algorithms.« less

  19. Draft genome sequence of Sulfurospirillum sp. strain MES, reconstructed from the metagenome of a microbial electrosynthesis system

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Ross, Daniel E.; Marshall, Christopher W.; May, Harold D.; Norman, R. Sean

    2015-01-15

    A draft genome of Sulfurospirillum sp. strain MES was isolated through taxonomic binning of a metagenome sequenced from a microbial electrosynthesis system (MES) actively producing acetate and hydrogen. The genome contains the nosZDFLY genes, which are involved in nitrous oxide reduction, suggesting the potential role of this strain in denitrification.

  20. Draft genome sequence of Sulfurospirillum sp. strain MES, reconstructed from the metagenome of a microbial electrosynthesis system

    SciTech Connect (OSTI)

    Ross, Daniel E.; Marshall, Christopher W.; May, Harold D.; Norman, R. Sean

    2015-01-15

    A draft genome of Sulfurospirillum sp. strain MES was isolated through taxonomic binning of a metagenome sequenced from a microbial electrosynthesis system (MES) actively producing acetate and hydrogen. The genome contains the nosZDFLY genes, which are involved in nitrous oxide reduction, suggesting the potential role of this strain in denitrification.

  1. Interactive effects of maternal and environmental exposure to coal combustion wastes decrease survival of larval southern toads (Bufo terrestris)

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Interactive effects of maternal and environmental exposure to coal combustion wastes decrease survival of larval southern toads (Bufo terrestris) Brian S. Metts a, * , Kurt A. Buhlmann a , David E. Scott a , Tracey D. Tuberville a , William A. Hopkins b a Savannah River Ecology Laboratory, Drawer E, Aiken, SC 29802, USA b Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA 24061, USA a r t i c l e i n f o Article history: Received 16 August 2011 Received in revised form

  2. SRS ECOLOGY ENVIRONMENTAL INFORMATION DOCUMENT -1997 UPDATE

    SciTech Connect (OSTI)

    Halverson, N.V.; Wike, L.D.; Patterson, K.K.; Bowers, J.A.; Bryan, A.L.; Chen, K.F.; Cummins, C.L.; deCarmen, B.R.; Dixon, K.L.; Dunn, D.L.

    1997-12-31

    The purpose of the SRS Ecology: Environmental Information Document is to provide a source of information on the ecology of the Savannah River Site.

  3. Solar terrestrial coupling through space plasma processes

    SciTech Connect (OSTI)

    Birn, J.

    2000-12-01

    This is the final report of a three-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The project investigates plasma processes that govern the interaction between the solar wind, charged particles ejected from the sun, and the earth's magnetosphere, the region above the ionosphere governed by the terrestrial magnetic field. Primary regions of interest are the regions where different plasma populations interact with each other. These are regions of particularly dynamic plasma behavior, associated with magnetic flux and energy transfer and dynamic energy release. The investigations concerned charged particle transport and energization, and microscopic and macroscopic instabilities in the magnetosphere and adjacent regions. The approaches combined space data analysis with theory and computer simulations.

  4. Assembly-driven metagenomics of a hypersaline microbial ecosystem (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Allen, Eric

    2013-03-01

    Eric Allen of Scripps and UC San Diego on "Assembly-driven metagenomics of a hypersaline microbial ecosystem" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  5. Synthetic Metagenomics: Converting digital information back to Biology (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Deutsch, Sam [DOE Joint Genome Institute

    2013-03-01

    Sam Deutsch of the DOE JGI on "Synthetic Metagenomics: Converting digital information back to Biology" at the 8th Annual Genomics of Energy & Environment Meeting in Walnut Creek, Calif.

  6. Comparison of Normalized and Unnormalized Single Cell and Population Assemblies (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Hugenholtz, Phil [University of Queensland

    2013-01-22

    University of Queensland's Phil Hugenholtz on "Comparison of Normalized and Unnormalized Single Cell and Population Assemblies" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  7. Sitewide biological risk assessment Eielson Air Force Base, Alaska: Risks to terrestrial receptors from diverse contaminants

    SciTech Connect (OSTI)

    Brandt, C.A.; Becker, J.M.

    1995-12-31

    Eielson Air Force Base (AFB) is located southeast of Fairbanks, Alaska. Eielson AFB was listed by the US Environmental Protection Agency on the National Priorities List with a total of 64 potential terrestrial and aquatic source areas. Contaminants of concern include fuel and fuel components, pesticides, polychlorinated biphenyls (PCBs), and lead. As part of the remedial investigations of these sites, a biological risk assessment (BRA) was conducted to estimate the risk of ecological effects on terrestrial receptors posed by contaminants in the Eielson environment. There are 32 mammal species, 117 bird species, 17 fish species, and 1 amphibian species known to inhabit Eielson AFB and vicinity. The BRA screened source areas based on completed biological exposure pathways, selected receptors for analysis, estimated exposure of receptors to contaminants, and compared these exposures to known toxicological effects. Lower Garrison Slough and Flightline Pond posed a substantial risk for shrikes and goshawks. Ingestion of PCBs constituted the primary pathway/contaminant combination contributing to this risk. The effects of the various sources of uncertainty in the ingestion exposure calculations for these sites were evaluated in a probabilistic risk assessment using Monte Carlo methods. There was an 11% risk of reproductive effects from PCBs for goshawks feeding from Flightline Pond and a 25 % risk from lower Garrison Slough. There was an 81 % risk of reproductive effects from PCB exposure for shrikes feeding near lower Garrison Slough.

  8. Women & the Department of Ecology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    30 * This permit will have about a 90-day comment period (closing Sept. 30 with the rest of the permit) * Ecology to offer webinar workshophearing on SST permit * Seeking HAB ...

  9. Ecology WTP Recovery Plan comments ...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    SSTs are to be retrieved during the coming year from the pool of tanks approved by Ecology (Appendix I, Section 2.1.2) have already been established to maintain and monitor...

  10. Ecology WTP Recovery Plan comments ...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    and the Hanford Site Integrated Priority List (IPL). Approvals Approved Disapproved Ecology Date Approved Disapproved DOE - ORP Date M-62-04-01 CR 1 Modifications to the M-62-00...

  11. Strategies for enhancing the effectiveness of metagenomic-based enzyme discovery in lignocellulytic microbial communities

    SciTech Connect (OSTI)

    DeAngelis, K.M.; Gladden, J.G.; Allgaier, M.; D'haeseleer, P.; Fortney, J.L.; Reddy, A.; Hugenholtz, P.; Singer, S.W.; Vander Gheynst, J.; Silver, W.L.; Simmons, B.; Hazen, T.C.

    2010-03-01

    Producing cellulosic biofuels from plant material has recently emerged as a key U.S. Department of Energy goal. For this technology to be commercially viable on a large scale, it is critical to make production cost efficient by streamlining both the deconstruction of lignocellulosic biomass and fuel production. Many natural ecosystems efficiently degrade lignocellulosic biomass and harbor enzymes that, when identified, could be used to increase the efficiency of commercial biomass deconstruction. However, ecosystems most likely to yield relevant enzymes, such as tropical rain forest soil in Puerto Rico, are often too complex for enzyme discovery using current metagenomic sequencing technologies. One potential strategy to overcome this problem is to selectively cultivate the microbial communities from these complex ecosystems on biomass under defined conditions, generating less complex biomass-degrading microbial populations. To test this premise, we cultivated microbes from Puerto Rican soil or green waste compost under precisely defined conditions in the presence dried ground switchgrass (Panicum virgatum L.) or lignin, respectively, as the sole carbon source. Phylogenetic profiling of the two feedstock-adapted communities using SSU rRNA gene amplicon pyrosequencing or phylogenetic microarray analysis revealed that the adapted communities were significantly simplified compared to the natural communities from which they were derived. Several members of the lignin-adapted and switchgrass-adapted consortia are related to organisms previously characterized as biomass degraders, while others were from less well-characterized phyla. The decrease in complexity of these communities make them good candidates for metagenomic sequencing and will likely enable the reconstruction of a greater number of full length genes, leading to the discovery of novel lignocellulose-degrading enzymes adapted to feedstocks and conditions of interest.

  12. Ecological safety of tidal-power projects

    SciTech Connect (OSTI)

    Fedorov, M. P.; Shilin, M. B.

    2010-07-15

    The operating regime of tidal power plants requires ecological monitoring of their associated water area.

  13. Isotope powered Stirling generator for terrestrial applications

    SciTech Connect (OSTI)

    Tingey, G.L.; Sorensen, G.C.; Ross, B.A.

    1995-01-01

    An electric power supply, small enough to be man-portable, is being developed for remote, terrestrial applications. This system is designed for an operating lifetime of five years without maintenance or refueling. A small Radioisotope Stirling Generator (RSG) has been developed. The energy source of the generator is a 60 watt plutonium-238 fuel clad used in the General Purpose Heat Sources (GPHS) developed for space applications. A free piston Stirling Engine drives a linear alternator to convert the heat to power. The system weighs about 7.5 kg and produces 11 watts AC power with a conversion efficiency of 18.5%. Two engine models have been designed, fabricated, and tested to date: (a) a developmental model instrumented to confirm and test parameters, and (b) an electrically heated model with an electrical heater equipped power input leads. Critical components have been tested for 10,000 to 20,000 hours. One complete generator has been operating for over 11,000 hours. Radioisotope heated prototypes are expected to be fabricated and tested in late 1995.

  14. Constraints on the bioavailability of trace elements to terrestrial fauna at mining and smelting sites

    SciTech Connect (OSTI)

    Pastorok, R.; Schoof, R.; LaTier, A.; Mellott, R.; Shields, W.; Ruby, M.

    1995-12-31

    At mining and smelting sites, the bioavailability of waste-related trace elements to terrestrial wildlife is limited by mineralogy of the waste material and the geochemistry of the waste-soil mixture. For example, encapsulation of trace elements in inert mineral matrices limits the assimilation of particle-associated trace elements that are ingested by wildlife. The bioavailability of arsenic, cadmium, copper, lead, silver, and zinc at mining and smelting sites in Oklahoma and Montana was evaluated based on analysis of waste material, soil chemistry, and concentrations of trace elements in whole-body samples of key food web species. Concentrations of trace elements were generally elevated relative to reference area values for selected species of vegetation, insects, spiders, and small mammals. Soil-to-tissue bioconcentration factors derived from field data at these sites were generally low (< 1), with the exception of cadmium in vegetation. For all of the trace elements evaluated, wildlife exposure models indicate that the potential for transfer of contaminants to wildlife species of public concern and high trophic-level predators is limited. Moreover, laboratory feeding experiments conducted with cadmium and lead indicate that the assimilation of waste-related trace elements by mammals is relatively low (24--47 percent for lead in blood and bone; 22--44 percent for cadmium in kidney). The relatively low bioavailability of trace elements at mining and smelting sites should be considered when estimating exposure of ecological receptors and when deriving soil cleanup criteria based on measured or modeled ecological risk.

  15. Tidal heating in multilayered terrestrial exoplanets

    SciTech Connect (OSTI)

    Henning, Wade G.; Hurford, Terry

    2014-07-01

    The internal pattern and overall magnitude of tidal heating for spin-synchronous terrestrial exoplanets from 1 to 2.5 R{sub E} is investigated using a propagator matrix method for a variety of layer structures. Particular attention is paid to ice-silicate hybrid super-Earths, where a significant ice mantle is modeled to rest atop an iron-silicate core, and may or may not contain a liquid water ocean. We find multilayer modeling often increases tidal dissipation relative to a homogeneous model, across multiple orbital periods, due to the ability to include smaller volume low viscosity regions, and the added flexure allowed by liquid layers. Gradations in parameters with depth are explored, such as allowed by the Preliminary Earth Reference Model. For ice-silicate hybrid worlds, dramatically greater dissipation is possible beyond the case of a silicate mantle only, allowing non-negligible tidal activity to extend to greater orbital periods than previously predicted. Surface patterns of tidal heating are found to potentially be useful for distinguishing internal structure. The influence of ice mantle depth and water ocean size and position are shown for a range of forcing frequencies. Rates of orbital circularization are found to be 10-100 times faster than standard predictions for Earth-analog planets when interiors are moderately warmer than the modern Earth, as well as for a diverse range of ice-silicate hybrid super-Earths. Circularization rates are shown to be significantly longer for planets with layers equivalent to an ocean-free modern Earth, as well as for planets with high fractions of either ice or silicate melting.

  16. Washington State Department of Ecology | Open Energy Information

    Open Energy Info (EERE)

    Ecology Jump to: navigation, search Logo: Washington State Department of Ecology Name: Washington State Department of Ecology Place: Lacey, Washington Zip: 98503 References:...

  17. Mexico National Institute of Ecology and Climate Change (INECC...

    Open Energy Info (EERE)

    Institute of Ecology and Climate Change (INECC) Jump to: navigation, search Logo: Mexico National Institute of Ecology Name: Mexico National Institute of Ecology Address:...

  18. Savannah River Ecology Laboratory Annual Technical Progress Report of Ecological Research, June 30, 2001

    SciTech Connect (OSTI)

    Bertsch, Paul M.; Janecek, Laura; Rosier, Brenda

    2001-06-30

    The Savannah River Ecology Laboratory (SREL) is a research unit of the University of Georgia (UGA) and has been conducting ecological research on the Savannah River Site (SRS) in South Carolina for 50 years. The overall mission of the Laboratory is to acquire and communicate knowledge of ecological processes and principles. SREL conducts fundamental and applied ecological research, as well as education and outreach programs, under a Cooperative Agreement with the U.S. Department of Energy (DOE) SRS near Aiken, South Carolina. The Laboratory's research mission during the 2001 fiscal year was fulfilled with the publication of one book and 83 journal articles and book chapters by faculty, technical staff, students, and visiting scientists. An additional 77 journal articles have been submitted or are in press. Other noteworthy events took place as faculty members and graduate students received awards. These are described in the section Special Accomplishments of Faculty, Staff, Students, and Administration on page 54. Notable scientific accomplishments include work conducted on contaminant transport, global reptile decline, phytoremediation, and radioecology. Dr. Domy Adriano authored the second edition of his book ''Trace Elements in Terrestrial Environments: Biogeochemistry, Bioavailability, and Risks of Metals'', which was recently published by Springer-Verlag. The book provides a comprehensive treatment of many important aspects of trace elements in the environment. The first edition of the book, published in 1986, has become a widely acclaimed and cited reference. International attention was focused on the problem of reptile species decline with the publication of an article on this topic in the journal ''Bioscience'' in August, 2000. The article's authors included Dr. Whit Gibbons and a number of other SREL herpetologists who researched the growing worldwide problem of decline of reptile species. Factors related to these declines include habitat loss and

  19. Kimberly Andrews | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Andrews with kingsnake Curriculum Vitae Faculty & Scientists SREL Home SREL Herpetology Kimberly Andrews Savannah River Ecology Laboratory P O Drawer E, Aiken, SC 29802 (803) 725-9793 office (803) 725-3309 fax andrews(at)srel.uga.edu Kimberly received her PhD in Ecology (2010) from the University of Georgia’s Odum School of Ecology through work at the Savannah River Ecology Laboratory (UGA SREL) under the advisement of Dr. Whit Gibbons. Kimberly also holds an M.S. in Conservation Ecology

  20. Observing terrestrial ecosystems and the carbon cycle from space

    SciTech Connect (OSTI)

    Schimel, David; Pavlick, Ryan; Fisher, Joshua B.; Asner, Gregory P.; Saatchi, Sassan; Townsend, Philip; Miller, Charles E.; Frankenberg, Christian; Hibbard, Kathleen A.; Cox, Peter

    2015-02-06

    Modeled terrestrial ecosystem and carbon cycle feedbacks contribute substantial uncertainty to projections of future climate. The limitations of current observing networks contribute to this uncertainty. Here we present a current climatology of global model predictions and observations for photosynthesis, biomass, plant diversity and plant functional diversity. Carbon cycle tipping points occur in terrestrial regions where fluxes or stocks are largest, and where biological variability is highest, the tropics and Arctic/Boreal zones. Global observations are predominately in the mid-latitudes and are sparse in high and low latitude ecosystems. Observing and forecasting ecosystem change requires sustained observations of sufficient density in time and space in critical regions. Using data and theory available now, we can develop a strategy to detect and forecast terrestrial carbon cycle-climate interactions, by combining in situ and remote techniques.

  1. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata

    SciTech Connect (OSTI)

    Fenner, Marsha W; Liolios, Konstantinos; Mavromatis, Konstantinos; Tavernarakis, Nektarios; Kyrpides, Nikos C.

    2007-12-31

    The Genomes On Line Database (GOLD) is a comprehensive resource of information for genome and metagenome projects world-wide. GOLD provides access to complete and ongoing projects and their associated metadata through pre-computed lists and a search page. The database currently incorporates information for more than 2900 sequencing projects, of which 639 have been completed and the data deposited in the public databases. GOLD is constantly expanding to provide metadata information related to the project and the organism and is compliant with the Minimum Information about a Genome Sequence (MIGS) specifications.

  2. Characterization of the bacterial metagenome in an industrial algae bioenergy production system

    SciTech Connect (OSTI)

    Huang, Shi; Fulbright, Scott P; Zeng, Xiaowei; Yates, Tracy; Wardle, Greg; Chisholm, Stephen T; Xu, Jian; Lammers, Peter

    2011-03-16

    Cultivation of oleaginous microalgae for fuel generally requires growth of the intended species to the maximum extent supported by available light. The presence of undesired competitors, pathogens and grazers in cultivation systems will create competition for nitrate, phosphate, sulfate, iron and other micronutrients in the growth medium and potentially decrease microalgal triglyceride production by limiting microalgal health or cell density. Pathogenic bacteria may also directly impact the metabolism or survival of individual microalgal cells. Conversely, symbiotic bacteria that enhance microalgal growth may also be present in the system. Finally, the use of agricultural and municipal wastes as nutrient inputs for microalgal production systems may lead to the introduction and proliferation of human pathogens or interfere with the growth of bacteria with beneficial effects on system performance. These considerations underscore the need to understand bacterial community dynamics in microalgal production systems in order to assess microbiome effects on microalgal productivity and pathogen risks. Here we focus on the bacterial component of microalgal production systems and describe a pipeline for metagenomic characterization of bacterial diversity in industrial cultures of an oleaginous alga, Nannochloropsis salina. Environmental DNA was isolated from 12 marine algal cultures grown at Solix Biofuels, a region of the 16S rRNA gene was amplified by PCR, and 16S amplicons were sequenced using a 454 automated pyrosequencer. The approximately 70,000 sequences that passed quality control clustered into 53,950 unique sequences. The majority of sequences belonged to thirteen phyla. At the genus level, sequences from all samples represented 169 different genera. About 52.94% of all sequences could not be identified at the genus level and were classified at the next highest possible resolution level. Of all sequences, 79.92% corresponded to 169 genera and 70 other taxa. We

  3. MCNP6 Cosmic & Terrestrial Background Particle Fluxes -- Release 4

    SciTech Connect (OSTI)

    McMath, Garrett E.; McKinney, Gregg W.; Wilcox, Trevor

    2015-01-23

    Essentially a set of slides, the presentation begins with the MCNP6 cosmic-source option, then continues with the MCNP6 transport model (atmospheric, terrestrial) and elevation scaling. It concludes with a few slides on results, conclusions, and suggestions for future work.

  4. T.G. Hinton: Radioactive Contaminants in Terrestrial Ecosystems...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Savannah River Ecology Laboratory P O Drawer E, Aiken, SC 29802 (803) 725-7454 office (803) 725-3309 fax thinton(at)uga.edu Dr. Hinton has published numerous papers on plant ...

  5. Metagenomic analysis of the microbiota in the highly compartmented hindguts of six wood- or soil-feeding higher termites

    SciTech Connect (OSTI)

    Rossmassler, Karen; Dietrich, Carsten; Thompson, Claire; Mikaelyan, Aram; Nonoh, James O.; Scheffrahn, Rudolf H.; Sillam-Dussès, David; Brune, Andreas

    2015-11-26

    Termites are important contributors to carbon and nitrogen cycling in tropical ecosystems. Higher termites digest lignocellulose in various stages of humification with the help of an entirely prokaryotic microbiota housed in their compartmented intestinal tract. Previous studies revealed fundamental differences in community structure between compartments, but the functional roles of individual lineages in symbiotic digestion are mostly unknown. Furthermore, we conducted a highly resolved analysis of the gut microbiota in six species of higher termites that feed on plant material at different levels of humification. Combining amplicon sequencing and metagenomics, we assessed similarities in community structure and functional potential between the major hindgut compartments (P1, P3, and P4). Cluster analysis of the relative abundances of orthologous gene clusters (COGs) revealed high similarities among woodand litter-feeding termites and strong differences to humivorous species. However, abundance estimates of bacterial phyla based on 16S rRNA genes greatly differed from those based on protein-coding genes. In conclusion, the community structure and functional potential of the microbiota in individual gut compartments are clearly driven by the digestive strategy of the host. The metagenomics libraries obtained in this study provide the basis for future studies that elucidate the fundamental differences in the symbiont-mediated breakdown of lignocellulose and humus by termites of different feeding groups. The high proportion of uncultured bacterial lineages in all samples calls for a reference-independent approach for the correct taxonomic assignment of protein-coding genes.

  6. Metagenomic analysis of the microbiota in the highly compartmented hindguts of six wood- or soil-feeding higher termites

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Rossmassler, Karen; Dietrich, Carsten; Thompson, Claire; Mikaelyan, Aram; Nonoh, James O.; Scheffrahn, Rudolf H.; Sillam-Dussès, David; Brune, Andreas

    2015-11-26

    Termites are important contributors to carbon and nitrogen cycling in tropical ecosystems. Higher termites digest lignocellulose in various stages of humification with the help of an entirely prokaryotic microbiota housed in their compartmented intestinal tract. Previous studies revealed fundamental differences in community structure between compartments, but the functional roles of individual lineages in symbiotic digestion are mostly unknown. Furthermore, we conducted a highly resolved analysis of the gut microbiota in six species of higher termites that feed on plant material at different levels of humification. Combining amplicon sequencing and metagenomics, we assessed similarities in community structure and functional potential betweenmore » the major hindgut compartments (P1, P3, and P4). Cluster analysis of the relative abundances of orthologous gene clusters (COGs) revealed high similarities among woodand litter-feeding termites and strong differences to humivorous species. However, abundance estimates of bacterial phyla based on 16S rRNA genes greatly differed from those based on protein-coding genes. In conclusion, the community structure and functional potential of the microbiota in individual gut compartments are clearly driven by the digestive strategy of the host. The metagenomics libraries obtained in this study provide the basis for future studies that elucidate the fundamental differences in the symbiont-mediated breakdown of lignocellulose and humus by termites of different feeding groups. The high proportion of uncultured bacterial lineages in all samples calls for a reference-independent approach for the correct taxonomic assignment of protein-coding genes.« less

  7. Educational Materials | Savannah River Ecology Laboratory Environmental

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Outreach Program Educational Materials southern hognose snake Ecology Fact Sheets Ready-to-use information on a variety of ecological topics alligator Ecoviews Dr. Whit Gibbons' weekly ecological commentaries Savannah River Site National Environmental Research Park Research Snapshots Information on a variety of research conducted at SREL cottonmouth Wildlife Safety • How to be safe around snakes • How to be safe around alligators

  8. Women & the Department of Ecology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    June 6, 2013 Hanford Permit Update  Working with EPA Region 10 and Ecology's Hazardous Waste and Toxics Reduction Program on technical evaluation, regulatory interpretation and statewide consistency for the draft permit.  Many of the discussion topics resulted from the public comments that we received during the public comment period. 'New' Ecology Director  Maia Bellon was appointed as Ecology director in mid-February (just days before the announcement of 6 leaking tanks).  Maia has

  9. I. Lehr Brisbin | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Brisbin Faculty & Scientists SREL Home I. Lehr Brisbin Savannah River Ecology Laboratory P O Drawer E, Aiken, SC 29802 (803) 725-5668 office (803) 725-3309 fax brisbin(at)uga.edu Research interests: Vertebrate ecology, radioecology, ecotoxicology, and animal behavior, particularly that related to canine olfaction. Current research is investigating ecological cycling processes; analyses of sigmoid curves and their application to studies of contaminant cycling and growth processes; biology of

  10. Larry Bryan | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Bryan Curriculum Vitae Faculty & Scientists SREL Home Larry Bryan Savannah River Ecology Laboratory P O Drawer E, Aiken, SC 29802 (803) 725-2907 office (803) 725-3309 fax lbryan(at)srel.uga.edu Research interests: Vertebrate ecology, habitat use, potential threats from contamination, rare species conservation. Current Research: Mycteria americana (endangered wood stork) Tracking large-scale movements via satellite telemetry Foraging ecology, behavior, and trophic position Breeding success

  11. Terrestrial Heat Flow In The North Island Of New Zealand | Open...

    Open Energy Info (EERE)

    Terrestrial Heat Flow In The North Island Of New Zealand Jump to: navigation, search OpenEI Reference LibraryAdd to library Journal Article: Terrestrial Heat Flow In The North...

  12. Erin Abernethy | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Erin Abernethy SREL Graduate Program Odum School of Ecology Erin Abernethy Masters Student Rhodes Lab Erin joined the Savannah River Ecology Lab in January 2013 as a Master’s student with Dr. Gene Rhodes through the Odum School of Ecology at the University of Georgia. Erin grew up in Aiken, SC, and is currently attending classes in Athens, Ga. She will be studying the scavenging ecology of invasive species in Hawai’i, as well as doing field and lab work at SREL. Before joining SREL, Erin lived

  13. Educational Materials | Savannah River Ecology Laboratory Environmenta...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Research Snapshots The Savannah River Site National Environmental Research Park The History of Radioecology Research at the Savannah River Ecology Laboratory Gray Foxes of the ...

  14. New Ecology Inc | Open Energy Information

    Open Energy Info (EERE)

    to: navigation, search Name: New Ecology Inc Address: 130 Bishop Allen Drive Place: Cambridge, Massachusetts Zip: 02139 Region: Greater Boston Area Sector: Buildings Product:...

  15. Beasley Lab | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    ... Sarah Webster returned to Belarus along with Cara Love to recover wolf GPS transmitters ... with Tom Hinton to conduct research on wolf spatial ecology and carnivore population ...

  16. Rich Biemiller | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    more effectively and efficiently. His primary research interests include aquatic invertebrate ecology, stream disturbance assessment and restoration, and headwater stream hydrology...

  17. STATE OF WASHINGTON DEPARTMENT OF ECOLOGY

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    " "'- STATE OF WASHINGTON DEPARTMENT OF ECOLOGY p.o. Box 47600 .Olympja, Washington 98504-7600 (360) 4076000 .TOD Only (Hearing Impaired) (360) 407-6006 ,'""""" .w.--.- ...

  18. Ecology Environment Inc | Open Energy Information

    Open Energy Info (EERE)

    Environment Inc Jump to: navigation, search Name: Ecology & Environment, Inc. Place: Seattle, Washington Zip: 98104 Product: Environmental consulting firm serving corporate and...

  19. Melissa Pilgrim | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    variation impact population level processes. Her research program integrates field ecology, biogeochemistry (e.g., stable isotopes), and ecophysiology. She uses herpetological...

  20. Greg Skupien | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Greg Skupien SREL Graduate Program Odum School of Ecology Greg Skupien Masters Student Odum School of Ecology, UGA Greg Skupien is currently pursuing a Master’s in Conservation Ecology and Sustainable Development in the Odum School of Ecology at the University of Georgia under the advisement of Dr. Kimberly Andrews. Greg graduated from the University of Wisconsin-Madison in 2008 where he received his B.S. in Zoology and a certificate in Environmental Studies. In 2011, Greg began work in the

  1. Rebecca Sharitz | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Faculty & Scientists SREL Home UGA Plant Biology Rebecca Sharitz Savannah River Ecology ... We are also conducting studies on the population biology and conservation of rare plants, ...

  2. Thomas G. Hinton | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    human and ecological risk analyses; remediation of radioactively contaminated wetlands; contaminant transport models; the use of radioactive tracers as a tool for...

  3. Michael E. Dorcas | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    as coauthors. He is involved in numerous research projects including studies of invasive Burmese pythons in Florida and the ecology and conservation of diamondback terrapins...

  4. EA-1964: National Ecological Observation Network (NEON)

    Broader source: Energy.gov [DOE]

    The National Science Foundation (NSF) prepared an EA that evaluated potential environmental impacts of the proposed National Ecological Observation Network (NEON), a continental-scale network of...

  5. Trends and Future Challenges in Sampling the Deep Terrestrial Biosphere

    SciTech Connect (OSTI)

    Wilkins, Michael J.; Daly, Rebecca; Mouser, Paula J.; Trexler, Ryan; Sharma, Shihka; Cole, David R.; Wrighton, Kelly C.; Biddle , Jennifer F.; Denis, Elizabeth; Fredrickson, Jim K.; Kieft, Thomas L.; Onstott, T. C.; Peterson, Lee; Pfiffner, Susan M.; Phelps, Tommy J.; Schrenk, Matthew O.

    2014-09-12

    Research in the deep terrestrial biosphere is driven by interest in novel biodiversity and metabolisms, biogeochemical cycling, and the impact of human activities on this ecosystem. As this interest continues to grow, it is important to ensure that when subsurface investigations are proposed, materials recovered from the subsurface are sampled and preserved in an appropriate manner to limit contamination and ensure preservation of accurate microbial, geochemical, and mineralogical signatures. On February 20th, 2014, a workshop on “Trends and Future Challenges in Sampling The Deep Subsurface” was coordinated in Columbus, Ohio by The Ohio State University and West Virginia University faculty, and sponsored by The Ohio State University and the Sloan Foundation’s Deep Carbon Observatory. The workshop aims were to identify and develop best practices for the collection, preservation, and analysis of terrestrial deep rock samples. This document summarizes the information shared during this workshop.

  6. Baseline measurements of terrestrial gamma radioactivity at the CEBAF site

    SciTech Connect (OSTI)

    Wollenberg, H.A.; Smith, A.R.

    1991-10-01

    A survey of the gamma radiation background from terrestrial sources was conducted at the CEBAF site, Newport News, Virginia, on November 12--16, 1990, to provide a gamma radiation baseline for the site prior to the startup of the accelerator. The concentrations and distributions of the natural radioelements in exposed soil were measured, and the results of the measurements were converted into gamma-ray exposure rates. Concurrently, samples were collected for laboratory gamma spectral analyses.

  7. Thermoelectrics: From Space Power Systems to Terrestrial Waste Heat

    Broader source: Energy.gov (indexed) [DOE]

    Recovery Applications | Department of Energy Progress in reliable high temperature segmented thermoelectric devices and potential for producing electricity from waste heat from energy intensive industrial processes and transportation vehicles exhaust are discussed fluerial.pdf (3.11 MB) More Documents & Publications Thermoelectrics: From Space Power Systems to Terrestrial Waste Heat Recovery Applications High Reliability, High TemperatureThermoelectric Power Generation Materials and

  8. Comparative Metagenomics of Gut and Ocean: Identification of Microbial Marker Genes for Complex Environmental Properties(2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Bork, Peer

    2011-06-03

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Peer Bork of the European Molecular Biology Laboratory on "Comparative Metagenomics of Gut and Ocean: Identification of Microbial Marker Genes for Complex Environmental Properties" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  9. Comparative Metagenomics of Gut and Ocean: Identification of Microbial Marker Genes for Complex Environmental Properties(2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Bork, Peer

    2011-03-23

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Peer Bork of the European Molecular Biology Laboratory on "Comparative Metagenomics of Gut and Ocean: Identification of Microbial Marker Genes for Complex Environmental Properties" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  10. The Center for Architecture, Science, and Ecology (CASE) | Open...

    Open Energy Info (EERE)

    Architecture, Science, and Ecology (CASE) Jump to: navigation, search Name: The Center for Architecture, Science, and Ecology Address: 14 Wall Street 24th Floor New York, NY 10005...

  11. Ecological Screening Values for Surface Water, Sediment, and...

    Office of Scientific and Technical Information (OSTI)

    Ecological Screening Values for Surface Water, Sediment, and Soil Citation Details In-Document Search Title: Ecological Screening Values for Surface Water, Sediment, and Soil ...

  12. Ecological Screening Values for Surface Water, Sediment, and...

    Office of Scientific and Technical Information (OSTI)

    Ecological Screening Values for Surface Water, Sediment, and Soil Friday, G. P. 54 ENVIRONMENTAL SCIENCES; SOILS; SURFACE WATERS; SEDIMENTS; ECOLOGICAL CONCENTRATION; ENVIRONMENTAL...

  13. Women & the Department of Ecology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    November 1, 2012 Agency Update Hanford Advisory Board Permit path forward Current status  Comment period closed October 22  Ecology working on comment responses Next steps  Permit will be revised, as needed  Ecology will send letter to DOE  Final permit to be issued 30 days later HAB advice  The Board's advice has been incorporated into permit comments  Ecology will respond to advice in the comment response document and in a separate letter to the Board when the

  14. Women & the Department of Ecology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    February 7, 2013 Agency Update Hanford Advisory Board Hanford Permit update Comments  Ecology received nearly 5,000 comments on the permit during last year's comment period (May 1-October 22). o Public comments: ~1,800 o DOE comments: ~3,000  Ecology staff working on comment responses. Next steps  Ecology estimates about a 2-year effort to: o Modify the permit to address substantial comments and issues. o Reissue draft permit with substantive changes & respond to initial

  15. Robert A. Kennamer | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Curriculum Vitae Faculty & Scientists SREL Home Robert A. Kennamer Savannah River Ecology Laboratory P O Drawer E, Aiken, SC 29802 (803) 725-0387 office (803) 725-3309 fax...

  16. Stacey Lance | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Lance Faculty & Scientists SREL Home Stacey Lance Savannah River Ecology Laboratory P O Drawer E, Aiken, SC 29802 (803) 725-0988 office (803) 725-3309 fax lance(at)srel.uga.edu...

  17. Peter Stangel | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Senior Vice President, U.S. Endowment for Forestry and Communities co Savannah River Ecology Laboratory P O Drawer E, Aiken, SC 29802 (404)-915-2763 (803) 725-8158...

  18. Tracey Tuberville | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Faculty & Scientists SREL Home SREL Herpetology Tracey D. Tuberville Savannah River Ecology Laboratory P O Drawer E, Aiken, SC 29802 (803) 725-5757office (803) 725-3309 fax...

  19. David E. Scott | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Scott Curriculum Vitae Faculty & Scientists SREL Home David E. Scott Savannah River Ecology Laboratory P O Drawer E, Aiken, SC 29802 (803) 725-5747 office (803) 725-3309 fax...

  20. Rebecca Sharitz: Teaching | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Teaching book cover I co-teach a graduate course in wetlands ecology (PBIO 8150) with Dr. Darold Batzer of the UGA Department of Entomology. The course objective is to describe...

  1. Women & the Department of Ecology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    March 6, 2014 Agency Update Hanford Advisory Board Key News Since Last HAB Meeting * Ecology letter on AY-102 pumping plan * Revised plan expected March 7 * Gov/AG letter requests new proposal on CD * Meeting possible later this month w/Governor & Moniz Key News cont. * Ecology, DOE finalize Agreed Order on CWC/WRAP * Annual TPA Public Involvement Survey conducted * More than 160 responses collected (new record!) Education & Outreach * Hanford email listserv keeps growing! * Subscribers

  2. J. Whitfield Gibbons | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Gibbons Curriculum Vitae Faculty & Scientists SREL Home SREL Herpetology J. Whitfield Gibbons Savannah River Ecology Laboratory P O Drawer E, Aiken, SC 29802 (803) 725-5852 / 725-5733 office (803) 725-3309 fax wgibbons(at)uga.edu My research interests focus on the population dynamics and ecology of aquatic and semiaquatic vertebrates and have involved detailed population studies of fish, amphibians, and reptiles, particularly turtles. One objective has been to determine functional

  3. James Beasley | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Beasley Curriculum Vitae Faculty & Scientists SREL Home James Beasley Savannah River Ecology Laboratory P O Drawer E, Aiken, SC 29802 (803) 725-5113 office (803) 725-3309 fax beasley(at)srel.uga.edu My research interests address both theoretical and applied questions in wildlife ecology and management. Within this framework, my research focuses on understanding the effects of habitat fragmentation and anthropogenic land use on the movement behavior, interspecific interactions, and population

  4. Judith L. Greene | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Greene Curriculum Vitae Faculty & Scientists SREL Home SREL Herpetology Judith L. Greene Savannah River Ecology Laboratory P O Drawer E, Aiken, SC 29802 (803) 725-7637 office (803) 725-3309 fax jgreene(at)srel.uga.edu My research interests include the population dynamics and ecology and of reptiles and amphibians, particularly turtles. Objectives have included documenting the distribution and abundance patterns of herpetofauna and relating this to conservation issues for herps , as well as

  5. Justin D. Congdon | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Congdon Curriculum Vitae Faculty & Scientists SREL Home SREL Herpetology Justin D. Congdon Savannah River Ecology Laboratory P O Drawer E, Aiken, SC 29802 (803) 725-5341 office (803) 725-3309 fax congdon(at)srel.uga.edu Justin Congdon is a Professor Emeritus at University of Georgia. For many years preceeding 2002 he was a senior research scientist at the Savannah River Ecology Laboratory and still participates in many of the studies being conducted at SREL. Justin earned an associate's

  6. Faculty and Scientists | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Faculty photo of Rhodes RHODES, Olin E. Jr. (Gene) Director, SREL Wildlife ecology and genetics, including the application of genetic tools to issues in wildlife management and conservation; disease ecology; molecular genetics as a tool for examining wildlife behavior and population structure; sustainability of wildlife species in human-dominated landscapes and resolution of human-wildlife conflicts photo of Seaman SEAMAN, John Assistant Director, SREL Research Professor of Biogeochemistry, UGA

  7. Beasley Lab | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Graduate Students EJ with sedated bobcat EJ Borchert is a Masters student in the Warnell School of Forestry and Natural Resources at the University of Georgia. His research interests include furbearer ecology and management, landscape ecology, ecotoxicology, wildlife habitat relationships, and wildlife health. He graduated from the SUNY College of Environmental Science and Forestry (SUNY-ESF) in 2013 with a B.S. in Conservation Biology. Before coming to SREL, he worked on projects focusing on

  8. Industrial ecology Prosperity Game{trademark}

    SciTech Connect (OSTI)

    Beck, D.; Boyack, K.; Berman, M.

    1998-03-01

    Industrial ecology (IE) is an emerging scientific field that views industrial activities and the environment as an interactive whole. The IE approach simultaneously optimizes activities with respect to cost, performance, and environmental impact. Industrial Ecology provides a dynamic systems-based framework that enables management of human activity on a sustainable basis by: minimizing energy and materials usage; insuring acceptable quality of life for people; minimizing the ecological impact of human activity to levels that natural systems can sustain; and maintaining the economic viability of systems for industry, trade and commerce. Industrial ecology applies systems science to industrial systems, defining the system boundary to incorporate the natural world. Its overall goal is to optimize industrial activities within the constraints imposed by ecological viability, globally and locally. In this context, Industrial systems applies not just to private sector manufacturing and services but also to government operations, including provision of infrastructure. Sandia conducted its seventeenth Prosperity Game{trademark} on May 23--25, 1997, at the Hyatt Dulles Hotel in Herndon, Virginia. The primary sponsors of the event were Sandia National Laboratories and Los Alamos National Laboratory, who were interested in using the format of a Prosperity Game to address some of the issues surrounding Industrial Ecology. Honorary game sponsors were: The National Science Foundation; the Committee on Environmental Improvement, American Chemical Society; the Industrial and Engineering Chemistry Division, American Chemical Society; the US EPA--The Smart Growth Network, Office of Policy Development; and the US DOE-Center of Excellence for Sustainable Development.

  9. High-throughput metagenomic technologies for complex microbial community analysis. Open and closed formats

    SciTech Connect (OSTI)

    Zhou, Jizhong; He, Zhili; Yang, Yunfeng; Deng, Ye; Tringe, Susannah G.; Alvarez-Cohen, Lisa

    2015-01-27

    Understanding the structure, functions, activities and dynamics of microbial communities in natural environments is one of the grand challenges of 21st century science. To address this challenge, over the past decade, numerous technologies have been developed for interrogating microbial communities, of which some are amenable to exploratory work (e.g., high-throughput sequencing and phenotypic screening) and others depend on reference genes or genomes (e.g., phylogenetic and functional gene arrays). Here, we provide a critical review and synthesis of the most commonly applied “open-format” and “closed-format” detection technologies. We discuss their characteristics, advantages, and disadvantages within the context of environmental applications and focus on analysis of complex microbial systems, such as those in soils, in which diversity is high and reference genomes are few. In addition, we discuss crucial issues and considerations associated with applying complementary high-throughput molecular technologies to address important ecological questions.

  10. Toward “optimal” integration of terrestrial biosphere models

    SciTech Connect (OSTI)

    Schwalm, Christopher R.; Huntingzger, Deborah; Fisher, Joshua B.; Michalak, A. M.; Bowman, Kevin; Cias, Philippe; Cook, Robert B.; El-Masri, Bassil; Hayes, Daniel J.; Huang, Maoyi; Ito, A.; Jain, Atul K.; King, Anthony W.; Lei, Huimin; Liu, Junjie; Lu, Chaoqun; Mao, Jiafu; Peng, Shushi; Poulter, Benjamin; Ricciuto, Daniel M.; Schaefer, Kevin; Shi, Xiaoying; Tao, Bo; Tian, Hanqin; Wang, Weile; Wei, Yaxing; Yang, Jia; Zeng, Ning

    2015-06-10

    Multi-model ensembles (MME) are commonplace in Earth system modeling. Here we perform MME integration using a 10-member ensemble of terrestrial biosphere models (TBMs) from the Multi-scale synthesis and Terrestrial Model Intercomparison Project (MsTMIP). We contrast optimal (skill-based for present-day carbon cycling) versus naïve (“one model – one vote”) integration. MsTMIP optimal and naïve mean land sink strength estimates (–1.16 vs. –1.15 Pg C per annum respectively) are statistically indistinguishable. This holds also for grid cell values and extends to gross uptake, biomass, and net ecosystem productivity. TBM skill is similarly indistinguishable. The added complexity of skill-based integration does not materially change MME values. This suggests that carbon metabolism has predictability limits and/or that all models and references are misspecified. Resolving this issue requires addressing specific uncertainty types (initial conditions, structure, references) and a change in model development paradigms currently dominant in the TBM community.

  11. Impacts of an oil well blowout near Trecate, Italy on ecological resources

    SciTech Connect (OSTI)

    Brandt, C.; Becker, J.; Dauble, D.

    1995-12-31

    An ecological risk assessment (ERA) was conducted after the February 1995 blowout of an oil well near Trecate, Italy to quantify injuries to terrestrial and aquatic biological resources from effects of oil and habitat changes. Avian surveys were conducted on a surrogate area near Varallino to estimate species and numbers potentially exposed to oil and displaced by habitat alteration in the affected area. Of the 43 avian species observed, 20 are considered protected by European Community laws. The most abundant species were passero domestico, fringuello, cornacchia grigia, rondine, piccione torraiolo, and cardellino. These species likely suffered the greatest losses due to inhalation of volatile aromatics, dermal loading of oil, and/or habitat loss in the affected area. Based on CHARM model outputs, inhalation exposures to volatile aromatics and oil aerosols occurred above LOELs for all receptors within 2 km of the blowout. The most significant exposure pathway to large birds was dermal loading, which likely exceeded LC50 levels within 900m of the well. Terrestrial insects seldom contained detectable levels of PAHs, consistent with their shorter life span and residence time in the contaminated area. The highest concentrations of PAHs were found in dike vegetation, frogs, and benthic invertebrates. Ingestion exposures of woodmice to PAHs exceeded toxic reference levels at one site and mice had EHQ = >1 at soil PAH concentrations >4.2 mg/kg. Based on known body burdens causing narcotic response, neither fish nor benthic invertebrates experienced toxic consequences from exposure to PAHs in irrigation canal sediments.

  12. The EMAP: Ecological indicators of condition

    SciTech Connect (OSTI)

    Austin, H.K.

    1995-12-01

    In 1988, the Science Advisory Board to the EPA recommended a program to monitor ecological status and trends, as well as the development of innovative methods, for anticipating emerging environmental problems before a crisis. The multi-agency Environmental Monitoring And Assessment Program (EMAP) evolved with the following program elements: (1) a focus on environmental values and policy-relevant questions; (2) an activity that monitors indicators of ecological condition rather than individual stressors or pollutants; (3) an assessment-driven approach that provides probability-based, scientific results with known certainty; and (4) an activity that translates results into information useful to environmental policy makers and managers. Establishing baseline environmental conditions has received increasing attention with the growing awareness of impacts on human health and environmental integrity from global atmospheric change, acidic deposition, the loss of wetland habitats, and decreasing biodiversity. Monitoring programs can provide critical, quantitative results for scientific assessments of the complex effects of pollutants and natural changes on ecosystems. The goal of the EPA component of EMAP is to conduct research to develop place-based (e.g., large and small geographic scales) ecological monitoring and assessment. EPA/EMAP conducts research to develop and evaluate indicators of ecological condition and to detect in the long-term changes and trends in indicators and associated stresses and develops monitoring strategies to identify conditions of ecological resources in larger, high priority regions or in smaller, regional studies, such as watersheds. With its focus on long-term monitoring and assessment research and research on indicators of ecological condition, the EPA/EMAP can better determine where environmental programs are working to protect, improve, and maintain the quality of our nation`s ecological resources.

  13. Savannah River Ecology Laboratory Annual Technical Progress Report of

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Ecological Research, June 30, 2001 (Technical Report) | SciTech Connect Savannah River Ecology Laboratory Annual Technical Progress Report of Ecological Research, June 30, 2001 Citation Details In-Document Search Title: Savannah River Ecology Laboratory Annual Technical Progress Report of Ecological Research, June 30, 2001 × You are accessing a document from the Department of Energy's (DOE) SciTech Connect. This site is a product of DOE's Office of Scientific and Technical Information

  14. High-throughput metagenomic technologies for complex microbial community analysis. Open and closed formats

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Zhou, Jizhong; He, Zhili; Yang, Yunfeng; Deng, Ye; Tringe, Susannah G.; Alvarez-Cohen, Lisa

    2015-01-27

    Understanding the structure, functions, activities and dynamics of microbial communities in natural environments is one of the grand challenges of 21st century science. To address this challenge, over the past decade, numerous technologies have been developed for interrogating microbial communities, of which some are amenable to exploratory work (e.g., high-throughput sequencing and phenotypic screening) and others depend on reference genes or genomes (e.g., phylogenetic and functional gene arrays). Here, we provide a critical review and synthesis of the most commonly applied “open-format” and “closed-format” detection technologies. We discuss their characteristics, advantages, and disadvantages within the context of environmental applications andmore » focus on analysis of complex microbial systems, such as those in soils, in which diversity is high and reference genomes are few. In addition, we discuss crucial issues and considerations associated with applying complementary high-throughput molecular technologies to address important ecological questions.« less

  15. Management Opportunities for Enhancing Terrestrial Carbon Dioxide Sinks

    SciTech Connect (OSTI)

    Post, W. M.; Izaurralde, Roberto C.; West, Tristram O.; Liebig, Mark A.; King, Anthony W.

    2012-12-01

    The potential for mitigating increasing atmospheric carbon dioxide concentrations through the use of terrestrial biological carbon (C) sequestration is substantial. Here, we estimate the amount of C being sequestered by natural processes at global, North American, and national US scales. We present and quantify, where possible, the potential for deliberate human actions through forestry, agriculture, and use of biomass-based fuels to augment these natural sinks. Carbon sequestration may potentially be achieved through some of these activities but at the expense of substantial changes in land-use management. Some practices (eg reduced tillage, improved silviculture, woody bioenergy crops) are already being implemented because of their economic benefits and associated ecosystem services. Given their cumulative greenhouse-gas impacts, other strategies (eg the use of biochar and cellulosic bioenergy crops) require further evaluation to determine whether widespread implementation is warranted.

  16. System, method, and apparatus for remote measurement of terrestrial biomass

    DOE Patents [OSTI]

    Johnson, Patrick W

    2011-04-12

    A system, method, and/or apparatus for remote measurement of terrestrial biomass contained in vegetative elements, such as large tree boles or trunks present in an area of interest, are provided. The method includes providing an airborne VHF radar system in combination with a LiDAR system, overflying the area of interest while directing energy toward the area of interest, using the VHF radar system to collect backscatter data from the trees as a function of incidence angle and frequency, and determining a magnitude of the biomass from the backscatter data and data from the laser radar system for each radar resolution cell. A biomass map is generated showing the magnitude of the biomass of the vegetative elements as a function of location on the map by using each resolution cell as a unique location thereon. In certain preferred embodiments, a single frequency is used with a linear array antenna.

  17. A Graded Approach for Evaluating Radiation Doses to Acquatic and Terrestrial Biota

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2012-08-14

    This technical standard provides methods, models, and guidance within a graded approach that the U.S. Department of Energy (DOE) and its contractors may use to evaluate doses of ionizing radiation to populations of aquatic animals, terrestrial plants, and terrestrial animals from DOE activities for the purpose of demonstrating protection relative to Dose Rate Guidelines.

  18. Linda Lee | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Lee Faculty & Scientists SREL Home Linda Lee Savannah River Ecology Laboratory P O Drawer E, Aiken, SC 29802 (803) 725-5883 office (803) 725-3309 fax lee(at)srel.uga.edu I have a broad range of interests including wetland ecology, habitat management and restoration, and plant conservation. One of my current projects is evaluating the erosion control potential of native grassland vegetation against two commonly-used turf grasses. I am also working with Audubon South Carolina on a new

  19. Conference Center | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    UGA-SREL Conference Center front view UGA-SREL Conference Center large conference room Large conference room small conference room Small conference room The University of Georgia - Savannah River Ecology Laboratory Conference Center is a 5,000-square-foot multi-purpose facility located on the U.S. Department of Energy's Savannah River Site (SRS) near Aiken, S.C. The facility is used by the Savannah River Ecology Laboratory, the Department of Energy, schools, businesses, and other groups, to host

  20. Ecological Research Division, Marine Research Program

    SciTech Connect (OSTI)

    Not Available

    1980-05-01

    This report presents program summaries of the various projects sponsored during 1979 by the Marine Research Program of the Ecological Research Division. Program areas include the effects of petroleum hydrocarbons on the marine environment; a study of the baseline ecology of a proposed OTEC site near Puerto Rico; the environmental impact of offshore geothermal energy development; the movement of radionuclides through the marine environment; the environmental aspects of power plant cooling systems; and studies of the physical and biological oceangraphy of the continental shelves bordering the United States.

  1. Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulphidic marine sediments

    SciTech Connect (OSTI)

    Glass, DR. Jennifer; Yu, DR. Hang; Steele, Joshua; Dawson, Katherine; Sun, S; Chourey, Karuna; Pan, Chongle; Hettich, Robert {Bob} L; Orphan, V

    2013-01-01

    Microbes have obligate requirements for trace metals in metalloenzymes that catalyse important biogeochemical reactions. In anoxic methane- and sulphiderich environments, microbes may have unique adaptations for metal acquisition and utilization because of decreased bioavailability as a result of metal sulphide precipitation. However, micronutrient cycling is largely unexplored in cold ( 10 C) and sulphidic (> 1 mM H2S) deep-sea methane seep ecosystems. We investigated trace metal geochemistry and microbial metal utilization in methane seeps offshore Oregon and California, USA, and report dissolved concentrations of nickel (0.5 270 nM), cobalt (0.5 6 nM), molybdenum (10 5600 nM) and tungsten (0.3 8 nM) in Hydrate Ridge sediment porewaters. Despite low levels of cobalt and tungsten, metagenomic and metaproteomic data suggest that microbial consortia catalysing anaerobic oxidation of methane (AOM) utilize both scarce micronutrients in addition to nickel and molybdenum. Genetic machinery for cobalt-containing vitamin B12 biosynthesis was present in both anaerobic methanotrophic archaea (ANME) and sulphate-reducing bacteria. Proteins affiliated with the tungsten-containing form of formylmethanofuran dehydrogenase were expressed in ANME from two seep ecosystems, the first evidence for expression of a tungstoenzyme in psychrophilic microorganisms. Overall, our data suggest that AOM consortia use specialized biochemical strategies to overcome the challenges of metal availability in sulphidic environments.

  2. Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulfidic marine sediments

    SciTech Connect (OSTI)

    Glass, DR. Jennifer; Yu, DR. Hang; Steele, Joshua; Dawson, Katherine; Sun, S; Chourey, Karuna; Hettich, Robert {Bob} L; Orphan, V

    2014-01-01

    Microbes have obligate requirements for trace metals in metalloenzymes that catalyze important biogeochemical reactions. In anoxic methane- and sulfide-rich environments, microbes may have unique adaptations for metal acquisition and utilization due to decreased bioavailability as a result of metal sulfide precipitation. However, micronutrient cycling is largely unexplored in cold ( 10 C) and sulfidic (>1 mM H2S) deep-sea methane seep ecosystems. We investigated trace metal geochemistry and microbial metal utilization in methane seeps offshore Oregon and California, USA, and report dissolved concentrations of nickel (0.5-270 nM), cobalt (0.5-6 nM), molybdenum (10-5,600 nM) and tungsten (0.3-8 nM) in Hydrate Ridge sediment porewaters. Despite low levels of cobalt and tungsten, metagenomic and metaproteomic data suggest that microbial consortia catalyzing anaerobic oxidation of methane utilize both scarce micronutrients in addition to nickel and molybdenum. Genetic machinery for cobalt-containing vitamin B12 biosynthesis was present in both anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB). Proteins affiliated with the tungsten-containing form of formylmethanofuran dehydrogenase were expressed in ANME from two seep ecosystems, the first evidence for expression of a tungstoenzyme in psychrotolerant microorganisms. Finally, our data suggest that chemical speciation of metals in highly sulfidic porewaters may exert a stronger influence on microbial bioavailability than total concentration

  3. Ecological Monitoring and Compliance Program 2007 Report

    SciTech Connect (OSTI)

    Hansen, Dennis; Anderson, David; Derek, Hall; Greger, Paul; Ostler, W. Kent

    2008-03-01

    In accordance with U.S. Department of Energy (DOE) Order 450.1, 'Environmental Protection Program', the Office of the Assistant Manager for Environmental Management of the DOE, National Nuclear Security Administration Nevada Site Office (NNSA/NSO) requires ecological monitoring and biological compliance support for activities and programs conducted at the Nevada Test Site (NTS). National Security Technologies, LLC (NSTec), Ecological Services has implemented the Ecological Monitoring and Compliance (EMAC) Program to provide this support. EMAC is designed to ensure compliance with applicable laws and regulations, delineate and define NTS ecosystems, and provide ecological information that can be used to predict and evaluate the potential impacts of proposed projects and programs on those ecosystems. This report summarizes the EMAC activities conducted by NSTec during calendar year 2007. Monitoring tasks during 2007 included eight program areas: (a) biological surveys, (b) desert tortoise compliance, (c) ecosystem mapping and data management, (d) sensitive plant monitoring, (e) sensitive and protected/regulated animal monitoring, (f) habitat monitoring, (g) habitat restoration monitoring, and (h) biological monitoring at the Nonproliferation Test and Evaluation Complex (NPTEC). The following sections of this report describe work performed under these eight areas.

  4. Make a Gift | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Make a Gift canopy photo photo of graduate student Ecologist for a Day photo photo of analytical facilities photo Contributions can be made online through the Georgia Fund, part of the Arch Foundation for the University of Georgia. Contributions are tax deductible. Give Online Thank you for supporting SREL's mission of ecological research, education, and environmental outreach.

  5. Applicability of 10 CFR 851 to Savannah River Ecology Laboratory

    Broader source: Energy.gov [DOE]

    Letter from Bruce Diamond, Assistant General Counsel for Environment, DOE, dated November 24, 2007 to Mr. Bertsch, Director and Professor, Savannah River Ecology Laboratory, regarding Savannah Riber Ecology Laboratory's Request for Interpretive Ruling under 10 CFR 851.

  6. START HERE 2014 Annual Ecology Report DVD 1.htm

    Office of Legacy Management (LM)

    Annual Ecology Report for the Rocky Flats Site Ecology DVD 1 Click on the links below to access different portions of the electronic annual report. 2014 Annual Report Sections...

  7. EcoCampus, Center for Creative Ecology, Kibbutz Lotan, Israel...

    Open Energy Info (EERE)

    EcoCampus, Center for Creative Ecology, Kibbutz Lotan, Israel Jump to: navigation, search Name EcoCampus, Center for Creative Ecology, Kibbutz Lotan, Israel Facility EcoCampus PV...

  8. START HERE 2013 Annual Ecology Report DVD 1.htm

    Office of Legacy Management (LM)

    3 Annual Ecology Report for the Rocky Flats Site Ecology DVD 1 Click on the links below to access different portions of the electronic annual report. 2013 Annual Report Sections...

  9. Savannah River Ecology Laboratory. Annual technical progress report of ecological research, period ending July 31, 1994

    SciTech Connect (OSTI)

    Not Available

    1994-07-31

    The Savannah River Ecology Laboratory (SREL) is a research unit of the University of Georgia (UGA) that is managed in conjunction with the University`s Institute of Ecology. The laboratory`s overall mission is to acquire and communicate knowledge of ecological processes and principles. SREL conducts basic and applied ecological research, as well as education and outreach programs, under an M&O contract with the US Department of Energy at the Savannah River Site. Significant accomplishments were made during the year ending July 31, 1994 in the areas of research, education and service. Reviewed in this document are research projects in the following areas: Environmental Operations Support (impacted wetlands, streams, trace organics, radioecology, database synthesis, wild life studies, zooplankton, safety and quality assurance); wood stork foraging and breeding ecology; defence waste processing facility; environmental risk assessment (endangered species, fish, ash basin studies); ecosystem alteration by chemical pollutants; wetlands systems; biodiversity on the SRS; Environmental toxicology; environmental outreach and education; Par Pond drawdown studies in wildlife and fish and metals; theoretical ecology; DOE-SR National Environmental Research Park; wildlife studies. Summaries of educational programs and publications are also give.

  10. Enforcement Letter, Savannah River Ecology Laboratory- June 7, 2000

    Broader source: Energy.gov [DOE]

    Issued to Savannah River Ecology Laboratory related to Radioactive Material Control Deficiencies at the Savannah River Site

  11. Functional Ecological Gene Networks to Reveal the Changes Among...

    Office of Scientific and Technical Information (OSTI)

    indicating the potential importance of network interactions in ecosystem functioning. ... aremore fundamentally important for research in microbial ecology, systems ...

  12. The Use of Ecological Restoration Principles To Achieve Remedy Protection

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    at the Fernald Preserve and Weldon Spring Sites | Department of Energy The Use of Ecological Restoration Principles To Achieve Remedy Protection at the Fernald Preserve and Weldon Spring Sites The Use of Ecological Restoration Principles To Achieve Remedy Protection at the Fernald Preserve and Weldon Spring Sites The Use of Ecological Restoration Principles To Achieve Remedy Protection at the Fernald Preserve and Weldon Spring Sites The Use of Ecological Restoration Principles To Achieve

  13. Disentangling climatic and anthropogenic controls on global terrestrial evapotranspiration trends

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Mao, Jiafu; Shi, Xiaoying; Ricciuto, Daniel M.; Wei, Yaxing; Thornton, Peter E.; Hoffman, Forrest M.; Fu, Wenting; Fisher, Joshua B.; Dickinson, Robert E.; Shem, Willis; et al

    2015-09-08

    Here, we examined natural and anthropogenic controls on terrestrial evapotranspiration (ET) changes from 1982-2010 using multiple estimates from remote sensing-based datasets and process-oriented land surface models. A significant increased trend of ET in each hemisphere was consistently revealed by observationally-constrained data and multi-model ensembles that considered historic natural and anthropogenic drivers. The climate impacts were simulated to determine the spatiotemporal variations in ET. Globally, rising CO2 ranked second in these models after the predominant climatic influences, and yielded a decreasing trend in canopy transpiration and ET, especially for tropical forests and high-latitude shrub land. Increased nitrogen deposition slightly amplified globalmore » ET via enhanced plant growth. Land-use-induced ET responses, albeit with substantial uncertainties across the factorial analysis, were minor globally, but pronounced locally, particularly over regions with intensive land-cover changes. Our study highlights the importance of employing multi-stream ET and ET-component estimates to quantify the strengthening anthropogenic fingerprint in the global hydrologic cycle.« less

  14. Disentangling climatic and anthropogenic controls on global terrestrial evapotranspiration trends

    SciTech Connect (OSTI)

    Mao, Jiafu; Shi, Xiaoying; Ricciuto, Daniel M.; Wei, Yaxing; Thornton, Peter E.; Hoffman, Forrest M.; Fu, Wenting; Fisher, Joshua B.; Dickinson, Robert E.; Shem, Willis; Piao, Shilong; Wang, Kaicun; Schwalm, Christopher R.; Tian, Hanqin; Mu, Mingquan; Arain, Altaf; Ciais, Philippe; Cook, Robert; Dai, Yongjiu; Hayes, Daniel; Huang, Maoyi; Huang, Suo; Huntzinger, Deborah N.; Ito, Akihiko; Jain, Atul; King, Anthony W.; Lei, Huimin; Lu, Chaoqun; Michalak, Anna M.; Parazoo, Nicholas; Peng, Changhui; Peng, Shushi; Poulter, Benjamin; Schaefer, Kevin; Jafarov, Elchin; Wang, Weile; Zeng, Ning; Zeng, Zhenzhong; Zhao, Fang; Zhu, Qiuan; Zhu, Zaichun

    2015-09-08

    Here, we examined natural and anthropogenic controls on terrestrial evapotranspiration (ET) changes from 1982-2010 using multiple estimates from remote sensing-based datasets and process-oriented land surface models. A significant increased trend of ET in each hemisphere was consistently revealed by observationally-constrained data and multi-model ensembles that considered historic natural and anthropogenic drivers. The climate impacts were simulated to determine the spatiotemporal variations in ET. Globally, rising CO2 ranked second in these models after the predominant climatic influences, and yielded a decreasing trend in canopy transpiration and ET, especially for tropical forests and high-latitude shrub land. Increased nitrogen deposition slightly amplified global ET via enhanced plant growth. Land-use-induced ET responses, albeit with substantial uncertainties across the factorial analysis, were minor globally, but pronounced locally, particularly over regions with intensive land-cover changes. Our study highlights the importance of employing multi-stream ET and ET-component estimates to quantify the strengthening anthropogenic fingerprint in the global hydrologic cycle.

  15. Definition, Capabilities, and Components of a Terrestrial Carbon Monitoring System

    SciTech Connect (OSTI)

    West, Tristram O.; Brown, Molly E.; Duran, Riley M.; Ogle, Stephen; Moss, Richard H.

    2013-08-08

    Research efforts for effectively and consistently monitoring terrestrial carbon are increasing in number. As such, there is a need to define carbon monitoring and how it relates to carbon cycle science and carbon management. There is also a need to identify intended capabilities of a carbon monitoring system and what system components are needed to develop the capabilities. This paper is intended to promote discussion on what capabilities are needed in a carbon monitoring system based on requirements for different areas of carbon-related research and, ultimately, for carbon management. While many methods exist to quantify different components of the carbon cycle, research is needed on how these methods can be coupled or integrated to obtain carbon stock and flux estimates regularly and at a resolution that enables attribution of carbon dynamics to respective sources. As society faces sustainability and climate change conerns, carbon management activities implemented to reduce carbon emissions or increase carbon stocks will become increasingly important. Carbon management requires moderate to high resolution monitoring. Therefore, if monitoring is intended to help inform management decisions, management priorities should be considered prior to development of a monitoring system.

  16. Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Lin, Kuei -Han; Liao, Ben -Yang; Chang, Hao -Wei; Huang, Shiao -Wei; Chang, Ting -Yan; Yang, Cheng -Yu; Wang, Yu -Bin; Lin, Yu-Teh Kirk; Wu, Yu -Wei; Tang, Sen -Lin; et al

    2015-12-03

    Microbial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys. However, our understanding regarding the interactions among microbes, or between microbes and environmental factors, remains limited. In the present study, a metagenomic approach, followed by bioinformatics analyses, were used to predict interactions within the microbial ecosystem in Shi-Huang-Ping (SHP), an acidic hot spring in northern Taiwan. Characterizing environmental parameters and potential metabolic pathways highlighted the importance of carbon assimilatory pathways. Four distinct carbon assimilatory pathways were identified in five dominant genera of bacteria. Of those dominant carbon fixers, Hydrogenobaculum bacteria outcompeted othermore » carbon assimilators and dominated the SHP, presumably due to their ability to metabolize hydrogen and to withstand an anaerobic environment with fluctuating temperatures. Furthermore, most dominant microbes were capable of metabolizing inorganic sulfur-related compounds (abundant in SHP). However, Acidithiobacillus ferrooxidans was the only species among key rare microbes with the capability to fix nitrogen, suggesting a key role in nitrogen cycling. In addition to potential metabolic interactions, based on the 16S rRNAs gene sequence of Nanoarchaeum-related and its potential host Ignicoccus-related archaea, as well as sequences of viruses and CRISPR arrays, we inferred that there were complex microbe-microbe interactions. In conclusion, our study provided evidence that there were numerous microbe-microbe and microbe-environment interactions within the microbial community in an acidic hot spring. We proposed that Hydrogenobaculum bacteria were the dominant microbial genus, as they were able to metabolize hydrogen, assimilate carbon and live in an anaerobic environment with fluctuating temperatures.« less

  17. 2011 Archaea: Ecology, Metabolism, & Molecular Biology

    SciTech Connect (OSTI)

    Keneth Stedman

    2011-08-05

    Archaea, one of three major evolutionary lineages of life, are a fascinating and diverse group of microbes with deep roots overlapping those of eukaryotes. The focus of the 'Archaea: Ecology Metabolism & Molecular Biology' GRC conference expands on a number of emerging topics highlighting new paradigms in archaeal metabolism, genome function and systems biology; information processing; evolution and the tree of life; the ecology and diversity of archaea and their viruses. The strength of this conference lies in its ability to couple a field with a rich history in high quality research with new scientific findings in an atmosphere of stimulating exchange. This conference remains an excellent opportunity for younger scientists to interact with world experts in this field.

  18. 2009 Archaea: Ecology, Metabolism & Molecular Biology GRC

    SciTech Connect (OSTI)

    Dr. Julie Maupin- Furlow

    2009-07-26

    Archaea, one of three major evolutionary lineages of life, are a fascinating and diverse group of microbes with deep roots overlapping those of eukaryotes. The focus of the 'Archaea: Ecology Metabolism & Molecular Biology' GRC conference expands on a number of emerging topics highlighting new paradigms in archaeal metabolism, genome function and systems biology; information processing; evolution and the tree of life; the ecology and diversity of archaea and their viruses; and industrial applications. The strength of this conference lies in its ability to couple a field with a rich history in high quality research with new scientific findings in an atmosphere of stimulating exchange. This conference remains an excellent opportunity for younger scientists to interact with world experts in this field.

  19. Science and technology for industrial ecology

    SciTech Connect (OSTI)

    Gilmartin, T.J.; Allenby, B.R.

    1996-07-10

    Scientific and technological communities have a significant role to play and responsibility for the evolution of global sustainability (continuously improving quality of life into the indefinite future). Sustainability is not possible without a substantially improved science and technology basis for industrial ecology. Society needs data and understanding of complex ecological issues to govern itself in a sustainable manner. We should: support and develop multi-disciplinary programs which create the scientific basis for understanding natural and anthropogenic complex systems and for developing environmentally and economically efficient technology; demonstrate a systems-based approach to science and technology issues which is life-cycle comprehensive, integrates environmental considerations, and promotes conservation of natural resources; and encourage development of responsible, technically and scientifically valid, cost-effective environmental laws and practices.

  20. Opportunies for Students | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Education catching alligators collecting microbes recording field data PCR coring trees releasing snapping turtle looking for rattlesnakes SREL offers outstanding research opportunities for students, including state-of-the-art laboratory facilities, nealy 300 square miles of habitat for field research, a wide range of faculty specializations under one roof, and more than 60 years of experience in ecological research. Although SREL is operated by the University of Georgia, students from any

  1. Women & the Department of Ecology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    September 5, 2013 Agency Update Hanford Advisory Board Top News for FY2013 * State leadership transitions * Governor Inslee took office in January * Maia Bellon appointed Ecology director in February * Leaking double-shell and single-shell tanks * Sitewide permit to be reissued for public comment * Consent Decree milestones in jeopardy? FY2013 Accomplishments  Reiussed Hanford Air Operating Permit April 1  Permit required to be renewed every 5 years  Nearly finished resolving comments

  2. Women & the Department of Ecology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    September 4, 2014 Agency Update Hanford Advisory Board Nuclear Waste Program News * TPA Public Involvement Calendar updated & posted on Ecology's website * State/DOE discussing path forward on AY-102 * Negotiations on possible amendments to the Consent Decree continuing Comment periods in progress  325 HWTU* Class 3 permit mod to add capacity to the Radiochemical Processing Lab (RPL or 325 building)  Comment period: August 18-October 17  LERF-ETF Class 2 mod to revise liner repair

  3. Women & the Department of Ecology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    June 4, 2014 Agency Update Hanford Advisory Board Key Events Since Last HAB Meeting * March 21: Ecology issues order to pump AY-102 * Order appealed by DOE * March 31: State/DOE propose amendments to CD * Agencies are in negotiations on proposals * May 1: Hanford Air Operating Permit revised * Added new federal engine emission requirements Sitewide Permit Update (Rev. 9) * Response to Public Comment: Continuing work on completing responses to public comment and identifying associated permit

  4. Tuberville Lab Personnel | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Lab Personnel RESEARCH STAFF Kimberly wih pine snake Kimberly Price is a new research technician in the Tuberville lab. Kimberly graduated in 2015 with her B.S. in Ecology from Augusta University in Augusta, Georgia. While a student working with Dr. Brandon R. Cromer, she focused her undergraduate research on contamination and maternal transfer of mercury in southeastern aquatic turtles using the yellow-bellied slider (Trachemys scripta scripta) and the eastern river cooter (Pseudemys concinna

  5. Gary Mills | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Mills Curriculum Vitae Faculty & Scientists SREL Home Gary Mills Savannah River Ecology Laboratory P O Drawer E, Aiken, SC 29802 (803) 725-5368 office (803) 725-3309 fax gmills(at)srel.uga.edu My research interest is in the biogeochemistry of aquatic ecosystems and my projects have included studies on stream, wetland, and estuarine systems as well as geothermal hot springs. My current research is focused on techniques for determining the bioavailable fraction of dissolved metals in wetland

  6. John Seaman | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Seaman Curriculum Vitae Faculty & Scientists SREL Home John Seaman Savannah River Ecology Laboratory P O Drawer E, Aiken, SC 29802 (803) 725-0977 office (803) 725-3309 fax seaman(at)uga.edu Dr. Seaman's research interests include a number of active agricultural and environmental research areas: the land application of animal waste and coal combustion by-products; solute and contaminant transport modeling; reclamation of Cr(VI) contaminated aquifers and soils; in situ contaminant

  7. Graduate Program | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Graduate Program catching alligators collecting microbes recording field data PCR coring trees releasing snapping turtle looking for rattlesnakes SREL offers outstanding research opportunities for students, including state-of-the-art laboratory facilities, nearly 300 square miles of habitat for field research, a wide range of faculty specializations under one roof, and more than 60 years of experience in ecological research. Although SREL is operated by the University of Georgia, students from

  8. Undergraduate Program | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Undergraduate Program catching alligators collecting microbes recording field data PCR coring trees releasing snapping turtle looking for rattlesnakes SREL offers outstanding research opportunities for students, including state-of-the-art laboratory facilities, nearly 300 square miles of habitat for field research, a wide range of faculty specializations under one roof, and more than 60 years of experience in ecological research. Although SREL is operated by the University of Georgia, students

  9. Upcoming Seminars | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Upcoming Seminars Seminars are held at the Savannah River Ecology Laboratory, Bldg. 737-A, in the Cypress Room. Snacks are provided 15 minutes prior to the beginning of each seminar. DATE SPEAKER TITLE 3:00 PM Wednesday, July 13, 2016 Dr. William Hopkins, Director, Global Change Center, Dept. of Fish and Wildlife Conservation, Virginia Tech Never Grow Up: Snot Otters, Blood Suckers, and a Smattering of Humble Advice for Aspiring Scientists SREL seminar committee: Dr. Doug Aubrey (chair),

  10. The Gut Microbiota: Ecology and Function

    SciTech Connect (OSTI)

    Willing, B.P.; Jansson, J.K.

    2010-06-01

    The gastrointestinal (GI) tract is teeming with an extremely abundant and diverse microbial community. The members of this community have coevolved along with their hosts over millennia. Until recently, the gut ecosystem was viewed as black box with little knowledge of who or what was there or their specific functions. Over the past decade, however, this ecosystem has become one of fastest growing research areas of focus in microbial ecology and human and animal physiology. This increased interest is largely in response to studies tying microbes in the gut to important diseases afflicting modern society, including obesity, allergies, inflammatory bowel diseases, and diabetes. Although the importance of a resident community of microorganisms in health was first hypothesized by Pasteur over a century ago (Sears, 2005), the multiplicity of physiological changes induced by commensal bacteria has only recently been recognized (Hooper et al., 2001). The term 'ecological development' was recently coined to support the idea that development of the GI tract is a product of the genetics of the host and the host's interactions with resident microbes (Hooper, 2004). The search for new therapeutic targets and disease biomarkers has escalated the need to understand the identities and functions of the microorganisms inhabiting the gut. Recent studies have revealed new insights into the membership of the gut microbial community, interactions within that community, as well as mechanisms of interaction with the host. This chapter focuses on the microbial ecology of the gut, with an emphasis on information gleaned from recent molecular studies.

  11. Mercury contamination of terrestrial vegetation near a caustic soda factory in Thailand

    SciTech Connect (OSTI)

    Suckcharoen, S.

    1980-03-01

    The present study is concerned with the fall-out of mercury on some terrestrial plants and one species of aquatic plant growing in the vicinity of the TACSCO factory.

  12. Savannah River Ecology Laboratory. Annual technical progress report of ecological research

    SciTech Connect (OSTI)

    Smith, M.H.

    1996-07-31

    The Savannah River Ecology Laboratory (SREL) is a research unit of the University of Georgia (UGA). The overall mission of the Laboratory is to acquire and communicate knowledge of ecological processes and principles. SREL conducts basic and applied ecological research, as well as education and outreach programs, under a contract with the U.S. Department of Energy (DOE) at the Savannah River Site (SRS) near Aiken, South Carolina. Significant accomplishments were made during the past year in the areas of research, education and service. The Laboratory`s research mission was fulfilled with the publication of two books and 143 journal articles and book chapters by faculty, technical and students, and visiting scientists. An additional three books and about 80 journal articles currently are in press. Faculty, technician and students presented 193 lectures, scientific presentations, and posters to colleges and universities, including minority institutions. Dr. J Vaun McArthur organized and conducted the Third Annual SREL Symposium on the Environment: New Concepts in Strewn Ecology: An Integrative Approach. Dr. Michael Newman conducted a 5-day course titled Quantitative Methods in Ecotoxicology, and Dr. Brian Teppen of The Advanced Analytical Center for Environmental Sciences (AACES) taught a 3-day short course titled Introduction to Molecular Modeling of Environmental Systems. Dr. I. Lehr Brisbin co-hosted a meeting of the Crocodile Special Interest Group. Dr. Rebecca Sharitz attended four symposia in Japan during May and June 1996 and conducted meetings of the Executive Committee and Board of the International Association for Ecology (ENTECOL).

  13. Relative importance of multiple factors on terrestrial loading of DOC to Arctic river networks

    SciTech Connect (OSTI)

    Kicklighter, David W.; Hayes, Daniel J; Mcclelland, James W; Peterson, Bruce; Mcguire, David; Melillo, Jerry

    2014-01-01

    Terrestrial carbon dynamics influence the contribution of dissolved organic carbon (DOC) to river networks in addition to controlling carbon fluxes between the land surface and the atmosphere. In this study, we use a biogeochemical process model to simulate the lateral transfer of DOC from land to the Arctic Ocean via riverine transport. We estimate that the pan-arctic watershed has contributed, on average, 32 Tg C/yr of DOC to the Arctic Ocean over the 20th century with most coming from the extensive area of boreal deciduous needle-leaved forests and forested wetlands in Eurasian watersheds. We also estimate that the rate of terrestrial DOC loading has been increasing by 0.037 Tg C/yr2 over the 20th century primarily as a result of increases in air temperatures and precipitation. These increases have been partially compensated by decreases in terrestrial DOC loading caused by wildfires. Other environmental factors (CO2 fertilization, ozone pollution, atmospheric nitrogen deposition, timber harvest, agriculture) are estimated to have relatively small effects on terrestrial DOC loading to arctic rivers. The effects of the various environmental factors on terrestrial carbon dynamics have both compensated and enhanced concurrent effects on hydrology to influence terrestrial DOC loading. Future increases in riverine DOC concentrations and export may occur from warming-induced increases in terrestrial DOC production associated with enhanced microbial metabolism and the exposure of additional organic matter from permafrost degradation along with decreases in water yield associated with warming-induced increases in evapotranspiration. Improvements in simulating terrestrial DOC loading to pan-arctic rivers in the future will require better information on the spatial distribution of precipitation and its temporal trends, carbon dynamics of larch-dominated ecosystems in eastern Siberia, and the role of industrial organic effluents on carbon budgets of rivers in western

  14. Excess /sup 129/Xe in terrestrial samples: A non-primordial hypothesis

    SciTech Connect (OSTI)

    Caffee, M.W.; Hudson, G.B.

    1987-03-01

    Excesses of /sup 129/Xe relative to the isotopic composition in air are observed in some terrestrial samples. Traditionally these /sup 129/Xe excesses have been thought to be related to /sup 129/I that was present in abundance in the early solar system. We propose an alternative hypothesis to explain terrestrial /sup 129/Xe excesses based on the production of /sup 129/I from the spontaneous fission of /sup 238/U.

  15. Terrestrial perturbation experiments as an environmental assessment tool

    SciTech Connect (OSTI)

    Suter, G.W. II

    1980-08-01

    The National Environmental Policy Act of 1969 (NEPA) was initially interpreted as requiring full disclosure of the environmental impacts of a federal action. Because of the limitations of time, money, and manpower, this requirement that all impacts be considered has led to superficial analysis of many important impacts. The President's Council on Environmental Quality (CEQ) has provided a solution to this problem by reinterpreting NEPA as requiring analysis of those impacts which have significant bearing on decision making. Because assessment resources can now be concentrated on a few critical issues, it should be possible to perform field perturbation experiments to provide direct evidence of the effects of a specific mixture of pollutants or physical disturbances on the specific receiving ecosystem. Techniques are described for field simulation of gaseous and particulate air pollution, soil pollutants, disturbance of the earth's surface, and disturbance of wildlife. These techniques are discussed in terms of their realism, cost, and the restrictions which they place on the measurement of ecological parameters.

  16. Women & the Department of Ecology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    June 7, 2012 Site-wide Permit Update Status:  Comment period began May 1*. Public meetings:  About 40 people attended public workshop May 3 at Ecology office.  Over 300 people total attended hearings May 15-16 in Seattle & Portland.  Spokane & Richland hearings held this week. *Except for Single-Shell Tanks. SST permit is on track to be released for public comment by July 1. River Corridor workshops June 12 - Seattle June 13 - Portland June 14 - Hood River Other comment

  17. Rebecca Sharitz: Publications | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Selected Publications (My full C.V. can be found here.) De Steven, D. and R. R. Sharitz. 2007. Transplanting native dominant plants to facilitate community development in restored Coastal Plain wetlands. Wetlands 27:972-978. Allen, B. P., R. R. Sharitz and P. C. Goebel. 2007. Are lianas increasing in importance in temperate floodplain forests in the southeastern United States? Forest Ecology and Management 242:17-23. Landman, G. B., R. K. Kolka and R. R. Sharitz. 2007. Soil seed bank analysis of

  18. Savannah River Ecology Laboratory annual technical progress report of ecological research, period ending July 31, 1993

    SciTech Connect (OSTI)

    Vaitkus, M.R.; Wein, G.R.; Johnson, G.

    1993-11-01

    This progress report gives an overview of research programs at the Savannah River Site. Topics include; environmental operations support, wood stork foraging and breeding, defense waste processing, environmental stresses, alterations in the environment due to pollutants, wetland ecology, biodiversity, pond drawdown studies, and environmental toxicology.

  19. Arid Lands Ecology Facility management plan

    SciTech Connect (OSTI)

    None

    1993-02-01

    The Arid Lands Ecology (ALE) facility is a 312-sq-km tract of land that lies on the western side of the Hanford Site in southcentral Washington. The US Atomic Energy Commission officially set aside this land area in 1967 to preserve shrub-steppe habitat and vegetation. The ALE facility is managed by Pacific Northwest Laboratory (PNL) for the US Department of Energy (DOE) for ecological research and education purposes. In 1971, the ALE facility was designated the Rattlesnake Hills Research Natural Area (RNA) as a result of an interagency federal cooperative agreement, and remains the largest RNA in Washington. it is also one of the few remaining large tracts of shrub-steppe vegetation in the state retaining a predominant preeuropean settlement character. This management plan provides policy and implementation methods for management of the ALE facilities consistent with both US Department of Energy Headquarters and the Richland Field Office decision (US Congress 1977) to designate and manage ALE lands as an RNA and as a component of the DOE National Environmental Research Park System.

  20. EcoTalks | Savannah River Ecology Laboratory Environmental Outreach...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    EcoTalks The Outreach Program at the Savannah River Ecology Laboratory annually presents about 300 talks to school, civic and professional groups. Educators give 45-minute to...

  1. 2006 Annual Ecology Report for the Rocky Flats Site

    Office of Legacy Management (LM)

    Ecology Report for the Rocky Flats Site Click on the links below to access different portions of the electronic annual report. 2006 Annual Report Sections Diffuse Knapweed...

  2. DOE Research Set-Aside Program | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Program Overview Set-Asides provide baseline information on ecological processes in SRS natural communities, ... to 1951, when the Atomic Energy Commission invited the ...

  3. LAND USE AND ECOLOGICAL IMPACTS FROM SHALE DEVELOPMENT IN THE...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    LAND USE AND ECOLOGICAL IMPACTS FROM SHALE DEVELOPMENT IN THE APPALACHIANS THE NATURE ... Research by The Nature Conservancy (Johnson et al. 2010; Johnson et al. 2011) indicates ...

  4. Enforcement Letter, Safety and Ecology Corporation- NEL-2011-04

    Broader source: Energy.gov [DOE]

    Issued to Safety and Ecology Corporation related to Two Radiological Contamination Events at the Separations Process Research Unit at the Knolls Atomic Power Laboratory

  5. Savannah River Ecology Laboratory, annual technical progress report of ecological research for the year ending June 30, 1997

    SciTech Connect (OSTI)

    Wein, G.; Rosier, B.

    1997-12-31

    This report provides an overview of the research programs and program components carried out by the Savannah River Ecology Laboratory. Research focused on the following: advanced analytical and spectroscopic techniques for developing novel waste isolation and stabilization technologies as well as cost-effective remediation strategies; ecologically sound management of damaged and remediation of ecological systems; ecotoxicology, remediation, and risk assessment; radioecology, including dose assessments for plants and animals exposed to environmental radiation; and other research support programs.

  6. The functional potential of microbial communities in hydraulic fracturing source water and produced water from natural gas extraction characterized by metagenomic sequencing

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Mohan, Arvind Murali; Bibby, Kyle J.; Lipus, Daniel; Hammack, Richard W.; Gregory, Kelvin B.; Forster, Robert J.

    2014-10-22

    Microbial activity in produced water from hydraulic fracturing operations can lead to undesired environmental impacts and increase gas production costs. However, the metabolic profile of these microbial communities is not well understood. Here, for the first time, we present results from a shotgun metagenome of microbial communities in both hydraulic fracturing source water and wastewater produced by hydraulic fracturing. Taxonomic analyses showed an increase in anaerobic/facultative anaerobic classes related to Clostridia, Gammaproteobacteria, Bacteroidia and Epsilonproteobacteria in produced water as compared to predominantly aerobic Alphaproteobacteria in the fracturing source water. Thus, the metabolic profile revealed a relative increase in genes responsiblemore » for carbohydrate metabolism, respiration, sporulation and dormancy, iron acquisition and metabolism, stress response and sulfur metabolism in the produced water samples. These results suggest that microbial communities in produced water have an increased genetic ability to handle stress, which has significant implications for produced water management, such as disinfection.« less

  7. Ecological Monitoring and Compliance Program 2012 Report

    SciTech Connect (OSTI)

    Hall, Derek B.; Anderson, David C.; Greger, Paul D.; Ostler, W. Kent; Hansen, Dennis J.

    2013-07-03

    The Ecological Monitoring and Compliance Program (EMAC), funded through the U.S. Department of Energy, National Nuclear Security Administration Nevada Field Office (NNSA/NFO, formerly Nevada Site Office), monitors the ecosystem of the Nevada National Security Site (NNSS) and ensures compliance with laws and regulations pertaining to NNSS biota. This report summarizes the program’s activities conducted by National Security Technologies, LLC (NSTec), during calendar year 2012. Program activities included (a) biological surveys at proposed construction sites, (b) desert tortoise compliance, (c) ecosystem monitoring, (d) sensitive plant species monitoring, (e) sensitive and protected/regulated animal monitoring, (f) habitat restoration monitoring, and (g) monitoring of the Nonproliferation Test and Evaluation Complex (NPTEC). During 2012, all applicable laws, regulations, and permit requirements were met, enabling EMAC to achieve its intended goals and objectives.

  8. Ecological Monitoring and Compliance Program 2009 Report

    SciTech Connect (OSTI)

    Hansen, J. Dennis; Anderson, David C.; Hall, Derek B.; Greger, Paul D.; Ostler, W. Kent

    2010-07-13

    The Ecological Monitoring and Compliance Program (EMAC), funded through the U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office, monitors the ecosystem of the Nevada Test Site and ensures compliance with laws and regulations pertaining to NTS biota. This report summarizes the program’s activities conducted by National Security Technologies, LLC, during calendar year 2009. Program activities included (a) biological surveys at proposed construction sites, (b) desert tortoise compliance, (c) ecosystem mapping and data management, (d) sensitive plant species monitoring, (e) sensitive and protected/regulated animal monitoring, (f) habitat monitoring, (g) habitat restoration monitoring, and (h) monitoring of the Nonproliferation Test and Evaluation Complex. During 2009, all applicable laws, regulations, and permit requirements were met, enabling EMAC to achieve its intended goals and objectives.

  9. Ecological Monitoring and Compliance Program 2011 Report

    SciTech Connect (OSTI)

    Hansen, D. J.; Anderson, D. C.; Hall, D. B.; Greger, P. D.; Ostler, W. K.

    2012-06-13

    The Ecological Monitoring and Compliance (EMAC) Program, funded through the U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office, monitors the ecosystem of the Nevada National Security Site and ensures compliance with laws and regulations pertaining to NNSS biota. This report summarizes the program's activities conducted by National Security Technologies, LLC, during calendar year 2011. Program activities included (a) biological surveys at proposed construction sites, (b) desert tortoise compliance, (c) ecosystem monitoring, (d) sensitive plant species monitoring, (e) sensitive and protected/regulated animal monitoring, (f) habitat restoration monitoring, and (g) monitoring of the Nonproliferation Test and Evaluation Complex. During 2011, all applicable laws, regulations, and permit requirements were met, enabling EMAC to achieve its intended goals and objectives.

  10. Ecological Monitoring and Compliance Program 2008 Report

    SciTech Connect (OSTI)

    Hansen, Dennis J.; Anderson, David C.; Hall, Derek B.; Greger, Paul D.; Ostler, W. Kent

    2009-04-30

    The Ecological Monitoring and Compliance Program, funded through the U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office (NNSA/NSO), monitors the ecosystem of the Nevada Test Site (NTS) and ensures compliance with laws and regulations pertaining to NTS biota. This report summarizes the program’s activities conducted by National Security Technologies, LLC (NSTec), during calendar year 2008. Program activities included (a) biological surveys at proposed construction sites, (b) desert tortoise compliance, (c) ecosystem mapping and data management, (d) sensitive plant species monitoring, (e) sensitive and protected/regulated animal monitoring, (f) habitat monitoring, (g) habitat restoration monitoring, and (h) monitoring of the Nonproliferation Test and Evaluation Complex (NPTEC).

  11. Ecological Monitoring and Compliance Program 2010 Report

    SciTech Connect (OSTI)

    Hansen, D.J.; Anderson, D.C.; Hall, D.B.; Greger, P.D.; Ostler, W.K.

    2011-07-01

    The Ecological Monitoring and Compliance (EMAC) Program, funded through the U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office (NNSA/NSO), monitors the ecosystem of the Nevada National Security Site (NNSS) and ensures compliance with laws and regulations pertaining to NNSS biota. This report summarizes the programs activities conducted by National Security Technologies, LLC (NSTec), during calendar year 2010. Program activities included (a) biological surveys at proposed construction sites, (b) desert tortoise compliance, (c) ecosystem monitoring, (d) sensitive plant species monitoring, (e) sensitive and protected/regulated animal monitoring, (f) habitat restoration monitoring, and (g) monitoring of the Nonproliferation Test and Evaluation Complex (NPTEC). During 2010, all applicable laws, regulations, and permit requirements were met, enabling EMAC to achieve its intended goals and objectives.

  12. Ecological Monitoring and Compliance Program 2013 Report

    SciTech Connect (OSTI)

    Hall, Derek B.; Anderson, David C.; Greger, Paul D.

    2014-06-05

    The Ecological Monitoring and Compliance Program (EMAC), funded through the U.S. Department of Energy, National Nuclear Security Administration Nevada Field Office (NNSA/NFO, formerly Nevada Site Office), monitors the ecosystem of the Nevada National Security Site (NNSS) and ensures compliance with laws and regulations pertaining to NNSS biota. This report summarizes the program’s activities conducted by National Security Technologies, LLC (NSTec), during calendar year 2013. Program activities included (a) biological surveys at proposed activity sites, (b) desert tortoise compliance, (c) ecosystem monitoring, (d) sensitive plant species monitoring, (e) sensitive and protected/regulated animal monitoring, and (f) habitat restoration monitoring. During 2013, all applicable laws, regulations, and permit requirements were met, enabling EMAC to achieve its intended goals and objectives.

  13. Modeling the role of terrestrial ecosystems in the global carbon cycle

    SciTech Connect (OSTI)

    Emanuel, W.R.; Post, W.M.; Shugart, H.H. Jr.

    1980-01-01

    A model for the global biogeochemical cycle of carbon which includes a five-compartment submodel for circulation in terrestrial ecosystems of the world is presented. Although this terrestrial submodel divides carbon into compartments with more functional detail than previous models, the variability in carbon dynamics among ecosystem types and in different climatic zones is not adequately treated. A new model construct which specifically treats this variability by modeling the distribution of ecosystem types as a function of climate on a 0.5/sup 0/ latitude by 0.5/sup 0/ longitude scale of resolution is proposed.

  14. Industrial ecology at Lawrence Livermore National Laboratory summary statement

    SciTech Connect (OSTI)

    Gilmartin, T.J.

    1996-06-04

    At Livermore our hope and our intention is to make important contributions to global sustainability by basing both our scientific and technological research and our business practices on the principles of industrial ecology. Current efforts in the following fields are documented: global security, global ecology, energy for transportation, fusion energy, materials sciences, environmental technology, and bioscience.

  15. Ecological risks of DOE`s programmatic environmental restoration alternatives

    SciTech Connect (OSTI)

    Not Available

    1994-06-01

    This report assesses the ecological risks of the Department of Energy`s (DOE) Environmental Restoration Program. The assessment is programmatic in that it is directed at evaluation of the broad programmatic alternatives outlined in the DOE Implementation Plan. It attempts to (1) characterize the ecological resources present on DOE facilities, (2) describe the occurrence and importance of ecologically significant contamination at major DOE facilities, (3) evaluate the adverse ecological impacts of habitat disturbance caused by remedial activities, and (4) determine whether one or another of the programmatic alternatives is clearly ecologically superior to the others. The assessment focuses on six representative facilities: the Idaho National Engineering Laboratory (INEL); the Fernald Environmental Management Project (FEMP); the Oak Ridge Reservation (ORR), including the Oak Ridge National Laboratory (ORNL), Y-12 plant, and K-25 plant; the Rocky Flats Plant; the Hanford Reservation; and the Portsmouth Gaseous Diffusion Plant.

  16. The Genomes and Metagenomes (GEM) Catalogue (first presentation) and The ISA-GCDML Workshop (second presentation) (GSC8 Meeting)

    ScienceCinema (OSTI)

    Field, Dawn [NERC Centre for Ecology and Hydrology]; Sansone, Susanna [EBI

    2011-04-29

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding ''Research Coordination Network'' from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Dawn Field of the NERC Centre for Ecology & Hydrology briefly introduces the GEM Catalogue, followed by Susanna Sansone of the European Bioinformatics Institute who talks about the ISA-GCDML workshop at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

  17. Terrestrial Ecosystem Science | U.S. DOE Office of Science (SC)

    Office of Science (SC) Website

    Terrestrial Ecosystem Science Biological and Environmental Research (BER) BER Home About Research Biological Systems Science Division (BSSD) Climate and Environmental Sciences Division (CESD) ARM Climate Research Facility Atmospheric System Research (ASR) Program Data Management Earth System Modeling (ESM) Program William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) Integrated Assessment of Global Climate Change Regional & Global Climate Modeling (RGCM) Program Subsurface

  18. Impacts of Environmental Nanoparticles on Chemical, Biological and Hydrological Processes in Terrestrial Ecosystems

    SciTech Connect (OSTI)

    Qafoku, Nikolla

    2012-01-01

    This chapter provides insights on nanoparticle (NP) influence or control on the extent and timescales of single or coupled physical, chemical, biological and hydrological reactions and processes that occur in terrestrial ecosystems. Examples taken from the literature that show how terrestrial NPs may determine the fate of the aqueous and sorbed (adsorbed or precipitated) chemical species of nutrients and contaminants, are also included in this chapter. Specifically, in the first section, chapter objectives, term definitions and discussions on size-dependent properties, the origin and occurrence of NP in terrestrial ecosystems and NP toxicity, are included. In the second section, the topic of the binary interactions of NPs of different sizes, shapes, concentrations and ages with the soil solution chemical species is covered, focusing on NP formation, stability, aggregation, ability to serve as sorbents, or surface-mediated precipitation catalysts, or electron donors and acceptors. In the third section, aspects of the interactions in the ternary systems composed of environmental NP, nutrient/contaminant chemical species, and the soil/sediment matrix are discussed, focusing on the inhibitory and catalytic effects of environmental NP on nutrient/contaminant advective mobility and mass transfer, adsorption and desorption, dissolution and precipitation and redox reactions that occur in terrestrial ecosystems. These three review sections are followed by a short summary of future research needs and directions, the acknowledgements, the list of the references, and the figures.

  19. Savannah River Ecology Laboratory, Annual Technical Progress Report of Ecological Research, June 30, 2002

    SciTech Connect (OSTI)

    Paul M. Bertsch,

    2002-06-30

    The Savannah River Ecology Laboratory (SREL) is a research unit of The University of Georgia (UGA) and has been conducting ecological research on the Savannah River Site (SRS) near Aiken, South Carolina for 50 years. The overall mission of the Laboratory is to acquire and communicate knowledge of ecological processes and principles. SREL conducts fundamental and applied ecological research, as well as education and outreach programs, under a Cooperative Agreement with the U.S. Department of Energy (DOE). The Laboratory's research mission during the 2002 fiscal year was fulfilled with the publication of 76 journal articles and book chapters by faculty, technical staff, students, and visiting scientists. An additional 50 journal articles have been submitted or are in press. Other noteworthy events took place as faculty members, staff, and graduate students received awards. These are described in the section titled Special Accomplishments of Faculty, Staff, Students, and Administration on page 51. Notable scientific accomplishments include work conducted on contaminant transport, stable isotopes, sandhills ecology, and phytoremediation: (1) A collaborative study between Dr. Tom Hinton at SREL and scientists at SRTC demonstrated the feasibility of using illite clay to sequester 137Cs in sediments along the P and R reactor cooling canal system, where approximately 3,000 acres of land are contaminated. Overall, the study showed significant decreases in cesium concentrations and bioavailability following the addition of illite with no sign of harm to the ecosystem. While the cesium remains sequestered from the biosphere, its radioactivity decays and the process progresses from contaminant immobilization to remediation. (2) SREL's stable isotope laboratory is now fully functional. Stable isotope distributions in nature can provide important insights into many historical and current environmental processes. Dr. Christopher Romanek is leading SREL's research in this area

  20. Baseline ecological footprint of Sandia National Laboratories, New Mexico.

    SciTech Connect (OSTI)

    Coplen, Amy K.; Mizner, Jack Harry,; Ubechel, Norion M.

    2009-01-01

    The Ecological Footprint Model is a mechanism for measuring the environmental effects of operations at Sandia National Laboratories in Albuquerque, New Mexico (SNL/NM). This analysis quantifies environmental impact associated with energy use, transportation, waste, land use, and water consumption at SNL/NM for fiscal year 2005 (FY05). Since SNL/NM's total ecological footprint (96,434 gha) is greater than the waste absorption capacity of its landholdings (338 gha), it created an ecological deficit of 96,096 gha. This deficit is equal to 886,470lha, or about 3,423 square miles of Pinyon-Juniper woodlands and desert grassland. 89% of the ecological footprint can be attributed to energy use, indicating that in order to mitigate environmental impact, efforts should be focused on energy efficiency, energy reduction, and the incorporation of additional renewable energy alternatives at SNL/NM.

  1. Savannah River Ecology Laboratory FY2006 Annual Technical Progress Report

    SciTech Connect (OSTI)

    Paul M. Bertsch

    2006-10-23

    FY2006 annual report of research conducted by the Savannah River Ecology Laboratory, a research unit of the University of Georgia operating on the Savannah River Site in Aiken, County, SC.

  2. The Importance of Traditional Ecological Knowledge in Adaptation Planning

    Broader source: Energy.gov [DOE]

    The National Adaptation Forum is hosting a webinar to focus on the importance and role of traditional ecological knowledge in adaptation planning at the local, regional, and national level.

  3. Long-Term Ecological Monitoring Field Sampling Plan for 2007

    SciTech Connect (OSTI)

    T. Haney R. VanHorn

    2007-07-31

    This field sampling plan describes the field investigations planned for the Long-Term Ecological Monitoring Project at the Idaho National Laboratory Site in 2007. This plan and the Quality Assurance Project Plan for Waste Area Groups 1, 2, 3, 4, 5, 6, 7, 10, and Removal Actions constitute the sampling and analysis plan supporting long-term ecological monitoring sampling in 2007. The data collected under this plan will become part of the long-term ecological monitoring data set that is being collected annually. The data will be used t determine the requirements for the subsequent long-term ecological monitoring. This plan guides the 2007 investigations, including sampling, quality assurance, quality control, analytical procedures, and data management. As such, this plan will help to ensure that the resulting monitoring data will be scientifically valid, defensible, and of known and acceptable quality.

  4. Savannah River Ecology Laboratory 2005 Annual Technical Progress Report

    SciTech Connect (OSTI)

    Paul M. Bertsch

    2005-07-19

    2005 annual report of research conducted by the Savannah River Ecology Laboratory, a research unit of The University of Georgia operating on the Savannah River Site, Aiken, South Carolina

  5. Savannah River Ecology Laboratory 2004 Annual Technical Progress Report

    SciTech Connect (OSTI)

    Paul M. Bertsch

    2004-07-29

    2004 annual report of research conducted by the Savannah River Ecology Laboratory, a research unit of The University of Georgia operating on the Savannah River Site in Aiken, South Carolina

  6. Washington State Department of Ecology: Replacement Wells Requiring...

    Open Energy Info (EERE)

    Ecology: Replacement Wells Requiring a Water Right Jump to: navigation, search OpenEI Reference LibraryAdd to library Legal Document- OtherOther: Washington State Department of...

  7. O. E. Rhodes, Jr. | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Curriculum Vitae Faculty & Scientists SREL Home Olin E. Rhodes, Jr. Savannah River Ecology Laboratory P O Drawer E, Aiken, SC 29802 (803) 725-8191 office (803) 725-3309 fax...

  8. Ecology Action: Small Market Advanced Retrofit Transformation Program (SMART)

    Broader source: Energy.gov [DOE]

    Lead Performer: Ecology Action – Santa Cruz, CA Partners: - New Buildings Institute – Portland, OR - Electric and Gas Industries Association (EGIA) – Sacramento, CA - Pacific Gas and Electric – San Francisco, CA - Sacramento Municipal Utility District – Sacramento, CA

  9. Preliminary Notice of Violation, Safety and Ecology Corporation...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Ecology Corporation related to a 10 CFR Part 708 Violation at the Portsmouth Gaseous Diffusion Project On June 14, 2005, the U.S. Department of Energy issued a Preliminary Notice...

  10. COLLOQUIUM: Ocean Acoustic Ecology: Great Whales, Ocean Scales...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    March 23, 2016, 4:15pm to 5:30pm Colloquia MBG Auditorium COLLOQUIUM: Ocean Acoustic Ecology: Great Whales, Ocean Scales, Big Data Dr. Christopher Clark Cornell University ...

  11. Ecological Principles and Guidelines for Managing the Use of Land

    SciTech Connect (OSTI)

    Dale, Virginia H; Brown, Sandra; Haeuber, R A; Hobbs, N T; Huntly, N; Naiman, R J; Riebsame, W E; Turner, M G; Valone, T J

    2014-01-01

    The many ways that people have used and managed land throughout history has emerged as a primary cause of land-cover change around the world. Thus, land use and land management increasingly represent a fundamental source of change in the global environment. Despite their global importance, however, many decisions about the management and use of land are made with scant attention to ecological impacts. Thus, ecologists' knowledge of the functioning of Earth's ecosystems is needed to broaden the scientific basis of decisions on land use and management. In response to this need, the Ecological Society of America established a committee to examine the ways that land-use decisions are made and the ways that ecologists could help inform those decisions. This paper reports the scientific findings of that committee. Five principles of ecological science have particular implications for land use and can assure that fundamental processes of Earth's ecosystems are sustained. These ecological principles deal with time, species, place, dis- turbance, and the landscape. The recognition that ecological processes occur within a temporal setting and change over time is fundamental to analyzing the effects of land use. In addition, individual species and networks of interacting species have strong and far-reaching effects on ecological processes. Furthermore, each site or region has a unique set of organisms and abiotic conditions influencing and constraining ecological processes. Distur- bances are important and ubiquitous ecological events whose effects may strongly influence population, com- munity, and ecosystem dynamics. Finally, the size, shape, and spatial relationships of habitat patches on the landscape affect the structure and function of ecosystems. The responses of the land to changes in use and management by people depend on expressions of these fundamental principles in nature. These principles dictate several guidelines for land use. The guidelines give practical

  12. Ecological function and resilience: Neglected criteria for environmental impact assessment and ecological risk analysis

    SciTech Connect (OSTI)

    Cairns, J. Jr.; Niederlehner, B.R. . Univ. Center for Environmental and Hazardous Materials Studies)

    1993-01-01

    The importance of establishing methods for determining ecological function and resilience transcends scientific interest; these methods are important to sustained societal use of ecosystems and long-term productivity. Essential services that ecosystems provide to human society include water purification, oxygen production, carbon storage, climate regulation, and production of food, wood, and medicinal drugs. Although man is dependent upon these services, human understanding of the dynamics of ecosystem function is limited. Man can detect gross impairment of ecosystem function or resilience after the fact. However, protecting ecosystem health necessitates detecting adverse trends in ecological function, rather than reacting when the system collapses. The information to date is inadequate for predicting subtle changes or incremental trends. Once ecosystems are damaged and therefore providing diminished services, it is important to determine when they will be restored to an approximation of their predisturbance condition. For those ecosystems unlikely to recover on their own, management techniques may enhance recovery processes. Information about response of ecosystem function to human actions and relative resilience of alternative ecosystems can facilitate decision-making under the National Environmental Policy Act (NEPA).

  13. Ecological perspectives of land use history: The Arid Lands Ecology (ALE) Reserve

    SciTech Connect (OSTI)

    Hinds, N R; Rogers, L E

    1991-07-01

    The objective of this study was to gather information on the land use history of the Arid Land Ecology (ALE) Reserve so that current ecological research could be placed within a historical perspective. The data were gathered in the early 1980s by interviewing former users of the land and from previously published research (where available). Interviews with former land users of the ALE Reserve in Benton County, Washington, revealed that major land uses from 1880 to 1940 were homesteading, grazing, oil/gas production, and road building. Land use practices associated with grazing and homesteading have left the greatest impact on the landscape. Disturbed sites where succession is characterized by non-native species, plots where sagebrush was railed away, and sheep trails are major indications today of past land uses. Recent estimates of annual bunchgrass production do ALE do not support the widespread belief that bunchgrass were more productive during the homesteading era, though the invasion of cheatgrass (Bromus tectorum), Jim Hill mustard (Sisymbrium altissium), and other European alien plant species has altered pre-settlement succession patterns. 15 refs., 6 figs., 1 tab.

  14. START HERE 2013 Annual Ecology Report DVD 1.htm

    Office of Legacy Management (LM)

    3 Annual Ecology Report for the Rocky Flats Site Ecology DVD 1 Click on the links below to access different portions of the electronic annual report. 2013 Annual Report Sections Revegetation Monitoring Report Vegetation Survey Report Wildlife Survey Report Wetland Mitigation Monitoring Report Rocky Flats Vascular Flora List (2013) 2013 Photopoint Monitoring Closure Revegetation Locations Post-Closure Revegetation Locations Wetland Mitigation Locations 2013 Wildlife Videos

  15. START HERE 2014 Annual Ecology Report DVD 1.htm

    Office of Legacy Management (LM)

    Annual Ecology Report for the Rocky Flats Site Ecology DVD 1 Click on the links below to access different portions of the electronic annual report. 2014 Annual Report Sections Revegetation Monitoring Report Vegetation Survey Report Wildlife Survey Report COU Vegetation Map 2014 Wetland Mitigation Monitoring Report Rocky Flats Vascular Flora List (2014) 2014 Photopoint Monitoring Closure Revegetation Locations Post-Closure Revegetation Locations Wetland Mitigation Locations

  16. Estimating and mapping ecological processes influencing microbial community assembly

    SciTech Connect (OSTI)

    Stegen, James C.; Lin, Xueju; Fredrickson, Jim K.; Konopka, Allan E.

    2015-05-01

    Ecological community assembly is governed by a combination of (i) selection resulting from among-taxa differences in performance; (ii) dispersal resulting from organismal movement; and (iii) ecological drift resulting from stochastic changes in population sizes. The relative importance and nature of these processes can vary across environments. Selection can be homogeneous or variable, and while dispersal is a rate, we conceptualize extreme dispersal rates as two categories; dispersal limitation results from limited exchange of organisms among communities, and homogenizing dispersal results from high levels of organism exchange. To estimate the influence and spatial variation of each process we extend a recently developed statistical framework, use a simulation model to evaluate the accuracy of the extended framework, and use the framework to examine subsurface microbial communities over two geologic formations. For each subsurface community we estimate the degree to which it is influenced by homogeneous selection, variable selection, dispersal limitation, and homogenizing dispersal. Our analyses revealed that the relative influences of these ecological processes vary substantially across communities even within a geologic formation. We further identify environmental and spatial features associated with each ecological process, which allowed mapping of spatial variation in ecological-process-influences. The resulting maps provide a new lens through which ecological systems can be understood; in the subsurface system investigated here they revealed that the influence of variable selection was associated with the rate at which redox conditions change with subsurface depth.

  17. Estimating and mapping ecological processes influencing microbial community assembly

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Stegen, James C.; Lin, Xueju; Fredrickson, Jim K.; Konopka, Allan E.

    2015-05-01

    Ecological community assembly is governed by a combination of (i) selection resulting from among-taxa differences in performance; (ii) dispersal resulting from organismal movement; and (iii) ecological drift resulting from stochastic changes in population sizes. The relative importance and nature of these processes can vary across environments. Selection can be homogeneous or variable, and while dispersal is a rate, we conceptualize extreme dispersal rates as two categories; dispersal limitation results from limited exchange of organisms among communities, and homogenizing dispersal results from high levels of organism exchange. To estimate the influence and spatial variation of each process we extend a recentlymore » developed statistical framework, use a simulation model to evaluate the accuracy of the extended framework, and use the framework to examine subsurface microbial communities over two geologic formations. For each subsurface community we estimate the degree to which it is influenced by homogeneous selection, variable selection, dispersal limitation, and homogenizing dispersal. Our analyses revealed that the relative influences of these ecological processes vary substantially across communities even within a geologic formation. We further identify environmental and spatial features associated with each ecological process, which allowed mapping of spatial variation in ecological-process-influences. The resulting maps provide a new lens through which ecological systems can be understood; in the subsurface system investigated here they revealed that the influence of variable selection was associated with the rate at which redox conditions change with subsurface depth.« less

  18. Single-junction solar cells with the optimum band gap for terrestrial concentrator applications

    DOE Patents [OSTI]

    Wanlass, Mark W.

    1994-01-01

    A single-junction solar cell having the ideal band gap for terrestrial concentrator applications. Computer modeling studies of single-junction solar cells have shown that the presence of absorption bands in the direct spectrum has the effect of "pinning" the optimum band gap for a wide range of operating conditions at a value of 1.14.+-.0.02 eV. Efficiencies exceeding 30% may be possible at high concentration ratios for devices with the ideal band gap.

  19. Reviews and syntheses: Four decades of modeling methane cycling in terrestrial ecosystems

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Xu, Xiaofeng; Yuan, Fengming; Hanson, Paul J.; Wullschleger, Stan D.; Thornton, Peter E.; Riley, William J.; Song, Xia; Graham, David E.; Song, Changchun; Tian, Hanqin

    2016-06-28

    Over the past 4 decades, a number of numerical models have been developed to quantify the magnitude, investigate the spatial and temporal variations, and understand the underlying mechanisms and environmental controls of methane (CH4) fluxes within terrestrial ecosystems. These CH4 models are also used for integrating multi-scale CH4 data, such as laboratory-based incubation and molecular analysis, field observational experiments, remote sensing, and aircraft-based measurements across a variety of terrestrial ecosystems. Here we summarize 40 terrestrial CH4 models to characterize their strengths and weaknesses and to suggest a roadmap for future model improvement and application. Our key findings are that (1) themore » focus of CH4 models has shifted from theoretical to site- and regional-level applications over the past 4 decades, (2) large discrepancies exist among models in terms of representing CH4 processes and their environmental controls, and (3) significant data–model and model–model mismatches are partially attributed to different representations of landscape characterization and inundation dynamics. Three areas for future improvements and applications of terrestrial CH4 models are that (1) CH4 models should more explicitly represent the mechanisms underlying land–atmosphere CH4 exchange, with an emphasis on improving and validating individual CH4 processes over depth and horizontal space, (2) models should be developed that are capable of simulating CH4 emissions across highly heterogeneous spatial and temporal scales, particularly hot moments and hotspots, and (3) efforts should be invested to develop model benchmarking frameworks that can easily be used for model improvement, evaluation, and integration with data from molecular to global scales. These improvements in CH4 models would be beneficial for the Earth system models and further simulation of climate–carbon cycle feedbacks.« less

  20. Reviews and syntheses: Four decades of modeling methane cycling in terrestrial ecosystems

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Xu, Xiaofeng; Yuan, Fengming; Hanson, Paul J.; Wullschleger, Stan D.; Thornton, Peter E.; Riley, William J.; Song, Xia; Graham, David E.; Song, Changchun; Tian, Hanqin

    2016-01-28

    A number of numerical models have been developed to quantify the magnitude, over the past 4 decades, such that we have investigated the spatial and temporal variations, and understand the underlying mechanisms and environmental controls of methane (CH4) fluxes within terrestrial ecosystems. These CH4 models are also used for integrating multi-scale CH4 data, such as laboratory-based incubation and molecular analysis, field observational experiments, remote sensing, and aircraft-based measurements across a variety of terrestrial ecosystems. Here we summarize 40 terrestrial CH4 models to characterize their strengths and weaknesses and to suggest a roadmap for future model improvement and application. Our keymore » findings are that (1) the focus of CH4 models has shifted from theoretical to site- and regional-level applications over the past 4 decades, (2) large discrepancies exist among models in terms of representing CH4 processes and their environmental controls, and (3) significant data–model and model–model mismatches are partially attributed to different representations of landscape characterization and inundation dynamics. Furthermore three areas for future improvements and applications of terrestrial CH4 models are that (1) CH4 models should more explicitly represent the mechanisms underlying land–atmosphere CH4 exchange, with an emphasis on improving and validating individual CH4 processes over depth and horizontal space, (2) models should be developed that are capable of simulating CH4 emissions across highly heterogeneous spatial and temporal scales, particularly hot moments and hotspots, and (3) efforts should be invested to develop model benchmarking frameworks that can easily be used for model improvement, evaluation, and integration with data from molecular to global scales. Finally, these improvements in CH4 models would be beneficial for the Earth system models and further simulation of climate–carbon cycle feedbacks.« less

  1. The use of microarrays in microbial ecology

    SciTech Connect (OSTI)

    Andersen, G.L.; He, Z.; DeSantis, T.Z.; Brodie, E.L.; Zhou, J.

    2009-09-15

    Microarrays have proven to be a useful and high-throughput method to provide targeted DNA sequence information for up to many thousands of specific genetic regions in a single test. A microarray consists of multiple DNA oligonucleotide probes that, under high stringency conditions, hybridize only to specific complementary nucleic acid sequences (targets). A fluorescent signal indicates the presence and, in many cases, the abundance of genetic regions of interest. In this chapter we will look at how microarrays are used in microbial ecology, especially with the recent increase in microbial community DNA sequence data. Of particular interest to microbial ecologists, phylogenetic microarrays are used for the analysis of phylotypes in a community and functional gene arrays are used for the analysis of functional genes, and, by inference, phylotypes in environmental samples. A phylogenetic microarray that has been developed by the Andersen laboratory, the PhyloChip, will be discussed as an example of a microarray that targets the known diversity within the 16S rRNA gene to determine microbial community composition. Using multiple, confirmatory probes to increase the confidence of detection and a mismatch probe for every perfect match probe to minimize the effect of cross-hybridization by non-target regions, the PhyloChip is able to simultaneously identify any of thousands of taxa present in an environmental sample. The PhyloChip is shown to reveal greater diversity within a community than rRNA gene sequencing due to the placement of the entire gene product on the microarray compared with the analysis of up to thousands of individual molecules by traditional sequencing methods. A functional gene array that has been developed by the Zhou laboratory, the GeoChip, will be discussed as an example of a microarray that dynamically identifies functional activities of multiple members within a community. The recent version of GeoChip contains more than 24,000 50mer

  2. The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classifications

    SciTech Connect (OSTI)

    Thomas, Alex D.; Stamatis, Dimitri; Bertsch, Jon; Isbandi, Michelle; Jansson, Jakob; Mallajosyula, Jyothi; Pagani, Ioanna; Lobos, Elizabeth A.; Kyrpides, Nikos C.; Reddy, Tatiparthi

    2014-10-29

    The Genomes OnLine Database (GOLD, http://www.genomesonline.org) is a comprehensive online resource to catalogue and monitor genetic studies worldwide. GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated metadata. Here we report version 5 (v.5) of the database. The newly designed database schema and web user interface supports several new features including the implementation of a four level (meta)genome project classification system and a simplified intuitive web interface to access reports and launch search tools. The database currently hosts information for about 19,200 studies, 56,000 Biosamples, 56,000 sequencing projects, and 39,400 analysis projects. More than just a catalogue of worldwide genome projects, GOLD is a manually curated, quality controlled metadata warehouse. The problems encountered in integrating disparate and varying quality data into GOLD are briefly highlighted. GOLD fully supports and follows the Genomic Standards Consortium (GSC) Minimum Information standards.

  3. The functional potential of microbial communities in hydraulic fracturing source water and produced water from natural gas extraction characterized by metagenomic sequencing

    SciTech Connect (OSTI)

    Mohan, Arvind Murali; Bibby, Kyle J.; Lipus, Daniel; Hammack, Richard W.; Gregory, Kelvin B.; Forster, Robert J.

    2014-10-22

    Microbial activity in produced water from hydraulic fracturing operations can lead to undesired environmental impacts and increase gas production costs. However, the metabolic profile of these microbial communities is not well understood. Here, for the first time, we present results from a shotgun metagenome of microbial communities in both hydraulic fracturing source water and wastewater produced by hydraulic fracturing. Taxonomic analyses showed an increase in anaerobic/facultative anaerobic classes related to Clostridia, Gammaproteobacteria, Bacteroidia and Epsilonproteobacteria in produced water as compared to predominantly aerobic Alphaproteobacteria in the fracturing source water. Thus, the metabolic profile revealed a relative increase in genes responsible for carbohydrate metabolism, respiration, sporulation and dormancy, iron acquisition and metabolism, stress response and sulfur metabolism in the produced water samples. These results suggest that microbial communities in produced water have an increased genetic ability to handle stress, which has significant implications for produced water management, such as disinfection.

  4. Terrestrial biogeochemical feedbacks in the climate system: from past to future

    SciTech Connect (OSTI)

    Arneth, A.; Harrison, S. P.; Zaehle, S.; Tsigaridis, K; Menon, S; Bartlein, P.J.; Feichter, J; Korhola, A; Kulmala, M; O'Donnell, D; Schurgers, G; Sorvari, S; Vesala, T

    2010-01-05

    The terrestrial biosphere plays a major role in the regulation of atmospheric composition, and hence climate, through multiple interlinked biogeochemical cycles (BGC). Ice-core and other palaeoenvironmental records show a fast response of vegetation cover and exchanges with the atmosphere to past climate change, although the phasing of these responses reflects spatial patterning and complex interactions between individual biospheric feedbacks. Modern observations show a similar responsiveness of terrestrial biogeochemical cycles to anthropogenically-forced climate changes and air pollution, with equally complex feedbacks. For future conditions, although carbon cycle-climate interactions have been a major focus, other BGC feedbacks could be as important in modulating climate changes. The additional radiative forcing from terrestrial BGC feedbacks other than those conventionally attributed to the carbon cycle is in the range of 0.6 to 1.6 Wm{sup -2}; all taken together we estimate a possible maximum of around 3 Wm{sup -2} towards the end of the 21st century. There are large uncertainties associated with these estimates but, given that the majority of BGC feedbacks result in a positive forcing because of the fundamental link between metabolic stimulation and increasing temperature, improved quantification of these feedbacks and their incorporation in earth system models is necessary in order to develop coherent plans to manage ecosystems for climate mitigation.

  5. Redefining fine roots improves understanding of belowground contributions to terrestrial biosphere processes

    SciTech Connect (OSTI)

    McCormack, M. Luke; Dickie, Ian A.; Eissenstat, David M.; Fahey, Timothy J.; Fernandez, Christopher W.; Guo, Dali; Helmisaari, Helja -Sisko; Hobbie, Erik A.; Iversen, Colleen M.; Jackson, Robert B.; Leppälammi-Kujansuu, Jaana; Norby, Richard J.; Phillips, Richard P.; Pregitzer, Kurt S.; Pritchard, Seth G.; Rewald, Boris; Zadworny, Marcin

    2015-03-10

    Fine roots acquire essential soil resources and mediate biogeochemical cycling in terrestrial ecosystems. Estimates of carbon and nutrient allocation to build and maintain these structures remain uncertain due to challenges in consistent measurement and interpretation of fine-root systems. We define fine roots as all roots less than or equal to 2 mm in diameter, yet it is now recognized that this approach fails to capture the diversity of form and function observed among fine-root orders. We demonstrate how order-based and functional classification frameworks improve our understanding of dynamic root processes in ecosystems dominated by perennial plants. In these frameworks, fine roots are separated into either individual root orders or functionally defined into a shorter-lived absorptive pool and a longer-lived transport fine root pool. Furthermore, using these frameworks, we estimate that fine-root production and turnover represent 22% of terrestrial net primary production globally a ca. 30% reduction from previous estimates assuming a single fine-root pool. In the future we hope to develop tools to rapidly differentiate functional fine-root classes, explicit incorporation of mycorrhizal fungi in fine-root studies, and wider adoption of a two-pool approach to model fine roots provide opportunities to better understand belowground processes in the terrestrial biosphere.

  6. Redefining fine roots improves understanding of belowground contributions to terrestrial biosphere processes

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    McCormack, M. Luke; Dickie, Ian A.; Eissenstat, David M.; Fahey, Timothy J.; Fernandez, Christopher W.; Guo, Dali; Helmisaari, Helja -Sisko; Hobbie, Erik A.; Iversen, Colleen M.; Jackson, Robert B.; et al

    2015-03-10

    Fine roots acquire essential soil resources and mediate biogeochemical cycling in terrestrial ecosystems. Estimates of carbon and nutrient allocation to build and maintain these structures remain uncertain due to challenges in consistent measurement and interpretation of fine-root systems. We define fine roots as all roots less than or equal to 2 mm in diameter, yet it is now recognized that this approach fails to capture the diversity of form and function observed among fine-root orders. We demonstrate how order-based and functional classification frameworks improve our understanding of dynamic root processes in ecosystems dominated by perennial plants. In these frameworks, finemore » roots are separated into either individual root orders or functionally defined into a shorter-lived absorptive pool and a longer-lived transport fine root pool. Furthermore, using these frameworks, we estimate that fine-root production and turnover represent 22% of terrestrial net primary production globally a ca. 30% reduction from previous estimates assuming a single fine-root pool. In the future we hope to develop tools to rapidly differentiate functional fine-root classes, explicit incorporation of mycorrhizal fungi in fine-root studies, and wider adoption of a two-pool approach to model fine roots provide opportunities to better understand belowground processes in the terrestrial biosphere.« less

  7. DOE Regional Partnership Successfully Demonstrates Terrestrial CO2 Storage Practices in Great Plains Region of U.S. and Canada

    Broader source: Energy.gov [DOE]

    A field test demonstrating the best approaches for terrestrial carbon dioxide storage in the heartland of North America has been successfully completed by one of the U.S. Department of Energy's seven Regional Carbon Sequestration Partnerships.

  8. PHOTOCHEMISTRY IN TERRESTRIAL EXOPLANET ATMOSPHERES. I. PHOTOCHEMISTRY MODEL AND BENCHMARK CASES

    SciTech Connect (OSTI)

    Hu Renyu; Seager, Sara; Bains, William

    2012-12-20

    We present a comprehensive photochemistry model for exploration of the chemical composition of terrestrial exoplanet atmospheres. The photochemistry model is designed from the ground up to have the capacity to treat all types of terrestrial planet atmospheres, ranging from oxidizing through reducing, which makes the code suitable for applications for the wide range of anticipated terrestrial exoplanet compositions. The one-dimensional chemical transport model treats up to 800 chemical reactions, photochemical processes, dry and wet deposition, surface emission, and thermal escape of O, H, C, N, and S bearing species, as well as formation and deposition of elemental sulfur and sulfuric acid aerosols. We validate the model by computing the atmospheric composition of current Earth and Mars and find agreement with observations of major trace gases in Earth's and Mars' atmospheres. We simulate several plausible atmospheric scenarios of terrestrial exoplanets and choose three benchmark cases for atmospheres from reducing to oxidizing. The most interesting finding is that atomic hydrogen is always a more abundant reactive radical than the hydroxyl radical in anoxic atmospheres. Whether atomic hydrogen is the most important removal path for a molecule of interest also depends on the relevant reaction rates. We also find that volcanic carbon compounds (i.e., CH{sub 4} and CO{sub 2}) are chemically long-lived and tend to be well mixed in both reducing and oxidizing atmospheres, and their dry deposition velocities to the surface control the atmospheric oxidation states. Furthermore, we revisit whether photochemically produced oxygen can cause false positives for detecting oxygenic photosynthesis, and find that in 1 bar CO{sub 2}-rich atmospheres oxygen and ozone may build up to levels that have conventionally been accepted as signatures of life, if there is no surface emission of reducing gases. The atmospheric scenarios presented in this paper can serve as the benchmark

  9. Nitrogen attenuation of terrestrial carbon cycle response to global environmental factors

    SciTech Connect (OSTI)

    Jain, Atul; Yang, Xiaojuan; Kheshgi, Haroon; Mcguire, David; Post, Wilfred M

    2009-01-01

    Nitrogen cycle dynamics have the capacity to attenuate the magnitude of global terrestrial carbon sinks and sources driven by CO2 fertilization and changes in climate. In this study, two versions of the terrestrial carbon and nitrogen cycle components of the Integrated Science Assessment Model (ISAM) are used to evaluate how variation in nitrogen availability influences terrestrial carbon sinks and sources in response to changes over the 20th century in global environmental factors including atmospheric CO2 concentration, nitrogen inputs, temperature, precipitation and land use. The two versions of ISAM vary in their treatment of nitrogen availability: ISAM-NC has a terrestrial carbon cycle model coupled to a fully dynamic nitrogen cycle while ISAM-C has an identical carbon cycle model but nitrogen availability is always in sufficient supply. Overall, the two versions of the model estimate approximately the same amount of global mean carbon uptake over the 20th century. However, comparisons of results of ISAM-NC relative to ISAM-C reveal that nitrogen dynamics: (1) reduced the 1990s carbon sink associated with increasing atmospheric CO2 by 0.53 PgC yr1 (1 Pg = 1015g), (2) reduced the 1990s carbon source associated with changes in temperature and precipitation of 0.34 PgC yr1 in the 1990s, (3) an enhanced sink associated with nitrogen inputs by 0.26 PgC yr1, and (4) enhanced the 1990s carbon source associated with changes in land use by 0.08 PgC yr1 in the 1990s. These effects of nitrogen limitation influenced the spatial distribution of the estimated exchange of CO2 with greater sink activity in high latitudes associated with climate effects and a smaller sink of CO2 in the southeastern United States caused by N limitation associated with both CO2 fertilization and forest regrowth. These results indicate that the dynamics of nitrogen availability are important to consider in assessing the spatial distribution and temporal dynamics of terrestrial carbon sources and

  10. Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche

    SciTech Connect (OSTI)

    Morin, Emmanuelle; Kohler, Annegret; Baker, Adam R.; Foulongne-Oriol, Marie; Lombard, Vincent; Nagy, Laszlo G.; Ohm, Robin A.; Patyshakuliyeva, Aleksandrina; Brun, Annick; Aerts, Andrea L.; Bailey, Andrew M.; Billette, Christophe; Coutinho, Pedro M.; Deakin, Greg; Doddapaneni, Harshavardhan; Floudas, Dimitrios; Grimwood, Jane; Hilden, Kristiina; Kues, Ursula; LaButti, Kurt M.; Lapidus, Alla; Lindquist, Erika A.; Lucas, Susan M.; Murat, Claude; Riley, Robert W.; Salamov, Asaf A.; Schmutz, Jeremy; Subramanian, Venkataramanan; Wosten, Han A. B.; Xu, Jianping; Eastwood, Daniel C.; Foster, Gary D.; Sonnenberg, Anton S. M.; Cullen, Dan; de Vries, Ronald P.; Lundell, Taina; Hibbett, David S.; Henrissat, Bernard; Burton, Kerry S.; Kerrigan, Richard W.; Challen, Michael P.; Grigoriev, Igor V.; Martin, Francis

    2012-04-27

    Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the button mushroom forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics.

  11. Studies of the terrestrial O{sub 2} and carbon cycles in sand dune gases and in biosphere 2

    SciTech Connect (OSTI)

    Severinghaus, J.P.

    1995-12-31

    Molecular oxygen in the atmosphere is coupled tightly to the terrestrial carbon cycle by the processes of photosynthesis, respiration, and burning. This dissertation examines different aspects of this coupling in four chapters. Chapter 1 explores the feasibility of using air from sand dunes to reconstruct atmospheric O{sub 2} composition centuries ago. Such a record would reveal changes in the mass of the terrestrial biosphere, after correction for known fossil fuel combustion, and constrain the fate of anthropogenic CO{sub 2}.

  12. Big Canyon Creek Ecological Restoration Strategy.

    SciTech Connect (OSTI)

    Rasmussen, Lynn; Richardson, Shannon

    2007-10-01

    He-yey, Nez Perce for steelhead or rainbow trout (Oncorhynchus mykiss), are a culturally and ecologically significant resource within the Big Canyon Creek watershed; they are also part of the federally listed Snake River Basin Steelhead DPS. The majority of the Big Canyon Creek drainage is considered critical habitat for that DPS as well as for the federally listed Snake River fall chinook (Oncorhynchus tshawytscha) ESU. The Nez Perce Soil and Water Conservation District (District) and the Nez Perce Tribe Department of Fisheries Resources Management-Watershed (Tribe), in an effort to support the continued existence of these and other aquatic species, have developed this document to direct funding toward priority restoration projects in priority areas for the Big Canyon Creek watershed. In order to achieve this, the District and the Tribe: (1) Developed a working group and technical team composed of managers from a variety of stakeholders within the basin; (2) Established geographically distinct sub-watershed areas called Assessment Units (AUs); (3) Created a prioritization framework for the AUs and prioritized them; and (4) Developed treatment strategies to utilize within the prioritized AUs. Assessment Units were delineated by significant shifts in sampled juvenile O. mykiss (steelhead/rainbow trout) densities, which were found to fall at fish passage barriers. The prioritization framework considered four aspects critical to determining the relative importance of performing restoration in a certain area: density of critical fish species, physical condition of the AU, water quantity, and water quality. It was established, through vigorous data analysis within these four areas, that the geographic priority areas for restoration within the Big Canyon Creek watershed are Big Canyon Creek from stream km 45.5 to the headwaters, Little Canyon from km 15 to 30, the mainstem corridors of Big Canyon (mouth to 7km) and Little Canyon (mouth to 7km). The District and the Tribe

  13. Ecological Monitoring and Compliance Program 2006 Report

    SciTech Connect (OSTI)

    David C. Anderson; Paul D. Greger; Derek B. Hall; Dennis J. Hansen; William K. Ostler

    2007-03-01

    The Ecological Monitoring and Compliance program (EMAC), funded through the U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office (NNSA/NSO), monitors the ecosystem of the Nevada Test Site (NTS) and ensures compliance with laws and regulations pertaining to NTS biota. This report summarizes the program's activities conducted by National Security Technologies LLC (NSTec) during the Calendar Year 2006. Program activities included: (a) biological surveys at proposed construction sites, (b) desert tortoise compliance, (c) ecosystem mapping and data management, (d) sensitive plant species monitoring, (e) sensitive and protected/regulated animal monitoring, (f) habitat monitoring, (g) habitat restoration monitoring, and (h) monitoring of the Nonproliferation Test and Evaluation Complex (NPTEC). Sensitive and protected/regulated species of the NTS include 44 plants, 1 mollusk, 2 reptiles, over 250 birds, and 26 mammals protected, managed, or considered sensitive as per state or federal regulations and natural resource agencies and organizations. The threatened desert tortoise (Gopherus agassizii) is the only species on the NTS protected under the Endangered Species Act. Biological surveys for the presence of sensitive and protected/regulated species and important biological resources on which they depend were conducted for 34 projects. A total of 342.1 hectares (ha) (845.37 acres [ac]) was surveyed for these projects. Sensitive and protected/regulated species and important biological resources found included: 2 inactive tortoise burrows, 2 western burrowing owls (Athene cunicularia hypugaea), several horses (Equus caballus), 2 active predator burrows, mature Joshua trees (Yucca brevifolia), yuccas and cacti; and also 1 bird nest (2 eggs), 1 barn owl (Tyto alba) and 2 great-horned owls (Bubo virginianus). NSTec provided a written summary report of all survey findings and mitigation recommendations, where applicable. All flagged burrows were

  14. Ecological Monitoring and Compliance Program 2006 Report

    SciTech Connect (OSTI)

    David C. Anderson; Paul D. Greger; Derek B. Hall; Dennis J. Hansen; William K. Ostler

    2007-03-01

    The Ecological Monitoring and Compliance program (EMAC), funded through the U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office (NNSA/NSO), monitors the ecosystem of the Nevada Test Site (NTS) and ensures compliance with laws and regulations pertaining to NTS biota. This report summarizes the program's activities conducted by National Security Technologies LLC (NSTec) during the Calendar Year 2006. Program activities included: (a) biological surveys at proposed construction sites, (b) desert tortoise compliance, (c) ecosystem mapping and data management, (d) sensitive plant species monitoring, (e) sensitive and protected/regulated animal monitoring, (f) habitat monitoring, (g) habitat restoration monitoring, and (h) monitoring of the Nonproliferation Test and Evaluation Complex (NPTEC). Sensitive and protected/regulated species of the NTS include 44 plants, 1 mollusk, 2 reptiles, over 250 birds, and 26 mammals protected, managed, or considered sensitive as per state or federal regulations and natural resource agencies and organizations. The threatened desert tortoise (Gopherus agassizii) is the only species on the NTS protected under the Endangered Species Act. Biological surveys for the presence of sensitive and protected/regulated species and important biological resources on which they depend were conducted for 34 projects. A total of 342.1 hectares (ha) (845.37 acres [ac]) was surveyed for these projects. Sensitive and protected/regulated species and important biological resources found included: 2 inactive tortoise burrows, 2 western burrowing owls (Athene cunicularia hypugaea), several horses (Equus caballus), 2 active predator burrows, mature Joshua trees (Yucca brevifolia), yuccas and cacti; and also 1 bird nest (2 eggs), 1 barn owl (Tyto alba) and 2 great-horned owls (Bubo virginianus). NSTec provided a written summary report of all survey findings and mitigation recommendations, where applicable. All flagged burrows were

  15. Ecological Monitoring and Compliance Program Fiscal Year 1998 Report

    SciTech Connect (OSTI)

    Bechtel Nevada Ecological Services

    1998-10-01

    The Ecological Monitoring and Compliance program, funded through the U. S. Department of Energy/Nevada Operations Office, monitors the ecosystem of the Nevada Test Site and ensures compliance with laws and regulations pertaining to NTS biota. This report summarizes the program's activities conducted by Bechtel Nevada during fiscal year 1998. Twenty-one sites for seven projects were surveyed for the presence of state or federally protected species. Three projects were in or near habitat of the threatened desert tortoise and required special clearance and transect surveys. All geospatial data collected were entered into Bechtel Nevada's Ecological Geographic Information system for use in ongoing ecosystem management of the NTS.

  16. Preliminary assessment of the ecological risks to wide-ranging wildlife species on the Oak Ridge Reservation. 1996 update

    SciTech Connect (OSTI)

    Sample, B.E.; Hinzman, R.L.; Jackson, B.L.; Baron, L.

    1996-09-01

    More than approximately 50 years of operations, storage, and disposal of wastes generated by the three facilities on the Oak Ridge Reservation (ORR) (the Oak Ridge K-25 Site, Oak Ridge National Laboratory, and the Oak Ridge Y-12 Plant) has resulted in a mosaic of uncontaminated property and lands that are contaminated to varying degrees. This contaminated property includes source areas and the terrestrial and aquatic habitats down gradient from these source areas. Although the integrator OUs generally contain considerable habitat for biota, the source OUs provide little or no suitable habitat. Historically, ecological risk assessment at Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) sites has focused on species that may be definitively associated with a contaminated area or source OU. Endpoints considered in source OUs include plants, soil/litter invertebrates and processes, aquatic biota found in on-OU sediments and surface waters, and small herbivorous, omnivorous, and vermivorous (i.e., feeding on ground, litter, or soil invertebrates) wildlife. All of these endpoints have limited spatial distributions or home ranges such that numerous individuals or a distinct population can be expected to reside within the boundaries of the source OU. Most analyses are not adequate for large sites with multiple, spatially separated contaminated areas such as the ORR that provide habitat for wide-ranging wildlife species. This report is a preliminary response to a plan for assessing risks to wide-ranging species.

  17. The terrestrial biosphere as a net source of greenhouse gases to the atmosphere

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Tian, Hanqin; Lu, Chaoqun; Ciais, Philippe; Michalak, Anna M.; Canadell, Josep G.; Saikawa, Eri; Huntzinger, Deborah N.; Gurney, Kevin R; Sitch, Stephen; Zhang, Bowen; et al

    2016-03-09

    The terrestrial biosphere can release or absorb the greenhouse gases, carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O), and therefore has an important role in regulating atmospheric composition and climate1. Anthropogenic activities such as land-use change, agriculture and waste management have altered terrestrial biogenic greenhouse gas fluxes, and the resulting increases in methane and nitrous oxide emissions in particular can contribute to climate change2, 3. The terrestrial biogenic fluxes of individual greenhouse gases have been studied extensively4, 5, 6, but the net biogenic greenhouse gas balance resulting from anthropogenic activities and its effect on the climate system remains uncertain.more » Here we use bottom-up (inventory, statistical extrapolation of local flux measurements, and process-based modelling) and top-down (atmospheric inversions) approaches to quantify the global net biogenic greenhouse gas balance between 1981 and 2010 resulting from anthropogenic activities and its effect on the climate system. We find that the cumulative warming capacity of concurrent biogenic methane and nitrous oxide emissions is a factor of about two larger than the cooling effect resulting from the global land carbon dioxide uptake from 2001 to 2010. This results in a net positive cumulative impact of the three greenhouse gases on the planetary energy budget, with a best estimate (in petagrams of CO2 equivalent per year) of 3.9 ± 3.8 (top down) and 5.4 ± 4.8 (bottom up) based on the GWP100 metric (global warming potential on a 100-year time horizon). Lastly, our findings suggest that a reduction in agricultural methane and nitrous oxide emissions, particularly in Southern Asia, may help mitigate climate change.« less

  18. Single-junction solar cells with the optimum band gap for terrestrial concentrator applications

    DOE Patents [OSTI]

    Wanlass, M.W.

    1994-12-27

    A single-junction solar cell is described having the ideal band gap for terrestrial concentrator applications. Computer modeling studies of single-junction solar cells have shown that the presence of absorption bands in the direct spectrum has the effect of ''pinning'' the optimum band gap for a wide range of operating conditions at a value of 1.14[+-]0.02 eV. Efficiencies exceeding 30% may be possible at high concentration ratios for devices with the ideal band gap. 7 figures.

  19. Ecological Monitoring and Compliance Program 2014 Report

    SciTech Connect (OSTI)

    Hall, Derek B.; Anderson, David C.; Greger, Paul D.; Ostler, W. Kent

    2015-05-12

    The Ecological Monitoring and Compliance Program (EMAC), funded through the U.S. Department of Energy, National Nuclear Security Administration Nevada Field Office (NNSA/NFO, formerly Nevada Site Office), monitors the ecosystem of the Nevada National Security Site (NNSS) and ensures compliance with laws and regulations pertaining to NNSS biota. This report summarizes the program’s activities conducted by National Security Technologies, LLC (NSTec), during calendar year 2014. Program activities included (a) biological surveys at proposed activity sites, (b) desert tortoise compliance, (c) ecosystem monitoring, (d) sensitive plant species monitoring, (e) sensitive and protected/regulated animal monitoring, and (f) habitat restoration monitoring. During 2014, all applicable laws, regulations, and permit requirements were met, enabling EMAC to achieve its intended goals and objectives. Sensitive and protected/regulated species of the NNSS include 42 plants, 1 mollusk, 2 reptiles, 236 birds, and 27 mammals. These species are protected, regulated, or considered sensitive according to state or federal regulations and natural resource agencies and organizations. The desert tortoise (Gopherus agassizii) and the western yellow-billed cuckoo (Coccyzus americanus) are the only species on the NNSS protected under the Endangered Species Act, both listed as threatened. However, only one record of the cuckoo has ever been documented on the NNSS, and there is no good habitat for this species on the NNSS. It is considered a rare migrant. Biological surveys for the presence of sensitive and protected/regulated species and important biological resources on which they depend were conducted for 18 projects. A total of 199.18 hectares (ha) was surveyed for these projects. Sensitive and protected/regulated species and important biological resources found during these surveys included a predator burrow, one sidewinder rattlesnake (Crotalus cerastes), two mating speckled rattlesnakes

  20. Role of basic ecological knowledge in environmental assessment

    SciTech Connect (OSTI)

    Hildebrand, S.G.; Barnthouse, L.W.; Suter, G.W.

    1984-01-01

    The role of basic ecological knowledge in environmental impact assessment was examined. The focus was primarily on the NEPA process. Experience in population biology and ecosystem studies is discussed, the successes and limits of applicability are highlighted, and implications for long-term research needs are identified. Current attempts to develop a national assessment of acid deposition impacts are reviewed. 48 refs. (ACR)

  1. Ecological Monitoring and Compliance Program Fiscal Year 2003 Report

    SciTech Connect (OSTI)

    Bechtel Nevada

    2003-12-01

    The Ecological Monitoring and Compliance program, funded through the U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office, monitors the ecosystem of the Nevada Test Site and ensures compliance with laws and regulations pertaining to Nevada Test Site biota. This report summarizes the program's activities conducted by Bechtel Nevada during fiscal year 2003.

  2. Ecological investigation of a hazardous waste site, Warner Robins, Georgia

    SciTech Connect (OSTI)

    Wade, M.C. ); Billig, P. )

    1993-01-01

    Zone 1, Robins Air Force Base, Georgia, has been designated a National Priorities List Site by the US Environmental Protection Agency. The Remedial Investigation for Zone 1 recommended a quantitative analysis of ecological risk. To accomplish this task a characterization of the bottomland hardwood forest ecosystem present on the base was required. This ecological characterization included the study of hydrology, aquatic and wildlife biology, and wetlands ecology where potential impacts were in question. In addition, a suitable reference area was studied. The hydrologic investigation consisted primarily of the installation of water level recorders and staff gauges, collection of surface water data, installation of piezometers and collection of groundwater data, and the collection of rainfall data. The aquatic biology investigation centered around the sampling of benthic macroinvertebrate communities, bioassay toxicity tests for surface water and sediment, fish sampling, aquatic macrophyte collection, macrophyte collection, and emergent and free-floating plant collection. The wildlife biology investigation focused on a breeding bird survey. The wetlands ecology investigation comprised the collection of soil and vegetation samples and using the Wetland Evaluation Technique (WET) to assess the functions and values of the wetlands present.

  3. Assessing ecological risks within a highly industrialized estuary

    SciTech Connect (OSTI)

    Bonnevie, N.L.; Iannuzzi, T.J.; Harman, C.H.

    1995-12-31

    Ecological assessment (EA) was conducted for a landfill located along an industrialized river within the NY/NJ Harbor Estuary. This estuary has been subjected to intense industrial and urban development throughout the past two centuries, resulting in alterations to the Site and regional ecology. For these reasons, consideration was given to the local and regional setting, and the relatively low quantity and degraded quality of habitats that exist in proximity to the Site. The EA focused on two ecological receptor groups: (1) aquatic receptors (i.e., benthic invertebrates and small forage fish) exposed primarily through direct contact with sediments and surface water; and (2) piscivorous species (i.e., great blue heron) for whom exposure is the result of trophic transfer through dietary intakes. Estimates of accumulation in prey species of the great blue heron were derived using a simplified food web model to predict trophic transfer. The primary chemicals of potential ecological concern (COPEC) included arsenic, selenium, mercury, as well as PCBs. Based on the results of this assessment, risk to piscivorous wildlife are very low; derived hazard quotients (HQ) were below one for all COPEC. HQ greater than one were observed for direct exposures to aquatic receptors, however, the HQ determined for exposures at the Site were generally within the range of those reported for sediments and surface waters throughout the NY/NJ Harbor Estuary. In addition, numerous non-chemical stressors were identified that likely significantly affect the health and abundance of aquatic organisms. For these reasons, the Site was determined not to contribute an increased risk to ecological receptors above a regional level.

  4. Terrestrial mapping of the Oak Ridge Reservation: Phase 1. Environmental Restoration Program

    SciTech Connect (OSTI)

    Washington-Allen, R.A.; Ashwood, T.L.; Christensen, S.W.; Offerman, H.; Scarbrough-Luther, P.

    1995-06-01

    This report presents the results of the first phase in development of a habitat map of the terrestrial ecosystem on the Oak Ridge Reservation (ORR). During this phase, a satellite image of the ORR was classified into land use/land cover types, the classified image was incorporated into a geographic information system map of the ORR, and the accuracy of the map was assessed. A habitat map is a critical foundation for evaluation of the potential impact of historical (or ongoing) contamination on terrestrial biota of the ORR. The abundance and distribution of wildlife species and plant communities of concern are intrinsically linked to the abundance and distribution of habitat on which those species and communities rely. Thus, the impact of spatially discrete patches of contamination on those biota is directly proportional to the degree of overlap between habitat and contamination. Landsat 5 Thematic Mapper satellite imagery was used to create the land use/land cover map. A Thematic Mapper image consists of seven images of the same point on the earth produced by seven separate sensors, each of which detects a unique part of the electromagnetic spectrum. Separately and in various combinations, these spectral images can be correlated with vegetation type or other land cover type. The image selected for this map was from April 13, 1994, and covers 189,000 ha.

  5. Survey of protected terrestrial vertebrates on the Oak Ridge Reservation 1995 annual progress report

    SciTech Connect (OSTI)

    Vail, E.R.; Mitchell, J.M.; Webb, J.W.; King, A.L.; Hamlett, P.A.

    1995-11-01

    This progress report discusses surveys of protected terrestrial vertebrates on the Oak Ridge Reservation (ORR) from October 1994 through September 1995. These surveys are important to help avoid or minimize potential impacts of projects on the ORR to species listed as threatened, endangered, or in need of management by the US Fish and Wildlife Service and the Tennessee Wildlife Resources Agency. Currently, there are 69 species of federally or state-listed terrestrial vertebrates that may occur in Tennessee. Not all of these are expected to occur on the ORR, nor do resources permit comprehensive sampling for all of them over the entire ORR. To effectively organize sampling efforts, listed animal species that might be present were targeted using a prioritization system based on historical and recent sightings, species distributions, literature reviews, and personal communications. Sampling was conducted during the time of the year when each targeted species would most likely be encountered. Several trapping and surveying methods were used, including pitfall traps, Sherman traps, seining, artificial covers, and cave and avian surveys.

  6. ORIGINS OF NON-MASS-DEPENDENT FRACTIONATION OF EXTRA-TERRESTRIAL OXYGEN

    SciTech Connect (OSTI)

    Barcena, Homar; Connolly, Harold C.

    2012-08-01

    The distribution of oxygen isotopes in meteorites and within the earliest solids that formed in the solar system hints that the precursors of these materials must have undergone a mass-independent process. The mass-independent process is specifically one that fractionates {sup 16}O from {sup 17}O and {sup 18}O. This chemical signature is indicative of non-equilibrium processing, which bear resemblance to some unusual terrestrial phenomenon such as fractionation of ozone in the upper Earth atmosphere. That the mass-independent fractionation of oxygen isotopes is preserved within petrological records presents planetary scientists interesting clues to the events that may have occurred during the formation of the solar system. Currently, there are several hypotheses on the origins of the oxygen isotope distribution within primitive planetary materials, which include both thermal and photochemical models. We present a new model based on a physico-chemical hypothesis for the origin of non-mass-dependent O-isotope distribution in oxygen-bearing extra-terrestrial materials, which originated from the disproportionation of CO in dark molecular clouds to create CO{sub 2} reservoirs. The disproportionation created a reservoir of heavy oxygen isotopes and could have occurred throughout the evolution of the disk. The CO{sub 2} was a carrier of the isotope anomaly in the solar nebula and we propose that non-steady-state mixing of these reservoirs with the early rock-forming materials during their formation corresponds with the birth and evolution of the solar system.

  7. Preliminary Notice of Violation, Safety and Ecology Corporation- EA-2005-03

    Broader source: Energy.gov [DOE]

    Issued to Safety and Ecology Corporation related to a 10 CFR Part 708 Violation at the Portsmouth Gaseous Diffusion Project

  8. North America's net terrestrial CO2 exchange with the atmosphere 1990–2009

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    King, Anthony W.; Andres, Robert; Davis, Kenneth J.; Hafer, M.; Hayes, Daniel J.; Huntzinger, Deborah N.; de Jong, Bernardus; Kurz, Werner; McGuire, A. David; Vargas, Rodrigo; et al

    2015-01-21

    Scientific understanding of the global carbon cycle is required for developing national and international policy to mitigate fossil fuel CO2 emissions by managing terrestrial carbon uptake. Toward that understanding and as a contribution to the REgional Carbon Cycle Assessment and Processes (RECCAP) project, this paper provides a synthesis of net land–atmosphere CO2 exchange for North America (Canada, United States, and Mexico) over the period 1990–2009. Only CO2 is considered, not methane or other greenhouse gases. This synthesis is based on results from three different methods: atmospheric inversion, inventory-based methods and terrestrial biosphere modeling. All methods indicate that the North Americanmore » land surface was a sink for atmospheric CO2, with a net transfer from atmosphere to land. Estimates ranged from -890 to -280 Tg C yr-1, where the mean of atmospheric inversion estimates forms the lower bound of that range (a larger land sink) and the inventory-based estimate using the production approach the upper (a smaller land sink). This relatively large range is due in part to differences in how the approaches represent trade, fire and other disturbances and which ecosystems they include. Integrating across estimates, \\"best\\" estimates (i.e., measures of central tendency) are -472 ± 281 Tg C yr-1 based on the mean and standard deviation of the distribution and -360 Tg C yr-1 (with an interquartile range of -496 to -337) based on the median. Considering both the fossil fuel emissions source and the land sink, our analysis shows that North America was, however, a net contributor to the growth of CO2 in the atmosphere in the late 20th and early 21st century. With North America's mean annual fossil fuel CO2 emissions for the period 1990–2009 equal to 1720 Tg C yr-1 and assuming the estimate of -472 Tg C yr-1 as an approximation of the true terrestrial CO2 sink, the continent's source : sink ratio for this time period was 1720:472, or nearly 4

  9. North America's net terrestrial CO2 exchange with the atmosphere 1990–2009

    SciTech Connect (OSTI)

    King, Anthony W.; Andres, Robert; Davis, Kenneth J.; Hafer, M.; Hayes, Daniel J.; Huntzinger, Deborah N.; de Jong, Bernardus; Kurz, Werner; McGuire, A. David; Vargas, Rodrigo; Wei, Yaxing; West, Tristram O.; Woodall, Chris W.

    2015-01-21

    Scientific understanding of the global carbon cycle is required for developing national and international policy to mitigate fossil fuel CO2 emissions by managing terrestrial carbon uptake. Toward that understanding and as a contribution to the REgional Carbon Cycle Assessment and Processes (RECCAP) project, this paper provides a synthesis of net land–atmosphere CO2 exchange for North America (Canada, United States, and Mexico) over the period 1990–2009. Only CO2 is considered, not methane or other greenhouse gases. This synthesis is based on results from three different methods: atmospheric inversion, inventory-based methods and terrestrial biosphere modeling. All methods indicate that the North American land surface was a sink for atmospheric CO2, with a net transfer from atmosphere to land. Estimates ranged from -890 to -280 Tg C yr-1, where the mean of atmospheric inversion estimates forms the lower bound of that range (a larger land sink) and the inventory-based estimate using the production approach the upper (a smaller land sink). This relatively large range is due in part to differences in how the approaches represent trade, fire and other disturbances and which ecosystems they include. Integrating across estimates, \\"best\\" estimates (i.e., measures of central tendency) are -472 ± 281 Tg C yr-1 based on the mean and standard deviation of the distribution and -360 Tg C yr-1 (with an interquartile range of -496 to -337) based on the median. Considering both the fossil fuel emissions source and the land sink, our analysis shows that North America was, however, a net contributor to the growth of CO2 in the atmosphere in the late 20th and early 21st century. With North America's mean annual fossil fuel CO2 emissions for the period 1990–2009 equal to 1720 Tg C yr-1 and assuming the estimate of -472 Tg C yr-1 as an approximation of the

  10. Industrial ecology: A basis for sustainable relations and cooperation

    SciTech Connect (OSTI)

    Blades, K.

    1996-07-19

    The Commission for Environmental Cooperation (CEC) seeks to address, in a cooperative manner, the environmental issues affecting the North American region and understand the linkages between environment and economy. Broadly, the goal of the CEC can be thought of as an attempt to achieve a sustainable economy concomitantly with continued economic, cultural, and technological evolution. The emerging field of industrial ecology provides a useful means for balancing the environmental and economical objectives of NAFTA. As NAFTA stimulates economic cooperation and growth, we must collectively develop mechanisms that enhance the environmental quality of the region. LLNL`s effort in industrial ecology provides the scientific basis and innovative use of technology to reconcile environmental and economic concerns. Nevertheless, these are not issues which can be resolved by a single institution. Efficient use of the linkages established by NAFTA is necessary to nurture our regional partnership which forms the basis for a sustainable environment, economy and relationship.

  11. Baseline ecological risk assessment Salmon Site, Lamar County, Mississippi

    SciTech Connect (OSTI)

    1995-04-01

    The Salmon Site (SS), formerly the Tatum Dome Test Site, located in Mississippi was the site of two nuclear and two gas explosion tests conducted between 1964 and 1970. A consequence of these testing activities is that radionuclides were released into the salt dome, where they are presently contained. During reentry drilling and other site activities, incidental liquid and solid wastes that contained radioactivity were generated, resulting in some soil, ground water and equipment contamination. As part of the remedial investigation effort, a Baseline Ecological Risk Assessment was conducted at the SS. The purpose is to gauge ecological and other environmental impacts attributable to past activities at the former test facility. The results of this facility-specific baseline risk assessment are presented in this document.

  12. Exhibits | Savannah River Ecology Laboratory Environmental Outreach Program

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Exhibits The SREL Outreach Program presents displays at many local and regional events to promote awareness of our extraordinary ecosystem to large numbers of people from many diverse backgrounds. The exhibits use live animals and plants to demonstrate the biodiversity of local ecosystems. If you are interested in having the Savannah River Ecology Laboratory participate in your event with a live animal and plant exhibit, you need to make your request well in advance. Exhibits are often scheduled

  13. ORNUTM-13249 DRAFT AN ECOLOGICAL INVESTIGATION OF A VANADIUM

    Office of Legacy Management (LM)

    ORNUTM-13249 DRAFT AN ECOLOGICAL INVESTIGATION OF A VANADIUM AND URANIUM MILL TAILINGS SITE 1. G. Smith, M. J. Peterson, and M. G. Ryon Biological Monitoring and Abatement Program Environmental Sciences Division Oak RidgeNational Laboratory Oak Ridge, Tennessee May 1996 Prepared for Gretchen A. Pierce Healthand Safety Research Division Environmental Technology Section Oak RidgeNational Laboratory GrandJunction, Colorado Prepared by the Environmental Sciences Division Oak RidgeNational Laboratory

  14. 2006 Annual Ecology Report for the Rocky Flats Site

    Office of Legacy Management (LM)

    Ecology Report for the Rocky Flats Site Click on the links below to access different portions of the electronic annual report. 2006 Annual Report Sections Diffuse Knapweed Biocontrol Monitoring Report Dalmatian Toadflax Monitoring Report High-Value Vegetation Monitoring Report Revegetation Monitoring Report Present and Original Landfill Revegetation Monitoring Report Frog Vocalization Monitoring Report Appendix A (Files below comprise Appendix A for the above listed reports.) Rocky Flats Flora

  15. START HERE 2015 Annual Ecology Report DVD 1.htm

    Office of Legacy Management (LM)

    Annual Ecology Report for the Rocky Flats Site DSCF8864resized Click on the links below to access different portions of the electronic annual report. 2015 Annual Report Sections Revegetation Monitoring Report Vegetation Survey Report Wildlife Survey Report Wetland Mitigation Monitoring Report Rocky Flats Vascular Flora List (2015) 2015 Photopoint Monitoring Closure Revegetation Locations Post-Closure Revegetation Locations Wetland Mitigation Locations Game Camera Video Bull Elk Video

  16. Ecological investigation of a hazardous waste site, Warner Robins, Georgia

    SciTech Connect (OSTI)

    Wade, M.; Billig, P.

    1993-05-01

    Landfill No. 4 and the sludge lagoon at Robins Air Force Base, Warner Robins, Georgia, were added to the United States Environmental Protection Agency (EPA) National Priorities List in 1987 because of highpotential for contaminant migration. Warner Robins is located approximately 90 miles southeast of Atlanta. In 1990 CH2M HILL conducted a Remedial Investigation at the base that recommended that further ecological assessment investigations be conducted (CH2M HILL 1990). The subject paper is the result of this recommendation. The ecological study was carried out by the Hazardous Waste Remedial Actions Program (HAZWRAP)Division of Martin Marietta Energy Systems, Inc., working jointly with its subcontractor CDM (CDM 1992a). The primary area of investigation (Zone 1) included the sludge lagoon, Landfill No. 4, the wetland area east of the landfill and west of Hannah Road (including two sewage treatment ponds), and the area between Hannah Road and Horse Creek (Fig. 1). The bottomland forest wetlands of Zone 1 extend from the landfill east to Horse Creek. Surface water and groundwater flow across Zone 1 is generally in an easterly direction toward Horse Creek. Horse Creek is a south-flowing tributary of the Ocmulgee River Floodplain. The objective of the study was to perform a quantitative analysis of ecological risk associated with the ecosystems present in Zone 1. This investigation was unique because the assessment was to be based upon many measurement endpoints resulting in both location-specific data and data that would assess the condition of the overall ecosystem. The study was segregated into five distinct field investigations: hydrology, surface water and sediment, aquatic biology, wetlands ecology, and wildlife biology.

  17. Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Wurch, Louie; Giannone, Richard J.; Belisle, Bernard S.; Swift, Carolyn; Utturkar, Sagar; Hettich, Robert L.; Reysenbach, Anna-Louise; Podar, Mircea

    2016-07-05

    Biological features can be inferred, based on genomic data, for many microbial lineages that remain uncultured. However, cultivation is important for characterizing an organism’s physiology and testing its genome-encoded potential. Here we use single-cell genomics to infer cultivation conditions for the isolation of an ectosymbiotic Nanoarchaeota (‘Nanopusillus acidilobi’) and its host (Acidilobus, a crenarchaeote) from a terrestrial geothermal environment. The cells of ‘Nanopusillus’ are among the smallest known cellular organisms (100–300 nm). They appear to have a complete genetic information processing machinery, but lack almost all primary biosynthetic functions as well as respiration and ATP synthesis. Lastly, genomic and proteomicmore » comparison with its distant relative, the marine Nanoarchaeum equitans illustrate an ancient, common evolutionary history of adaptation of the Nanoarchaeota to ectosymbiosis, so far unique among the Archaea.« less

  18. A Preliminary Survey of Terrestrial Plant Communities in the Sierra de los Valles

    SciTech Connect (OSTI)

    Randy G. Balice

    1998-10-01

    To more fully understand the species compositions and environmental relationships of high-elevation terrestrial plant communities in the Los Alamos region, 30 plots in randomly selected, upland locations were sampled for vegetation, topographic, and soils characteristics. The locations of these plots were constrained to be above 2,134 m (7,000 ft) above mean sea level. The field results were summarized, analyzed, and incorporated into a previously developed classification of vegetation and land cover types. The revised and updated discussions of the environmental relationships at these sites and their associated species compositions are included in this report. A key to the major land cover types in the Los Alamos region was also revised in accordance with the new information and included herein its entirety.

  19. Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris

    SciTech Connect (OSTI)

    Berka, Randy M.; Grigoriev, Igor V.; Otillar, Robert; Salamov, Asaf; Grimwood, Jane; Reid, Ian; Ishmael, Nadeeza; John, Tricia; Darmond, Corinne; Moisan, Marie-Claude; Henrissat, Bernard; Coutinho, Pedro M.; Lombard, Vincent; Natvig, Donald O.; Lindquist, Erika; Schmutz, Jeremy; Lucas, Susan; Harris, Paul; Powlowski, Justin; Bellemare, Annie; Taylor, David; Butler, Gregory; de Vries, Ronald P.; Allijn, Iris E.; van den Brink, Joost; Ushinsky, Sophia; Storms, Reginald; Powell, Amy J.; Paulsen, Ian T.; Elbourne, Liam D. H.; Baker, Scott. E.; Magnuson, Jon; LaBoissiere, Sylvie; Clutterbuck, A. John; Martinez, Diego; Wogulis, Mark; Lopez de Leon, Alfredo; Rey, Michael W.; Tsang, Adrian

    2011-05-16

    Thermostable enzymes and thermophilic cell factories may afford economic advantages in the production of many chemicals and biomass-based fuels. Here we describe and compare the genomes of two thermophilic fungi, Myceliophthora thermophila and Thielavia terrestris. To our knowledge, these genomes are the first described for thermophilic eukaryotes and the first complete telomere-to-telomere genomes for filamentous fungi. Genome analyses and experimental data suggest that both thermophiles are capable of hydrolyzing all major polysaccharides found in biomass. Examination of transcriptome data and secreted proteins suggests that the two fungi use shared approaches in the hydrolysis of cellulose and xylan but distinct mechanisms in pectin degradation. Characterization of the biomass-hydrolyzing activity of recombinant enzymes suggests that these organisms are highly efficient in biomass decomposition at both moderate and high temperatures. Furthermore, we present evidence suggesting that aside from representing a potential reservoir of thermostable enzymes, thermophilic fungi are amenable to manipulation using classical and molecular genetics.

  20. Terrestrial Carbon Management Data from the Carbon Dioxide Information Analysis Center (CDIAC)

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    CDIAC products are indexed and searchable through a customized interface powered by ORNL's Mercury search engine. Products include numeric data packages, publications, trend data, atlases, and models and can be searched for by subject area, keywords, authors, product numbers, time periods, collection sites, spatial references, etc. Some of the collections may also be included in the CDIAC publication Trends Online: A Compendium of Global Change Data. Most data sets, many with numerous data files, are free to download from CDIAC's ftp area. Collections under the broad heading of Terrestrial Carbon Management are organized as Carbon Accumulation with Cropland Management, Carbon Accumulation with Grassland Management, Carbon Loss Following Cultivation, Carbon Accumulation Following Afforestation, and Carbon Sources and Sinks Associated with U.S. Cropland Production.

  1. Estimated dose to man from uranium milling via the terrestrial food-chain pathway

    SciTech Connect (OSTI)

    Rayno, D.R.

    1982-01-01

    One of the major pathways of radiological exposure to man from uranium milling operations is through the terrestrial food chain. Studies by various investigators have shown the extent of uptake and distribution of U-238, U-234, Th-230, Ra-226, Pb-210, and Po-210 in plants and animals. These long-lived natural radioisotopes, all nuclides of the uranium decay series, are found in concentrated amounts in uranium mill tailings. Data from these investigations are used to estimate the dose to man from consumption of beef and milk contaminated by the tailings. This dose estimate from this technologically enhanced source is compared with that from average normal dietary intake of these radionuclides from natural sources.

  2. Preliminary systems engineering evaluations for the National Ecological Observatory Network.

    SciTech Connect (OSTI)

    Robertson, Perry J.; Kottenstette, Richard Joseph; Crouch, Shannon M.; Brocato, Robert Wesley; Zak, Bernard Daniel; Osborn, Thor D.; Ivey, Mark D.; Gass, Karl Leslie; Heller, Edwin J.; Dishman, James Larry; Schubert, William Kent; Zirzow, Jeffrey A.

    2008-11-01

    The National Ecological Observatory Network (NEON) is an ambitious National Science Foundation sponsored project intended to accumulate and disseminate ecologically informative sensor data from sites among 20 distinct biomes found within the United States and Puerto Rico over a period of at least 30 years. These data are expected to provide valuable insights into the ecological impacts of climate change, land-use change, and invasive species in these various biomes, and thereby provide a scientific foundation for the decisions of future national, regional, and local policy makers. NEON's objectives are of substantial national and international importance, yet they must be achieved with limited resources. Sandia National Laboratories was therefore contracted to examine four areas of significant systems engineering concern; specifically, alternatives to commercial electrical utility power for remote operations, approaches to data acquisition and local data handling, protocols for secure long-distance data transmission, and processes and procedures for the introduction of new instruments and continuous improvement of the sensor network. The results of these preliminary systems engineering evaluations are presented, with a series of recommendations intended to optimize the efficiency and probability of long-term success for the NEON enterprise.

  3. Ecological Characterization Data for the 2004 Composite Analysis

    SciTech Connect (OSTI)

    Downs, Janelle L.; Simmons, Mary A.; Stegen, Jennifer A.; Bunn, Amoret L.; Tiller, Brett L.; Thorsten, Susan L.; Zufelt, Rhett K.

    2004-11-01

    A composite analysis is required by U.S. Department of Energy (DOE) Order 435.1 to ensure public safety through the management of active and planned low-level radioactive waste disposal facilities associated with the Hanford Site. The original Hanford Site Composite Analysis of 1998 must be revised and submitted to DOE Headquarters (DOE-HQ) in 2004 because of revisions to waste site information in the 100, 200, and 300 Areas, updated performance assessments and environmental impact statements (EIS), changes in inventory estimates for key sites and constituents, and a change in the definition of offsite receptors. Beginning in fiscal year (FY) 2003, the DOE Richland Operations Office (DOE-RL) initiated activities, including the development of data packages, to support the 2004 Composite Analysis. This report describes the data compiled in FY 2003 to support ecological site assessment modeling for the 2004 Composite Analysis. This work was conducted as part of the Characterization of Systems Task of the Groundwater Remediation Project (formerly the Groundwater Protection Program) managed by Fluor Hanford, Inc., Richland, Washington. The purpose of this report is to provide summaries of the characterization information and available spatial data on the biological resources and ecological receptors found in the upland, riparian, aquatic, and island habitats on the Hanford Site. These data constitute the reference information used to establish parameters for the ecological risk assessment module of the System Assessment Capability and other assessment activities requiring information on the presence and distribution of biota on the Hanford Site.

  4. Multi-level effects of low dose rate ionizing radiation on southern toad, Anaxyrus [Bufo] terrestris

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Stark, Karolina; Scott, David E.; Tsyusko, Olga; Coughlin, Daniel P.; Hinton, Thomas G.; Amendola, Roberto

    2015-04-30

    Despite their potential vulnerability to contaminants from exposure at multiple life stages, amphibians are one of the least studied groups of vertebrates in ecotoxicology, and research on radiation effects in amphibians is scarce. We used multiple endpoints to assess the radiosensitivity of the southern toad (Anaxyrus [Bufo] terrestris) during its pre-terrestrial stages of development –embryonic, larval, and metamorphic. Toads were exposed, from several hours after oviposition through metamorphosis (up to 77 days later), to four low dose rates of ¹³⁷Cs at 0.13, 2.4, 21, and 222 mGy d⁻¹, resulting in total doses up to 15.8 Gy. Radiation treatments did notmore » affect hatching success of embryos, larval survival, or the length of the larval period. The individual family variation in hatching success of embryos was larger than the radiation response. In contrast, newly metamorphosed individuals from the higher dose-rate treatments had higher mass and mass/length body indices, a measure which may relate to higher post-metamorphic survival. The increased mass and index at higher dose rates may indicate that the chronic, low dose rate radiation exposures triggered secondary responses. Additionally, the increases in growth were linked to a decrease in DNA damage (as measured by the Comet Assay) in red blood cells at a dose rate of 21mGy d⁻¹ and a total dose of 1.1 Gy. In conclusion, the complex effects of low dose rates of ionizing radiation may trigger growth and cellular repair mechanisms in amphibian larvae.« less

  5. CAN THE MASSES OF ISOLATED PLANETARY-MASS GRAVITATIONAL LENSES BE MEASURED BY TERRESTRIAL PARALLAX?

    SciTech Connect (OSTI)

    Freeman, M.; Botzler, C. S.; Bray, J. C.; Cherrie, J. M.; Rattenbury, N. J.; Philpott, L. C.; Abe, F.; Muraki, Y.; Albrow, M. D.; Bennett, D. P.; Bond, I. A.; Christie, G. W.; Natusch, T.; Dionnet, Z.; Gould, A.; Han, C.; Heyrovský, D.; McCormick, J. M.; Skowron, J.; and others

    2015-02-01

    Recently Sumi et al. reported evidence for a large population of planetary-mass objects (PMOs) that are either unbound or orbit host stars in orbits ≥10 AU. Their result was deduced from the statistical distribution of durations of gravitational microlensing events observed by the MOA collaboration during 2006 and 2007. Here we study the feasibility of measuring the mass of an individual PMO through microlensing by examining a particular event, MOA-2011-BLG-274. This event was unusual as the duration was short, the magnification high, the source-size effect large, and the angular Einstein radius small. Also, it was intensively monitored from widely separated locations under clear skies at low air masses. Choi et al. concluded that the lens of the event may have been a PMO but they did not attempt a measurement of its mass. We report here a re-analysis of the event using re-reduced data. We confirm the results of Choi et al. and attempt a measurement of the mass and distance of the lens using the terrestrial parallax effect. Evidence for terrestrial parallax is found at a 3σ level of confidence. The best fit to the data yields the mass and distance of the lens as 0.80 ± 0.30 M {sub J} and 0.80 ± 0.25 kpc respectively. We exclude a host star to the lens out to a separation ∼40 AU. Drawing on our analysis of MOA-2011-BLG-274 we propose observational strategies for future microlensing surveys to yield sharper results on PMOs including those down to super-Earth mass.

  6. The sensitivity of the terrestrial biosphere to climatic change: A simulation of the middle Holocene

    SciTech Connect (OSTI)

    Foley, J.A.

    1994-12-01

    A process-based ecosystem model, DEMETER, is used to simulate the sensitivity of the terrestrial biosphere to changes in climate. In this study, DEMETER is applied to the two following climatic regimes: (1) the modern observed climate and (2) a simulated mid-Holocene climate (6000 years before present). The mid-Holocene climate is simulated using the GENESIS global climate model, where shifts in the Earth`s orbital parameters result in warmer northern continents and enhanced monsoons in Asia, North Africa, and North America. DEMETER simulates large differences between modern and mid-Holocene vegetation cover: (1) mid-Holocene boreal forests extend farther poleward than present in much of Europe, Asia, and North America, and (2) mid-Holocene North African grasslands extend substantially farther north than present. The simulated patterns of mid-Holocene vegetation are consistent with many features of the paleobotanical record. Simulated mid-Holocene global net primary productivity is approximately 3% larger than present, largely due to the increase of boreal forest and tropical grasslands relative to tundra and desert. Global vegetation carbon is higher at 6 kyr B.P. compared to present by roughly the same amount (4%). Mid-Holocene global litter carbon is larger than present by 10%, while global soil carbon is approximately 1% less. Despite the regional changes in productivity and carbon storage the simulated total carbon storage potential of the terrestrial biosphere (not including changes in peat) does not change significantly between the two simulations. 53 refs., 12 figs., 4 tabs.

  7. North America's net terrestrial carbon exchange with the atmosphere 1990-2009

    SciTech Connect (OSTI)

    King, Anthony W.; Andres, Robert; Davis, Kenneth J.; Hafer, M.; Hayes, Daniel J.; Huntzinger, Deborah N.; de Jong, Bernardus; Kurz, Werner; McGuire, A. David; Vargas, Rodrigo; Wei, Yaxing; West, Tristram O.; Woodall, Chris W.

    2015-01-01

    Scientific understanding of the global carbon cycle is required for developing national and international policy to mitigate fossil-fuel CO2 emissions by managing terrestrial carbon uptake. Toward that understanding and as a contribution to the REgional Carbon Cycle Assessment and Processes (RECCAP) project, this paper provides a synthesis of net land-atmosphere CO2 exchange for North America over the period (1990-2009). This synthesis is based on results from three different methods: atmospheric inversion, inventory-based methods and terrestrial biosphere modeling. All methods indicate that the North America land surface was a sink for atmospheric CO2, with a net transfer from atmosphere to land. Estimates ranged from -890 to -280 Tg C yr-1, where the atmospheric inversion estimate forms the lower bound of that range (a larger land-sink) and the inventory-based estimate the upper (a smaller land sink). Integrating across estimates, a best estimates (i.e., measures of central tendency) are -472 281 Tg C yr-1 based on the mean and standard deviation of the distribution and -360 Tg C yr-1 (with an interquartile range of -496 to -337) based on the median. Considering both the fossil-fuel emissions source and the land sink, our analysis shows that North America was, however, a net contributor to the growth of CO2 in the atmosphere in the late 20th and early 21st century. The continents CO2 source to sink ratio for this time period was likely in the range of 4:1 to 3:1.

  8. Potential land competition between open-pond microalgae production and terrestrial dedicated feedstock supply systems in the U.S.

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Coleman, Andre M.; Wigmosta, Mark S.; Hellwinckel, Chad M.; Brandt, Craig C.; Langholtz, Matthew H.; Eaton, Laurence M.

    2016-03-03

    To date, feedstock resource assessments have evaluated cellulosic and algal feedstocks independently, without consideration of demands for, and resource allocation to, each other. We assess potential land competition between algal and terrestrial feedstocks in the United States, and evaluate a scenario in which 41.5 × 109 L yr–1 of second-generation biofuels are produced on pastureland, the most likely land base where both feedstock types may be deployed. Under this scenario, open-pond microalgae production is projected to use 1.2 × 106 ha of private pastureland, while terrestrial biomass feedstocks would use 14.0 × 106 ha of private pastureland. A spatial meta-analysismore » indicates that potential competition for land under this scenario would be concentrated in 110 counties, containing 1.0 and 1.7 × 106 ha of algal and terrestrial dedicated feedstock production, respectively. Furthermore, a land competition index applied to these 110 counties suggests that 38 to 59 counties could experience competition for upwards of 40% of a county's pastureland, representing 2%–5% of total pastureland in the U.S.; therefore suggesting little overall competition between algae production, terrestrial energy feedstocks and alternative uses for existing agricultural production such as livestock grazing.« less

  9. Savannah River Ecology Laboratory annual technical progress report of ecological research for the year ending July 31, 1995

    SciTech Connect (OSTI)

    Smith, M.H.

    1995-07-01

    The Savannah River Ecology Laboratory (SREL) is a research unit of the University of Georgia (UGA). The overall mission of the Laboratory is to acquire and communicate knowledge of ecological processes and principles. SREL conducts basic and applied ecological research, as well as education and outreach programs, under a contract with the US Department of Energy (DOE) at the Savannah River Site near Aiken, South Carolina. Significant accomplishments were made during the past year in the areas of research, education and service. Major additions to SREL Facilities were completed that will enhance the Laboratory`s work in the future. Following several years of planning, opening ceremonies were held for the 5000 ft{sup 2} multi-purpose conference center that was funded by the University of Georgia Research Foundation (UGARF). The center is located on 68 acres of land that was provided by the US Department of Energy. This joint effort between DOE and UGARF supports DOE`s new initiative to develop partnerships with the private sector and universities. The facility is being used for scientific meetings and environmental education programs for students, teachers and the general public. A 6000 ft{sup 2} office and library addition to S@s main building officially opened this year, and construction plans are underway on a new animal care facility, laboratory addition, and receiving building.

  10. Kenneth W. McLeod | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    McLeod Faculty & Scientists SREL Home Kenneth W. McLeod Savannah River Ecology Laboratory P O Drawer E, Aiken, SC 29802 (803) 725-5309 office (803) 725-3309 fax kwmcleod(at)srel.uga.edu As a plant ecophysiologist, I am interested in the unique mechanisms that allow plant species to inhabit marginal habitats and which contributes to their individual distribution patterns, from large-scale continental patterns to patterns of individual trees in a forest. The elucidation of these mechanisms has

  11. Savannah River Ecology Laboratory - Touch An Animal Day 2016

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Return to Photo Album Savannah River Ecology Laboratory's 8th Annual "Touch An Animal Day!" August 20, 2016 Once again a fun day was had by all! Click on an image for a larger view. Special thanks to the following individuals for their help with this event: Matt Baker Dr. I. Lehr Brisbin Dr. Kurt Buhlmann Joseph Colbert Zoë Cooper Fanny Coutelot Mackenzie Dix Carol Eldridge Larry Eldridge Dean Fletcher Wes Flynn Dr. Whit Gibbons Judy Greene-McLeod Matt Hamilton David Keiter Linda Lee

  12. ECOLOGICAL MONITORING AND COMPLIANCE PROGRAM CALENDAR YEAR 2005 REPORT

    SciTech Connect (OSTI)

    BECHTEL NEVADA ECOLOGICAL SERVICES

    2006-03-01

    The Ecological Monitoring and Compliance program (EMAC), funded through the U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office (NNSA/NSO), monitors the ecosystem of the Nevada Test Site (NTS) and ensures compliance with laws and regulations pertaining to NTS biota. This report summarizes the program’s activities conducted by Bechtel Nevada (BN) during the Calendar Year 2005. Program activities included: (1) biological surveys at proposed construction sites, (2) desert tortoise compliance, (3) ecosystem mapping and data management, (4) sensitive and protected/regulated species and unique habitat monitoring, (5) habitat restoration monitoring, and (6) biological monitoring at the Non-Proliferation Test and Evaluation Complex (NPTEC).

  13. Population and community ecology of the rare plant amsinckia grandiflora

    SciTech Connect (OSTI)

    Carlsen, T.M.

    1996-11-01

    Research was conducted between the fall of 1992 and the spring on the population and community ecology of the rare annual plant, Amsinckia glandiflora (Gray) Kleeb. ex Greene (Boraginaceae). The research goal was to investigate the causes of the species rarity, data useful to restorative efforts. The work focused on the examination of competitive suppression by exotic annual grasses; comparisons with common, weedy congener; and the role of litter cover and seed germination and seedling establishment. Annual exotic grasses reduced A. grandiflora reproductive output to a greater extent than did the native perennial bunch grass.

  14. Comparative metagenomics of microbial communities

    SciTech Connect (OSTI)

    Tringe, Susannah Green; von Mering, Christian; Kobayashi, Arthur; Salamov, Asaf A.; Chen, Kevin; Chang, Hwai W.; Podar, Mircea; Short, Jay M.; Mathur, Eric J.; Detter, John C.; Bork, Peer; Hugenholtz, Philip; Rubin, Edward M.

    2004-12-15

    The predicted proteins encoded in DNA isolated from environmental microbial community samples reveal habitat-specific metabolic demands.

  15. Soil metagenomics and carbon cycling

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Establishing a foundational understanding of the microbial and ecosystem factors that ... understanding of the microbial and ecosystem factors that control carbon partitioning ...

  16. Soil metagenomics and carbon cycling

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Services » Soil and Groundwater Soil and Groundwater Soil and Groundwater Legacy soil and groundwater remediation activities at Los Alamos National Laboratory (LANL) are conducted in accordance with regulatory requirements, DOE regulations, and other applicable environmental laws. The scope of work requires investigation and remediation of contaminated sites known as solid waste management units (SWMUs) or areas of concern (AOCs). The protection of surface water and groundwater is also within

  17. N-body simulations of terrestrial planet formation under the influence of a hot Jupiter

    SciTech Connect (OSTI)

    Ogihara, Masahiro; Kobayashi, Hiroshi; Inutsuka, Shu-ichiro E-mail: ogihara@nagoya-u.jp

    2014-06-01

    We investigate the formation of multiple-planet systems in the presence of a hot Jupiter (HJ) using extended N-body simulations that are performed simultaneously with semianalytic calculations. Our primary aims are to describe the planet formation process starting from planetesimals using high-resolution simulations, and to examine the dependences of the architecture of planetary systems on input parameters (e.g., disk mass, disk viscosity). We observe that protoplanets that arise from oligarchic growth and undergo type I migration stop migrating when they join a chain of resonant planets outside the orbit of an HJ. The formation of a resonant chain is almost independent of our model parameters, and is thus a robust process. At the end of our simulations, several terrestrial planets remain at around 0.1 AU. The formed planets are not equal mass; the largest planet constitutes more than 50% of the total mass in the close-in region, which is also less dependent on parameters. In the previous work of this paper, we have found a new physical mechanism of induced migration of the HJ, which is called a crowding-out. If the HJ opens up a wide gap in the disk (e.g., owing to low disk viscosity), crowding-out becomes less efficient and the HJ remains. We also discuss angular momentum transfer between the planets and disk.

  18. Convergence of microbial assimilations of soil carbon, nitrogen, phosphorus, and sulfur in terrestrial ecosystems

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Xu, Xiaofeng; Hui, Dafeng; King, Anthony Wayne; Song, Xia; Thornton, Peter E.; Zhang, Lihua

    2015-11-27

    How soil microbes assimilate carbon-C, nitrogen-N, phosphorus-P, and sulfur-S is fundamental for understanding nutrient cycling in terrestrial ecosystems. We compiled a global database of C, N, P, and S concentrations in soils and microbes and developed relationships between them by using a power function model. The C:N:P:S was estimated to be 287:17:1:0.8 for soils, and 42:6:1:0.4 for microbes. We found a convergence of the relationships between elements in soils and in soil microbial biomass across C, N, P, and S. The element concentrations in soil microbial biomass follow a homeostatic regulation curve with soil element concentrations across C, N, Pmore » and S, implying a unifying mechanism of microbial assimilating soil elements. This correlation explains the well-constrained C:N:P:S stoichiometry with a slightly larger variation in soils than in microbial biomass. Meanwhile, it is estimated that the minimum requirements of soil elements for soil microbes are 0.8 mmol C Kg–1 dry soil, 0.1 mmol N Kg–1 dry soil, 0.1 mmol P Kg–1 dry soil, and 0.1 mmol S Kg–1 dry soil, respectively. Lastly, these findings provide a mathematical explanation of element imbalance in soils and soil microbial biomass, and offer insights for incorporating microbial contribution to nutrient cycling into Earth system models.« less

  19. Are GRACE-era Terrestrial Water Trends Driven by Anthropogenic Climate Change?

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Fasullo, J. T.; Lawrence, D. M.; Swenson, S. C.

    2016-01-01

    To provide context for observed trends in terrestrial water storage (TWS) during GRACE (2003–2014), trends and variability in the CESM1-CAM5 Large Ensemble (LE) are examined. Motivated in part by the anomalous nature of climate variability during GRACE, the characteristics of both forced change and internal modes are quantified and their influences on observations are estimated. Trends during the GRACE era in the LE are dominated by internal variability rather than by the forced response, with TWS anomalies in much of the Americas, eastern Australia, Africa, and southwestern Eurasia largely attributable to the negative phases of the Pacific Decadal Oscillation (PDO)more » and Atlantic Multidecadal Oscillation (AMO). While similarities between observed trends and the model-inferred forced response also exist, it is inappropriate to attribute such trends mainly to anthropogenic forcing. For several key river basins, trends in the mean state and interannual variability and the time at which the forced response exceeds background variability are also estimated while aspects of global mean TWS, including changes in its annual amplitude and decadal trends, are quantified. The findings highlight the challenge of detecting anthropogenic climate change in temporally finite satellite datasets and underscore the benefit of utilizing models in the interpretation of the observed record.« less

  20. Terrestrial Sequestration of CO2 – An Assessment of Research Needs

    SciTech Connect (OSTI)

    Dove, Patricia; Richter, Frank; Rudnicki, John W; Harris, Jerry; Logan, John M.; Warpinski, Norman R; Wawersik, Wolfgang R; Wilson, John L; Wong, Teng-Fong; Ortoleva, Peter J; Orr, Jr., Franklin M; Pyrak-Nolte, Laura

    1998-11-02

    Scientific debate about global warming prompted the Office of Basic Energy Sciences (OBES) of the U.S. Department of Energy to assess a broad range of research possibilities that might result in more efficient energy and reduce the amount of greenhouse gases emitted to the atmosphere. Therefore, in May 1998, the Geosciences Research Program of OBES invited eleven panelists to a workshop in order to address the potential for the sequestration of CO2 in geologic formations as part of a possible OBES initiative on climate change technology. Starting with knowledge gained from the industrial use of CO2 for enhanced oil recovery, the panelists were asked to identify the fundamental scientific and technical issues that would enhance the safety, efficiency and predictability of terrestrial CO2 sequestration. This report is the product of the May, 1998 workshop and subsequent discussions among the panelists. Although many of the problems discussed cut across traditional geoscience disciplines, the background of the workshop participants naturally lead to a paper with four sections representing the perspectives of geohydrology, geochemistry, geomechanics, and geophysics.

  1. Biotransformation and Incorporation into Proteins along a Simulated Terrestrial Food Chain

    SciTech Connect (OSTI)

    Unrine, J.M., B.P. Jackson and W.A. Hopkins

    2007-01-01

    Selenium is an essential trace element in vertebrates, but there is a narrow concentration range between dietary requirement and toxicity threshold. Although a great deal is known about the biochemistry of Se from a nutritional perspective, considerably less attention has been focused on the specific biochemistry of Se as an environmental toxicant. Recent advances in hyphenated analytical techniques have provided the capability of quantifying specific chemical forms of Se in biological tissues as well as the distribution of Se among macromolecules. We applied liquid chromatography coupled to inductively coupled plasma mass spectrometry to investigate biotransformations of selenomethionine along a simulated terrestrial food chain consisting of selenomethionine exposed crickets (Acheta domesticus) fed to western fence lizards (Sceloporus occidentalis). Evidence was obtained for selenomethionine biotransformation as well as for sex-specific differences in the metabolism of Se compounds and their subsequent incorporation into proteins in the lizard. The results demonstrate the complexities involved in trophic transfer of Se due to the potential for extensive biotransformation and the species- and even sex-specific nature of these biotransformations.

  2. Collaborative Research. Quantifying Climate Feedbacks of the Terrestrial Biosphere under Thawing Permafrost Conditions in the Arctic

    SciTech Connect (OSTI)

    Zhuang, Qianlai; Schlosser, Courtney; Melillo, Jerry; Walter, Katey

    2015-09-15

    Our overall goal is to quantify the potential for threshold changes in natural emission rates of trace gases, particularly methane and carbon dioxide, from pan-arctic terrestrial systems under the spectrum of anthropogenically-forced climate warming, and the conditions under which these emissions provide a strong feedback mechanism to global climate warming. This goal is motivated under the premise that polar amplification of global climate warming will induce widespread thaw and degradation of the permafrost, and would thus cause substantial changes to the landscape of wetlands and lakes, especially thermokarst (thaw) lakes, across the Arctic. Through a suite of numerical experiments that encapsulate the fundamental processes governing methane emissions and carbon exchanges – as well as their coupling to the global climate system - we intend to test the following hypothesis in the proposed research: There exists a climate warming threshold beyond which permafrost degradation becomes widespread and stimulates large increases in methane emissions (via thermokarst lakes and poorly-drained wetland areas upon thawing permafrost along with microbial metabolic responses to higher temperatures) and increases in carbon dioxide emissions from well-drained areas. Besides changes in biogeochemistry, this threshold will also influence global energy dynamics through effects on surface albedo, evapotranspiration and water vapor. These changes would outweigh any increased uptake of carbon (e.g. from peatlands and higher plant photosynthesis) and would result in a strong, positive feedback to global climate warming.

  3. CONDITIONS OF PASSAGE AND ENTRAPMENT OF TERRESTRIAL PLANETS IN SPIN-ORBIT RESONANCES

    SciTech Connect (OSTI)

    Makarov, Valeri V.

    2012-06-10

    The dynamical evolution of terrestrial planets resembling Mercury in the vicinity of spin-orbit resonances is investigated using comprehensive harmonic expansions of the tidal torque taking into account the frequency-dependent quality factors and Love numbers. The torque equations are integrated numerically with a small step in time, including the oscillating triaxial torque components but neglecting the layered structure of the planet and assuming a zero obliquity. We find that a Mercury-like planet with a current value of orbital eccentricity (0.2056) is always captured in 3:2 resonance. The probability of capture in the higher 2:1 resonance is approximately 0.23. These results are confirmed by a semi-analytical estimation of capture probabilities as functions of eccentricity for both prograde and retrograde evolutions of spin rate. As follows from analysis of equilibrium torques, entrapment in 3:2 resonance is inevitable at eccentricities between 0.2 and 0.41. Considering the phase space parameters at the times of periastron, the range of spin rates and phase angles for which an immediate resonance passage is triggered is very narrow, and yet a planet like Mercury rarely fails to align itself into this state of unstable equilibrium before it traverses 2:1 resonance.

  4. Argonne Terrestrial Carbon Cycle Data from Batavia Prairie and Agricultural Sites

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Matamala, Roser [ANL; Jastrow, Julie D.; Lesht, Barry [ANL; Cook, David [ANL; Pekour, Mikhail [ANL; Gonzalez-Meler, Miquel A. [University of Illinois at Chicago

    Carbon dioxide fluxes and stocks in terrestrial ecosystems are key measurements needed to constrain quantification of regional carbon sinks and sources and the mechanisms controlling them. This information is required to produce a sound carbon budget for North America. This project examines CO2 and energy fluxes from agricultural land and from restored tallgrass prairie to compare their carbon sequestration potentials. The study integrates eddy covariance measurements with biometric measurements of plant and soil carbon stocks for two systems in northeastern Illinois: 1) long-term cultivated land in corn-soybean rotation with conventional tillage, and 2) a 15 year-old restored prairie that represents a long-term application of CRP conversion of cultivated land to native vegetation. The study contributes to the North American Carbon Program (NACP) by providing information on the magnitude and distribution of carbon stocks and the processes that control carbon dynamics in cultivated and CRP-restored land in the Midwest. The prairie site has been functioning since October 2004 and the agricultural site since July 2005. (From http://www.atmos.anl.gov/ FERMI/index.html)

  5. Convergence of microbial assimilations of soil carbon, nitrogen, phosphorus, and sulfur in terrestrial ecosystems

    SciTech Connect (OSTI)

    Xu, Xiaofeng; Hui, Dafeng; King, Anthony Wayne; Song, Xia; Thornton, Peter E.; Zhang, Lihua

    2015-11-27

    How soil microbes assimilate carbon-C, nitrogen-N, phosphorus-P, and sulfur-S is fundamental for understanding nutrient cycling in terrestrial ecosystems. We compiled a global database of C, N, P, and S concentrations in soils and microbes and developed relationships between them by using a power function model. The C:N:P:S was estimated to be 287:17:1:0.8 for soils, and 42:6:1:0.4 for microbes. We found a convergence of the relationships between elements in soils and in soil microbial biomass across C, N, P, and S. The element concentrations in soil microbial biomass follow a homeostatic regulation curve with soil element concentrations across C, N, P and S, implying a unifying mechanism of microbial assimilating soil elements. This correlation explains the well-constrained C:N:P:S stoichiometry with a slightly larger variation in soils than in microbial biomass. Meanwhile, it is estimated that the minimum requirements of soil elements for soil microbes are 0.8 mmol C Kg–1 dry soil, 0.1 mmol N Kg–1 dry soil, 0.1 mmol P Kg–1 dry soil, and 0.1 mmol S Kg–1 dry soil, respectively. Lastly, these findings provide a mathematical explanation of element imbalance in soils and soil microbial biomass, and offer insights for incorporating microbial contribution to nutrient cycling into Earth system models.

  6. Terrestrial planet formation in the presence of migrating super-Earths

    SciTech Connect (OSTI)

    Izidoro, Andr; Morbidelli, Alessandro; Raymond, Sean N. E-mail: morbidelli@oca.eu

    2014-10-10

    Super-Earths with orbital periods less than 100 days are extremely abundant around Sun-like stars. It is unlikely that these planets formed at their current locations. Rather, they likely formed at large distances from the star and subsequently migrated inward. Here we use N-body simulations to study the effect of super-Earths on the accretion of rocky planets. In our simulations, one or more super-Earths migrate inward through a disk of planetary embryos and planetesimals embedded in a gaseous disk. We tested a wide range of migration speeds and configurations. Fast-migrating super-Earths (?{sub mig} ? 0.01-0.1 Myr) only have a modest effect on the protoplanetary embryos and planetesimals. Sufficient material survives to form rocky, Earth-like planets on orbits exterior to the super-Earths'. In contrast, slowly migrating super-Earths shepherd rocky material interior to their orbits and strongly deplete the terrestrial planet-forming zone. In this situation any Earth-sized planets in the habitable zone are extremely volatile-rich and are therefore probably not Earth-like.

  7. PART FOUR INTEGRATION OF EPA AND ECOLOGY RESPONSIBILITIES ARTICLE XXIII. RCRA/CERCLA INTERFACE

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    49- PART FOUR INTEGRATION OF EPA AND ECOLOGY RESPONSIBILITIES ARTICLE XXIII. RCRA/CERCLA INTERFACE 86. Part Two of this Agreement requires DOE to carry out RCRA TSD work under the direction and authority of Ecology. Part Three of this Agreement requires DOE to carry out investigations and cleanup of past- practice units through the CERCLA process under the authority of EPA, or through the RCRA Corrective Action process under the authority of Ecology. This Part Four establishes the framework for

  8. DOE Cites Safety and Ecology Corp. for Violating Nuclear Safety Rules |

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Department of Energy Safety and Ecology Corp. for Violating Nuclear Safety Rules DOE Cites Safety and Ecology Corp. for Violating Nuclear Safety Rules June 14, 2005 - 4:53pm Addthis WASHINGTON, D.C. -- The Department of Energy (DOE) today notified Safety and Ecology Corporation, the contractor responsible for radiological safety at the Portsmouth Gaseous Diffusion Project in Portsmouth, Ohio, that it will fine the company $55,000 for violating the department's regulations prohibiting

  9. Microsoft PowerPoint - Ecology update for HAB 2-5-2015.pptx

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    February 5, 2015 Jane Hedges Manager, Nuclear Waste Program National Remedy Review Board * Ecology and Yakama Nation presented to board Jan. 27 on 100 D/H Proposed Plan * NRRB is EPA board, but Ecology is lead regulatory agency on this project * NRRB comments expected in about 6 weeks * Ecology will review comments & determine potential impacts to proposed plan * Public comment period on proposed plan could be ready to start June 2015 * Copies on back table * Posted on ECY website Updated

  10. Guidance Manual for Conducting Screening Level Ecological Risk Assessments at the INEL

    SciTech Connect (OSTI)

    R. L. VanHorn; N. L. Hampton; R. C. Morris

    1995-06-01

    This document presents reference material for conducting screening level ecological risk assessments (SLERAs)for the waste area groups (WAGs) at the Idaho National Engineering Laboratory. Included in this document are discussions of the objectives of and processes for conducting SLERAs. The Environmental Protection Agency ecological risk assessment framework is closely followed. Guidance for site characterization, stressor characterization, ecological effects, pathways of contaminant migration, the conceptual site model, assessment endpoints, measurement endpoints, analysis guidance, and risk characterization are included.

  11. The United States Regional Association of the International Association for Landscape Ecology

    SciTech Connect (OSTI)

    Not Available

    1993-06-01

    Abstracts are presented from a meeting on landscape ecology. Topics include: conservation, climatic change, forest management, aquatic, wetland, rural and urban landscapes, land use, and biodiversity.

  12. The United States Regional Association of the International Association for Landscape Ecology

    SciTech Connect (OSTI)

    Not Available

    1993-01-01

    Abstracts are presented from a meeting on landscape ecology. Topics include: conservation, climatic change, forest management, aquatic, wetland, rural and urban landscapes, land use, and biodiversity.

  13. Ethnic differences in ecological concerns: Spanish-speaking Hispanics are more concerned than others

    SciTech Connect (OSTI)

    Burger, Joanna . E-mail: burger@biology.rutgers.edu; Greenberg, Michael

    2006-09-15

    We postulated that environmental concern encompasses a wide range of different issues, often lumping pollution with habitat loss (or land use) and ecological resources (fish and wildlife). In this paper, we compare perceptions about a range of environmental and ecological resource issues, and explore ethnic/racial differences. We surveyed 1513 residents of New Jersey about 'environmental concerns', using both general environmental questions (two questions: How serious are environmental problems in New Jersey? Are you concerned about the loss of open space?) and ecological resource questions (12 questions: e.g., how important is planting trees in your neighborhood, how concerned are you about loss of breeding and feeding habitat for fish and birds?) in New Jersey. Not all concerns were rated equally. For the ecological questions, there were no ethnic differences in concerns over preserving areas around water supplies, loss of places to hunt and fish, and loss of places for quiet walks and cycling, but there were for the other 9 ecological concerns. For eight of these nine concerns, Spanish-speaking Hispanics were more concerned than others (including English-speaking Hispanics). We divided the ecological resources into three categories: ecological services (clean water and safety), ecological resources (fish and wildlife), and recreational services. The strongest correlates of people's association with enlarging and enhancing recreational services were Spanish-speaking Hispanics, who are supportive of regulations and believe local government is not doing enough for environmental problems. People concerned about the loss of ecological resources and open space believe the federal government and the state are not doing enough for the environment, were non-Hispanic White, want continued environmental regulations, were longer-term residents, were high school graduates, and were older (45-54 years). People interested in ecological services were college-educated, non

  14. Sensitivity of Global Terrestrial Gross Primary Production to Hydrologic States Simulated by the Community Land Model Using Two Runoff Parameterizations

    SciTech Connect (OSTI)

    Lei, Huimin; Huang, Maoyi; Leung, Lai-Yung R.; Yang, Dawen; Shi, Xiaoying; Mao, Jiafu; Hayes, Daniel J.; Schwalm, C.; Wei, Yaxing; Liu, Shishi

    2014-09-01

    The terrestrial water and carbon cycles interact strongly at various spatio-temporal scales. To elucidate how hydrologic processes may influence carbon cycle processes, differences in terrestrial carbon cycle simulations induced by structural differences in two runoff generation schemes were investigated using the Community Land Model 4 (CLM4). Simulations were performed with runoff generation using the default TOPMODEL-based and the Variable Infiltration Capacity (VIC) model approaches under the same experimental protocol. The comparisons showed that differences in the simulated gross primary production (GPP) are mainly attributed to differences in the simulated leaf area index (LAI) rather than soil moisture availability. More specifically, differences in runoff simulations can influence LAI through changes in soil moisture, soil temperature, and their seasonality that affect the onset of the growing season and the subsequent dynamic feedbacks between terrestrial water, energy, and carbon cycles. As a result of a relative difference of 36% in global mean total runoff between the two models and subsequent changes in soil moisture, soil temperature, and LAI, the simulated global mean GPP differs by 20.4%. However, the relative difference in the global mean net ecosystem exchange between the two models is small (2.1%) due to competing effects on total mean ecosystem respiration and other fluxes, although large regional differences can still be found. Our study highlights the significant interactions among the water, energy, and carbon cycles and the need for reducing uncertainty in the hydrologic parameterization of land surface models to better constrain carbon cycle modeling.

  15. Ecological Monitoring and Compliance Program Fiscal Year 2002 Report

    SciTech Connect (OSTI)

    C. A. Wills

    2002-12-01

    The Ecological Monitoring and Compliance program, funded through the U.S. Department of Energy, National Nuclear Security Administration Nevada Operations Office, monitors the ecosystem of the Nevada Test Site (NTS) and ensures compliance with laws and regulations pertaining to NTS biota. This report summarizes the program's activities conducted by Bechtel Nevada (BN) during fiscal year 2002. Program activities included: (1) biological surveys at proposed construction sites, (2) desert tortoise compliance, (3) ecosystem mapping and data management, (4) sensitive species and unique habitat monitoring, and (5) biological monitoring at the HAZMAT Spill Center. Biological surveys for the presence of sensitive species and important biological resources were conducted for 26 NTS projects. These projects have the potential to disturb a total of 374 acres. Thirteen of the projects were in desert tortoise habitat, and 13.38 acres of desert tortoise habitat were disturbed. No tortoises were found in or displaced from project areas, and no tortoises were accidentally injured or killed at project areas or along paved roads. Compilation of historical wildlife data continued this year in efforts to develop faunal distribution maps for the NTS. Photographs associated with the NTS ecological landform units sampled to create the NTS vegetation maps were cataloged for future retrieval and analysis. The list of sensitive plant species for which long-term population monitoring is scheduled was revised. Six vascular plants and five mosses were added to the list. Plant density estimates from ten populations of Astragalus beatleyae were collected, and eight known populations of Eriogonum concinnum were visited to assess plant and habitat status. Minimal field monitoring of western burrowing owl burrows occurred. A report relating to the ecology of the western burrowing owl on the Nevada Test Site was prepared which summarizes four years of data collected on this species' distribution

  16. Terrestrial fate of coal-liquid constituents: behavior of alkyl anilines in soil

    SciTech Connect (OSTI)

    Felice, L.J.; Zachara, J.M.; Rogers, J.E.

    1982-07-01

    The low molecular weight aromatic amines (anilines) are important water soluble constituents of coal liquids. The impact of anilines released to the terrestrial environment will largely depend on their mobility and persistence. Studies were conducted to investigate those processes governing the mobility and persistence of the alkylanilines, namely, soil sorption and chemical/microbial degradation. Soil sorption measurements were conducted on aniline and several methyl substituted anilines on A and B horizons of a soil profile collected from Davies County, Kentucky. The magnitude of sorption was large in all horizons. Sorption in the B horizons was larger than in the A horizon for many of the anilines studied, indicating the importance of both the mineral matrix and organic carbon content of the soil in determining the magnitude of sorption. Results of these measurements indicate that movement of the anilines through the soil would be significantly attenuated by sorption reactions. Aniline sorption measurement in the A horizon after removal of the organic matter and in the B/sub 22/ horizon after removal of amorphous iron oxides and crystalline iron oxides indicate that organic matter largely controls aniline sorption in the A horizon, while crystalline iron oxides and phyllosilicates are important in the B horizons. The effects of pH on aniline sorption was also examined and shown to have significant effects on the magnitude of sorption in both A and B horizons. Soil degradation studies using /sup 14/C-3-methylaniline as a model for alkyl aniline degradation show that 3-methylaniline is readily metabolized by soil microorganisms during the 32-day period examined.

  17. Marker-free registration of forest terrestrial laser scanner data pairs with embedded confidence metrics

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Van Aardt, Jan; Romanczyk, Paul; van Leeuwen, Martin; Kelbe, David; Cawse-Nicholson, Kerry

    2016-04-04

    Terrestrial laser scanning (TLS) has emerged as an effective tool for rapid comprehensive measurement of object structure. Registration of TLS data is an important prerequisite to overcome the limitations of occlusion. However, due to the high dissimilarity of point cloud data collected from disparate viewpoints in the forest environment, adequate marker-free registration approaches have not been developed. The majority of studies instead rely on the utilization of artificial tie points (e.g., reflective tooling balls) placed within a scene to aid in coordinate transformation. We present a technique for generating view-invariant feature descriptors that are intrinsic to the point cloud datamore » and, thus, enable blind marker-free registration in forest environments. To overcome the limitation of initial pose estimation, we employ a voting method to blindly determine the optimal pairwise transformation parameters, without an a priori estimate of the initial sensor pose. To provide embedded error metrics, we developed a set theory framework in which a circular transformation is traversed between disjoint tie point subsets. This provides an upper estimate of the Root Mean Square Error (RMSE) confidence associated with each pairwise transformation. Output RMSE errors are commensurate with the RMSE of input tie points locations. Thus, while the mean output RMSE=16.3cm, improved results could be achieved with a more precise laser scanning system. This study 1) quantifies the RMSE of the proposed marker-free registration approach, 2) assesses the validity of embedded confidence metrics using receiver operator characteristic (ROC) curves, and 3) informs optimal sample spacing considerations for TLS data collection in New England forests. Furthermore, while the implications for rapid, accurate, and precise forest inventory are obvious, the conceptual framework outlined here could potentially be extended to built environments.« less

  18. THE INFLUENCE OF THERMAL EVOLUTION IN THE MAGNETIC PROTECTION OF TERRESTRIAL PLANETS

    SciTech Connect (OSTI)

    Zuluaga, Jorge I.; Bustamante, Sebastian; Cuartas, Pablo A.; Hoyos, Jaime H. E-mail: sbustama@pegasus.udea.edu.co E-mail: jhhoyos@udem.edu.co

    2013-06-10

    Magnetic protection of potentially habitable planets plays a central role in determining their actual habitability and/or the chances of detecting atmospheric biosignatures. Here we develop a thermal evolution model of potentially habitable Earth-like planets and super-Earths (SEs). Using up-to-date dynamo-scaling laws, we predict the properties of core dynamo magnetic fields and study the influence of thermal evolution on their properties. The level of magnetic protection of tidally locked and unlocked planets is estimated by combining simplified models of the planetary magnetosphere and a phenomenological description of the stellar wind. Thermal evolution introduces a strong dependence of magnetic protection on planetary mass and rotation rate. Tidally locked terrestrial planets with an Earth-like composition would have early dayside magnetopause distances between 1.5 and 4.0 R{sub p} , larger than previously estimated. Unlocked planets with periods of rotation {approx}1 day are protected by magnetospheres extending between 3 and 8 R{sub p} . Our results are robust in comparison with variations in planetary bulk composition and uncertainties in other critical model parameters. For illustration purposes, the thermal evolution and magnetic protection of the potentially habitable SEs GL 581d, GJ 667Cc, and HD 40307g were also studied. Assuming an Earth-like composition, we found that the dynamos of these planets are already extinct or close to being shut down. While GL 581d is the best protected, the protection of HD 40307g cannot be reliably estimated. GJ 667Cc, even under optimistic conditions, seems to be severely exposed to the stellar wind, and, under the conditions of our model, has probably suffered massive atmospheric losses.

  19. Actual versus predicted impacts of three ethanol plants on aquatic and terrestrial resources

    SciTech Connect (OSTI)

    Eddlemon, G.K.; Webb, J.W.; Hunsaker, D.B. Jr.; Miller, R.L.

    1993-03-15

    To help reduce US dependence on imported petroleum, Congress passed the Energy Security Act of 1980 (public Law 96-294). This legislation authorized the US Department of Energy (DOE) to promote expansion of the fuel alcohol industry through, among other measures, its Alcohol Fuels Loan Guarantee Program. Under this program, selected proposals for the conversion of plant biomass into fuel-grade ethanol would be granted loan guarantees. of 57 applications submitted for loan guarantees to build and operate ethanol fuel projects under this program, 11 were considered by DOE to have the greatest potential for satisfying DOE`s requirements and goals. In accordance with the National Environmental Policy Act (NEPA), DOE evaluated the potential impacts of proceeding with the Loan Guarantee Program in a programmatic environmental assessment (DOE 1981) that resulted in a finding of no significant impact (FANCY) (47 Federal Register 34, p. 7483). The following year, DOE conducted site-specific environmental assessments (EAs) for 10 of the proposed projects. These F-As predicted no significant environmental impacts from these projects. Eventually, three ethanol fuel projects received loan guarantees and were actually built: the Tennol Energy Company (Tennol; DOE 1982a) facility near Jasper in southeastern Tennessee; the Agrifuels Refining Corporation (Agrifuels; DOE 1985) facility near New Liberia in southern Louisiana; and the New Energy Company of Indiana (NECI; DOE 1982b) facility in South Bend, Indiana. As part of a larger retrospective examination of a wide range of environmental effects of ethanol fuel plants, we compared the actual effects of the three completed plants on aquatic and terrestrial resources with the effects predicted in the NEPA EAs several years earlier. A secondary purpose was to determine: Why were there differences, if any, between actual effects and predictions? How can assessments be improved and impacts reduced?

  20. Packaging and distributing ecological data from multisite studies

    SciTech Connect (OSTI)

    Olson, R.J.; Voorhees, L.D.; Field, J.M.; Gentry, M.J.

    1996-10-01

    Studies of global change and other regional issues depend on ecological data collected at multiple study areas or sites. An information system model is proposed for compiling diverse data from dispersed sources so that the data are consistent, complete, and readily available. The model includes investigators who collect and analyze field measurements, science teams that synthesize data, a project information system that collates data, a data archive center that distributes data to secondary users, and a master data directory that provides broader searching opportunities. Special attention to format consistency is required, such as units of measure, spatial coordinates, dates, and notation for missing values. Often data may need to be enhanced by estimating missing values, aggregating to common temporal units, or adding other related data such as climatic and soils data. Full documentation, an efficient data distribution mechanism, and an equitable way to acknowledge the original source of data are also required.

  1. Ecology problems associated with geothermal development in California

    SciTech Connect (OSTI)

    Shinn, J.H.; Ireland, R.R.

    1980-08-04

    Geothermal power plants have the potential for supplying about 5% of the US electrical generating needs by 1985, and are even now supplying about one third of San Francisco's electricity. Investigations have shown that the typical geothermal field, such as the hot water resource of Imperial Valley, can be developed in an environmentally sound manner when proper considerations are made for ecosystem problems. Experimental evidence is presented pro and con for potential impacts due to habitat disturbance, powerline corridors, noise effects, trace element emissions from cooling towers, accidental brine discharges into aquatic or soil systems, competition for water and H/sub 2/S effects on vegetation. A mitigation and control strategy is recommended for each ecological issue and it is shown where effects are likely to be irreversible.

  2. Environmental audit of the Savannah River Ecology Laboratory (SREL)

    SciTech Connect (OSTI)

    Not Available

    1993-09-01

    This report documents the results of the environmental audit conducted at the Savannah River Ecology Laboratory (SREL) at the Savannah River Site (SRS), principally in Aiken and Barnwell Counties, South Carolina. The audit was conducted by the US Department of Energy`s (DOE`s), Office of Environmental Audit (EH-24), beginning September 13, 1993, and ending September 23, 1993. The scope of the audit at SREL was comprehensive, addressing environmental activities in the technical areas of air; surface water/drinking water; groundwater/soil, sediment, and biota; waste management; toxic and chemical materials; inactive Waste sites; radiation; quality assurance; and environmental management. Specifically assessed was the compliance of SREL operations and activities with Federal, state, and local regulations; DOE Orders; and best management practices.

  3. The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution and Metabolism

    SciTech Connect (OSTI)

    Armbrust, E V; Berges, J A; Bowler, C; Green, B R; Martinez, D; Putnam, N H; Zhou, S; Allen, A E; Apt, K E; Bechner, M; Brzezinski, M A; Chaal, B K; Chiovitti, A; Davis, A K; Demarest, M S; Detter, J C; del Rio, T G; Goodstein, D; Hadi, M Z; Hellsten, U; Hildebrand, M; Jenkins, B D; Jurka, J; Kapitonov, V V; Kroger, N; Lau, W Y; Lane, T W; Larimer, F W; Lippmeier, J C; Lucas, S; Medina, M; Montsant, A; Obornik, M; Parker, M S; Palenik, B; Pazour, G J; Richardson, P M; Rynearson, T A; Saito, M A; Schwartz, D C; Thamatrakoln, K; Valentin, K; Vardi, A; Wilkerson, F P; Rokhsar, D S

    2005-11-14

    Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for {approx}20% of global carbon fixation. We report the 34 Mbp draft nuclear genome of the marine diatom, Thalassiosira pseudonana and its 129 Kbp plastid and 44 Kbp mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, utilization of a range of nitrogenous compounds and a complete urea cycle, all attributes that allow diatoms to prosper in the marine environment. Diatoms are unicellular, photosynthetic, eukaryotic algae found throughout the world's oceans and freshwater systems. They form the base of short, energetically-efficient food webs that support large-scale coastal fisheries. Photosynthesis by marine diatoms generates as much as 40% of the 45-50 billion tonnes of organic carbon produced each year in the sea (1), and their role in global carbon cycling is predicted to be comparable to that of all terrestrial rainforests combined (2, 3). Over geological time, diatoms may have influenced global climate by changing the flux of atmospheric carbon dioxide into the oceans (4). A defining feature of diatoms is their ornately patterned silicified cell wall or frustule, which displays species-specific nano-structures of such fine detail that diatoms have long been used to test the resolution of optical microscopes. Recent attention has focused on biosynthesis of these nano-structures as a paradigm for future silica nanotechnology (5). The long history (over 180 million years) and dominance of diatoms in the oceans is reflected by their contributions to vast deposits of diatomite, most cherts and a significant fraction of current petroleum reserves (6). As photosynthetic heterokonts, diatoms reflect a fundamentally different

  4. The genome of the diatom Thalassiosira pseudonana: Ecology,evolution, and metabolism

    SciTech Connect (OSTI)

    Ambrust, E.V.; Berges, J.; Bowler, C.; Green, B.; Martinez, D.; Putnam, N.; Zhou, S.; Allen, A.; Apt, K.; Bechner, M.; Brzezinski, M.; Chaal, B.; Chiovitti, A.; Davis, A.; Goodstein, D.; Hadi, M.; Hellsten,U.; Hildebrand, M.; Jenkins, B.; Jurka, J.; Kapitonov, V.; Kroger, N.; Lau, W.; Lane, T.; Larimer, F.; Lippmeier, J.; Lucas, S.; Medina, M.; Montsant, A.; Obornik, M.; Parker, M. Schnitzler; Palenik, B.; Pazour,G.; Richardson, P.; Rynearson, T.; Saito, M.; Schwartz, D.; Thamatrakoln,K.; Valentin, K.; Vardi, A.; Wilkerson, F.; Rokhsar, D.; Vardi, A.; Wilkerson, F.P.; Rokhsar, D.S.

    2004-09-01

    Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for {approx}20% of global carbon fixation. We report the 34 Mbp draft nuclear genome of the marine diatom, Thalassiosira pseudonana and its 129 Kbp plastid and 44 Kbp mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, utilization of a range of nitrogenous compounds and a complete urea cycle, all attributes that allow diatoms to prosper in the marine environment. Diatoms are unicellular, photosynthetic, eukaryotic algae found throughout the world's oceans and freshwater systems. They form the base of short, energetically-efficient food webs that support large-scale coastal fisheries. Photosynthesis by marine diatoms generates as much as 40% of the 45-50 billion tonnes of organic carbon produced each year in the sea (1), and their role in global carbon cycling is predicted to be comparable to that of all terrestrial rainforests combined (2, 3). Over geological time, diatoms may have influenced global climate by changing the flux of atmospheric carbon dioxide into the oceans (4). A defining feature of diatoms is their ornately patterned silicified cell wall or frustule, which displays species-specific nano-structures of such fine detail that diatoms have long been used to test the resolution of optical microscopes. Recent attention has focused on biosynthesis of these nano-structures as a paradigm for future silica nanotechnology (5). The long history (over 180 million years) and dominance of diatoms in the oceans is reflected by their contributions to vast deposits of diatomite, most cherts and a significant fraction of current petroleum reserves (6). As photosynthetic heterokonts, diatoms reflect a fundamentally different

  5. Technical Report Department of Energy Grant #SC0004335 “Tracking Down Cheaters. Molecular Analysis of Carbon Consumption by Organisms That Do Not Contribute to Extracellular Enzyme Pools”

    SciTech Connect (OSTI)

    Blackwood, Christopher

    2015-05-31

    The overriding objective of our work is to integrate physiological and community ecology of belowground organisms into understanding of soil carbon dynamics to improve predictions of terrestrial ecosystem models. This includes using metagenomics and metatranscriptomics-based methods to understand microbial interactions affecting decomposition and soil carbon dynamics. The focus of the majority of the work directly related to this project was on “cheating”, a poorly understood microbial interaction with a potentially large effect on decomposition. Model organisms were used to determine the types of organisms that cheat based on their known niche and genomic characteristics. In addition, we study plant and microbial traits and plant-microbe interactions that affect species distributions and soil carbon, and also develop bioinformatics tools to increase the power of ecological inferences that can be obtained from omics-based sequence data.

  6. Separating stressor influences from environmental variability: eight case studies from aquatic and terrestrial ecosystems

    SciTech Connect (OSTI)

    Luoma, Samuel N.; Clements, Will; Gerritsen, Jeroen; Hatch, Audrey; Jepson, Paul; Reynoldson, Trefor; Thom, Ronald M.

    2001-12-03

    It can be difficult to unambiguously establish the influences of a particular stressor or group of stressors in a complex ecosystem, except, perhaps, when the effects are extreme (Luoma and Carter, 1991). Yet this is a critical problem we face when attempting to understand the influences of human activities on ecosystems. Single experiments or studies are rarely adequate to establish cause and effect in complex ecosystems, and many of the individual approaches available to demonstrate stressor effects have important inadequacies. A multi-faceted body of work is usually at the center of most examples where stressor effects are explained. In this chapter seven case studies are presented where effects or influences of multiple stressors were explained and separated from natural variability. The goal of this chapter is to demonstrate that identification of stressor effects is tractable, although not necessarily simple; and to illustrate some specific strategies that have worked. We also present one case study where the quest for cause and effect is just beginning, to illustrate the range of challenges involved as a body of work begins to be established. The examples are from several different fields of ecology, they cover a variety of scales and a mix of disciplines.

  7. Contents of risk assessments to support the retrieval and closure of tanks for the Washington State Department of Ecology

    SciTech Connect (OSTI)

    MANN, F.M.

    2003-03-21

    Before the Integrated Mission Acceleration Plan can be performed, risk assessments of various options must be performed for ORP, DOE Headquarters, and the Washington State Dept. of Ecology. This document focuses on the risk assessments for Ecology.

  8. Toxicity Bioassays for Ecological Risk Assessment in Arid and Semiarid Ecosystems. Reviews Environmental Contamination and Toxicology 168:43-98.

    SciTech Connect (OSTI)

    Markwiese, J.T.; Ryti, R.T.; Hooten, M.M.; Michael, D.I.; Hlohowskyj, I.

    2001-02-01

    This paper discusses current limitations for performing ecological risk assessments in dry environments (i.e., ecosystems that are characteristic of many DOE Facilities) and presents novel approaches to addressing ecological risk in such systems.

  9. ENHANCEMENT OF TERRESTRIAL CARBON SINKS THROUGH RECLAMATION OF ABANDONED MINE LANDS IN THE APPALACHIAN REGION

    SciTech Connect (OSTI)

    Gary D. Kronrad

    2002-12-01

    The U.S.D.I. Office of Surface Mining (OSM) estimates that there are approximately 1 million acres of abandoned mine land (AML) in the Appalachian region. AML lands are classified as areas that were inadequately reclaimed or were left unreclaimed prior to the passage of the 1977 Surface Mining Control and Reclamation Act, and where no federal or state laws require any further reclamation responsibility to any company or individual. Reclamation and afforestation of these sites have the potential to provide landowners with cyclical timber revenues, generate environmental benefits to surrounding communities, and sequester carbon in the terrestrial ecosystem. Through a memorandum of understanding, the OSM and the U.S. Department of Energy (DOE) have decided to investigate reclaiming and afforesting these lands for the purpose of mitigating the negative effects of anthropogenic carbon dioxide in the atmosphere. This study determined the carbon sequestration potential of northern red oak (Quercus rubra L.), one of the major reclamation as well as commercial species, planted on West Virginia AML sites. Analyses were conducted to (1) calculate the total number of tons that can be stored, (2) determine the cost per ton to store carbon, and (3) calculate the profitability of managing these forests for timber production alone and for timber production and carbon storage together. The Forest Management Optimizer (FORMOP) was used to simulate growth data on diameter, height, and volume for northern red oak. Variables used in this study included site indices ranging from 40 to 80 (base age 50), thinning frequencies of 0, 1, and 2, thinning percentages of 20, 25, 30, 35, and 40, and a maximum rotation length of 100 years. Real alternative rates of return (ARR) ranging from 0.5% to 12.5% were chosen for the economic analyses. A total of 769,248 thinning and harvesting combinations, net present worths, and soil expectation values were calculated in this study. Results indicate that

  10. Controls on terrestrial carbon feedbacks by productivity vs. turnover in the CMIP5 Earth System Models

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Koven, C. D.; Chambers, J. Q.; Georgiou, K.; Knox, R.; Negron-Juarez, R.; Riley, W. J.; Arora, V. K.; Brovkin, V.; Friedlingstein, P.; Jones, C. D.

    2015-04-16

    To better understand sources of uncertainty in projections of terrestrial carbon cycle feedbacks, we present an approach to separate the controls on modeled carbon changes. We separate carbon changes into 4 categories using a linearized, equilibrium approach: those arising from changed inputs (productivity-driven changes), and outputs (turnover-driven changes), and apply the analysis separately to the live and dead carbon pools. Using Coupled Model Intercomparison Project Phase 5 (CMIP5) simulations for 5 models, we find that changes to the live pools are primarily explained by productivity-driven changes, with only one model showing large compensating changes to live carbon turnover times. Formore » dead carbon pools, the situation is more complex as all models predict a large reduction in turnover times in response to increases in productivity. This responses arises from the common representation of a broad spectrum of decomposition turnover times via a multi-pool approach, in which flux-weighted turnover times are faster than mass-weighted turnover times. This leads to a shift in the distribution of carbon among dead pools in response to changes in inputs, and therefore a transient but long-lived reduction in turnover times in response to increases in productivity. Since this behavior, a reduction in inferred turnover times resulting from an increase in inputs, is superficially similar to priming processes, but occurring without the mechanisms responsible for priming, we call the phenomenon "false priming", and show that it masks much of the intrinsic changes to dead carbon turnover times as a result of changing climate. These patterns hold across the fully-coupled, biogeochemically-coupled, and radiatively-coupled 1% yr−1 increasing CO2 experiments. We disaggregate inter-model uncertainty in the globally-integrated equilibrium carbon responses to initial turnover times, inital productivity, fractional changes in turnover, and fractional changes in

  11. Controls on terrestrial carbon feedbacks by productivity versus turnover in the CMIP5 Earth System Models

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Koven, C. D.; Chambers, J. Q.; Georgiou, K.; Knox, R.; Negron-Juarez, R.; Riley, W. J.; Arora, V. K.; Brovkin, V.; Friedlingstein, P.; Jones, C. D.

    2015-09-07

    To better understand sources of uncertainty in projections of terrestrial carbon cycle feedbacks, we present an approach to separate the controls on modeled carbon changes. We separate carbon changes into four categories using a linearized, equilibrium approach: those arising from changed inputs (productivity-driven changes), and outputs (turnover-driven changes), of both the live and dead carbon pools. Using Coupled Model Intercomparison Project Phase 5 (CMIP5) simulations for five models, we find that changes to the live pools are primarily explained by productivity-driven changes, with only one model showing large compensating changes to live carbon turnover times. For dead carbon pools, themore » situation is more complex as all models predict a large reduction in turnover times in response to increases in productivity. This response arises from the common representation of a broad spectrum of decomposition turnover times via a multi-pool approach, in which flux-weighted turnover times are faster than mass-weighted turnover times. This leads to a shift in the distribution of carbon among dead pools in response to changes in inputs, and therefore a transient but long-lived reduction in turnover times. Since this behavior, a reduction in inferred turnover times resulting from an increase in inputs, is superficially similar to priming processes, but occurring without the mechanisms responsible for priming, we call the phenomenon "false priming", and show that it masks much of the intrinsic changes to dead carbon turnover times as a result of changing climate. These patterns hold across the fully coupled, biogeochemically coupled, and radiatively coupled 1 % yr−1 increasing CO2 experiments. We disaggregate inter-model uncertainty in the globally integrated equilibrium carbon responses to initial turnover times, initial productivity, fractional changes in turnover, and fractional changes in productivity. For both the live and dead carbon pools, inter

  12. BIO-MONITORING FOR URANIUM USING STREAM-SIDE TERRESTRIAL PLANTS AND MACROPHYTES

    SciTech Connect (OSTI)

    Caldwell, E.; Duff, M.; Hicks, T.; Coughlin, D.; Hicks, R.; Dixon, E.

    2012-01-12

    This study evaluated the abilities of various plant species to act as bio-monitors for environmental uranium (U) contamination. Vegetation and soil samples were collected from a U processing facility. The water-way fed from facility storm and processing effluents was the focal sample site as it represented a primary U transport mechanism. Soils and sediments from areas exposed to contamination possessed U concentrations that averaged 630 mg U kg{sup -1}. Aquatic mosses proved to be exceptional accumulators of U with dry weight (dw) concentrations measuring as high as 12500 mg U kg{sup -1} (approximately 1% of the dw mass was attributable to U). The macrophytes (Phragmites communis, Scripus fontinalis and Sagittaria latifolia) were also effective accumulators of U. In general, plant roots possessed higher concentrations of U than associated upper portions of plants. For terrestrial plants, the roots of Impatiens capensis had the highest observed levels of U accumulation (1030 mg kg{sup -1}), followed by the roots of Cyperus esculentus and Solidago speciosa. The concentration ratio (CR) characterized dry weight (dw) vegetative U levels relative to that in associated dw soil. The plant species that accumulated U at levels in excess of that found in the soil were: P. communis root (CR, 17.4), I. capensis root (CR, 3.1) and S. fontinalis whole plant (CR, 1.4). Seven of the highest ten CR values were found in the roots. Correlations with concentrations of other metals with U were performed, which revealed that U concentrations in the plant were strongly correlated with nickel (Ni) concentrations (correlation: 0.992; r-squared: 0.984). Uranium in plant tissue was also strongly correlated with strontium (Sr) (correlation: 0.948; r-squared: 0.899). Strontium is chemically and physically similar to calcium (Ca) and magnesium (Mg), which were also positively-correlated with U. The correlation with U and these plant nutrient minerals, including iron (Fe), suggests that active

  13. Effects of climate change, land-use change, and invasive species on the ecology of the Cumberland forests

    SciTech Connect (OSTI)

    Dale, Virginia H; Lannom, Karen O.; Hodges, Donald G.; Tharp, M Lynn; Fogel, Jonah

    2009-02-01

    Effects of climate change, land-use change, and invasive species on the ecology of the Cumberland forests

  14. The North American Carbon Program Multi-scale Synthesis and Terrestrial Model Intercomparison Project – Part 2: Environmental driver data

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Wei, Yaxing; Liu, Shishi; Huntzinger, Deborah N.; Michalak, Anna M.; Viovy, Nicolas; Post, Wilfred M.; Schwalm, Christopher R.; Schaeffer, Kevin; Jacobson, Andrew R.; Lu, Chaoqun; et al

    2014-12-05

    Ecosystems are important and dynamic components of the global carbon cycle, and terrestrial biospheric models (TBMs) are crucial tools in further understanding of how terrestrial carbon is stored and exchanged with the atmosphere across a variety of spatial and temporal scales. Improving TBM skills, and quantifying and reducing their estimation uncertainties, pose significant challenges. The Multi-scale Synthesis and Terrestrial Model Intercomparison Project (MsTMIP) is a formal multi-scale and multi-model intercomparison effort set up to tackle these challenges. The MsTMIP protocol prescribes standardized environmental driver data that are shared among model teams to facilitate model model and model observation comparisons. Inmore » this article, we describe the global and North American environmental driver data sets prepared for the MsTMIP activity to both support their use in MsTMIP and make these data, along with the processes used in selecting/processing these data, accessible to a broader audience. Based on project needs and lessons learned from past model intercomparison activities, we compiled climate, atmospheric CO2 concentrations, nitrogen deposition, land use and land cover change (LULCC), C3 / C4 grasses fractions, major crops, phenology and soil data into a standard format for global (0.5⁰ x 0.5⁰ resolution) and regional (North American: 0.25⁰ x 0.25⁰ resolution) simulations. In order to meet the needs of MsTMIP, improvements were made to several of the original environmental data sets, by improving the quality, and/or changing their spatial and temporal coverage, and resolution. The resulting standardized model driver data sets are being used by over 20 different models participating in MsTMIP. Lastly, the data are archived at the Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC, http://daac.ornl.gov) to provide long-term data management and distribution.« less

  15. Predicting ecological roles in the rhizosphere using metabolome and transportome modeling

    SciTech Connect (OSTI)

    Larsen, Peter E.; Collart, Frank R.; Dai, Yang; Blanchard, Jeffrey L.

    2015-09-02

    The ability to obtain complete genome sequences from bacteria in environmental samples, such as soil samples from the rhizosphere, has highlighted the microbial diversity and complexity of environmental communities. New algorithms to analyze genome sequence information in the context of community structure are needed to enhance our understanding of the specific ecological roles of these organisms in soil environments. We present a machine learning approach using sequenced Pseudomonad genomes coupled with outputs of metabolic and transportomic computational models for identifying the most predictive molecular mechanisms indicative of a Pseudomonad’s ecological role in the rhizosphere: a biofilm, biocontrol agent, promoter of plant growth, or plant pathogen. Computational predictions of ecological niche were highly accurate overall with models trained on transportomic model output being the most accurate (Leave One Out Validation F-scores between 0.82 and 0.89). The strongest predictive molecular mechanism features for rhizosphere ecological niche overlap with many previously reported analyses of Pseudomonad interactions in the rhizosphere, suggesting that this approach successfully informs a system-scale level understanding of how Pseudomonads sense and interact with their environments. The observation that an organism’s transportome is highly predictive of its ecological niche is a novel discovery and may have implications in our understanding microbial ecology. The framework developed here can be generalized to the analysis of any bacteria across a wide range of environments and ecological niches making this approach a powerful tool for providing insights into functional predictions from bacterial genomic data.

  16. PHOTOCHEMISTRY IN TERRESTRIAL EXOPLANET ATMOSPHERES. II. H{sub 2}S AND SO{sub 2} PHOTOCHEMISTRY IN ANOXIC ATMOSPHERES

    SciTech Connect (OSTI)

    Hu Renyu; Seager, Sara; Bains, William

    2013-05-20

    Sulfur gases are common components in the volcanic and biological emission on Earth, and are expected to be important input gases for atmospheres on terrestrial exoplanets. We study the atmospheric composition and the spectra of terrestrial exoplanets with sulfur compounds (i.e., H{sub 2}S and SO{sub 2}) emitted from their surfaces. We use a comprehensive one-dimensional photochemistry model and radiative transfer model to investigate the sulfur chemistry in atmospheres ranging from reducing to oxidizing. The most important finding is that both H{sub 2}S and SO{sub 2} are chemically short-lived in virtually all types of atmospheres on terrestrial exoplanets, based on models of H{sub 2}, N{sub 2}, and CO{sub 2} atmospheres. This implies that direct detection of surface sulfur emission is unlikely, as their surface emission rates need to be extremely high (>1000 times Earth's volcanic sulfur emission) for these gases to build up to a detectable level. We also find that sulfur compounds emitted from the surface lead to photochemical formation of elemental sulfur and sulfuric acid in the atmosphere, which would condense to form aerosols if saturated. For terrestrial exoplanets in the habitable zone of Sun-like stars or M stars, Earth-like sulfur emission rates result in optically thick haze composed of elemental sulfur in reducing H{sub 2}-dominated atmospheres for a wide range of particle diameters (0.1-1 {mu}m), which is assumed as a free parameter in our simulations. In oxidized atmospheres composed of N{sub 2} and CO{sub 2}, optically thick haze, composed of elemental sulfur aerosols (S{sub 8}) or sulfuric acid aerosols (H{sub 2}SO{sub 4}), will form if the surface sulfur emission is two orders of magnitude more than the volcanic sulfur emission of Earth. Although direct detection of H{sub 2}S and SO{sub 2} by their spectral features is unlikely, their emission might be inferred by observing aerosol-related features in reflected light with future generation space

  17. Microbial ecology and genomics: A crossroads of opportunity

    SciTech Connect (OSTI)

    Stahl, David A.; Tiedje, James M.

    2002-08-30

    Microbes have dominated life on Earth for most of its 4.5 billionyear history. They are the foundation of the biosphere, controlling the biogeochemical cycles and affecting geology, hydrology, and local and global climates. All life is completely dependent upon them. Humans cannot survive without the rich diversity of microbes, but most microbial species can survive without humans. Extraordinary advances in molecular technology have fostered an explosion of information in microbial biology. It is now known that microbial species in culture poorly represent their natural diversity—which dwarfs conventions established for the visible world. This was revealed over the last decade using newer molecular tools to explore environmental diversity and has sparked an explosive growth in microbial ecology and technologies that may profit from the bounty of natural biochemical diversity. Several colloquia and meetings have helped formulate policy recommendations to enable sustained research programs in these areas. One such colloquium organized by the American Academy of Microbiology (“The Microbial World: Foundation of the Biosphere,” 1997) made two key recommendations: (1) develop a more complete inventory of living organisms and the interagency cooperation needed to accomplish this goal, and (2) develop strategies to harvest this remarkable biological diversity for the benefit of science, technology, and society. Complete genome sequence information was identified as an essential part of strategy development, and the recommendation was made to sequence the genome of at least one species of each of the major divisions of microbial life.

  18. Integrating ecological and engineering concepts of resilience in microbial communities

    SciTech Connect (OSTI)

    Song, Hyun -Seob; Renslow, Ryan S.; Fredrickson, Jim K.; Lindemann, Stephen R.

    2015-12-01

    We note that many definitions of resilience have been proffered for natural and engineered ecosystems, but a conceptual consensus on resilience in microbial communities is still lacking. Here, we argue that the disconnect largely results from the wide variance in microbial community complexity, which range from simple synthetic consortia to complex natural communities, and divergence between the typical practical outcomes emphasized by ecologists and engineers. Viewing microbial communities as elasto-plastic systems, we argue that this gap between the engineering and ecological definitions of resilience stems from their respective emphases on elastic and plastic deformation, respectively. We propose that the two concepts may be fundamentally united around the resilience of function rather than state in microbial communities and the regularity in the relationship between environmental variation and a community’s functional response. Furthermore, we posit that functional resilience is an intrinsic property of microbial communities, suggesting that state changes in response to environmental variation may be a key mechanism driving resilience in microbial communities.

  19. Integrating ecological and engineering concepts of resilience in microbial communities

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Song, Hyun -Seob; Renslow, Ryan S.; Fredrickson, Jim K.; Lindemann, Stephen R.

    2015-12-01

    We note that many definitions of resilience have been proffered for natural and engineered ecosystems, but a conceptual consensus on resilience in microbial communities is still lacking. Here, we argue that the disconnect largely results from the wide variance in microbial community complexity, which range from simple synthetic consortia to complex natural communities, and divergence between the typical practical outcomes emphasized by ecologists and engineers. Viewing microbial communities as elasto-plastic systems, we argue that this gap between the engineering and ecological definitions of resilience stems from their respective emphases on elastic and plastic deformation, respectively. We propose that the twomore » concepts may be fundamentally united around the resilience of function rather than state in microbial communities and the regularity in the relationship between environmental variation and a community’s functional response. Furthermore, we posit that functional resilience is an intrinsic property of microbial communities, suggesting that state changes in response to environmental variation may be a key mechanism driving resilience in microbial communities.« less

  20. Ecological compensation and Environmental Impact Assessment in Spain

    SciTech Connect (OSTI)

    Villarroya, Ana; Puig, Jordi

    2010-11-15

    To achieve meaningful sustainable development, Environmental Impact Assessment (EIA) should avoid the net losses in the environment resource base. But EIA practice does not always avoid the losses caused by the implementation of the projects under EIA regulation. Some environmental impacts are, simply, admitted, even without enforcing any form of compensation. When applied, compensation is sometimes just a monetary payment to offset the environmental loss. This paper looks for evidence on the role that compensation is given at present in EIA practice in Spain, and for some of its conceptual and regulatory roots. Specifically, it explores how compensation is addressed in 1302 records of decision (RODs) on those projects subject to the Spanish EIA regulation published during the years 2006 and 2007, to know how far Spain is from preserving the environmental resource base managed through this particular aspect of EIA practice. As a result, it is concluded that the practice of ecological compensation in EIA in Spain is much lower than it could be expected in a theoretical sustainability context committed to avoid net losses in the environment resource base, mainly due to an EIA practice focused on on-site mitigation that allows these net losses.

  1. Ecological measures for converter steelmaking emphasizing process integration

    SciTech Connect (OSTI)

    Wiesinger, H.A.; Patuzzi, A.A.; Gara, S.P. )

    1994-09-01

    Integrated technological and environmental solutions have become a key challenge, particularly for the iron and steel industry. End of pipe thinking, or the approach to solve all emission-related problems solely by exp-process cleaning systems is neither a long-term economic solution nor a satisfactory environmental answer. In addition, dealing with the problem of emissions must be redirected to the source. Optimized technologies and systems must be increasingly employed which not only maximizes production and product quality, but also minimizes the overall environmental impact for converter steelmaking. This presentation focuses on state of the art technologies emphasizing process integration. Various technological alternatives for converter steelmaking are discussed in terms of best available solutions for minimized overall environmental impact. Effective implementation of ecological measures for converter steelmaking are to be achieved through total view strategies which take into account the entire production process route from raw material preparation to steelmaking, including by-product management up to the final and safe disposal of waste. Future-oriented technologies include: Airfine for integrated gas cleaning and waste management for sinter plants; Corex featuring the lowest rate of environmental emissions for the production of hot metal; LT (Lurgi-Thyssen) steel gas process for emission control, energy recovery and dust recycling in BOF vessels.

  2. From Fjords to Open Seas: Ecological Genomics of Expanding Oxygen Minimum Zones (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Hallam, Steven

    2011-04-26

    Steven Hallam of the University of British Columbia talks "From Fjords to Open Seas: Ecological Genomics of Expanding Oxygen Minimum Zones" on March 24, 2010 at the 5th Annual DOE JGI User Meeting

  3. Rocky Flats Environmental Technology Site Ecological Monitoring Program 1995 annual report

    SciTech Connect (OSTI)

    1995-05-31

    The Ecological Monitoring Program (ECMP) was established at the Rocky Flats Environmental Technology Site (Site) in September 1992. At that time, EcMP staff developed a Program Plan that was peer-reviewed by scientists from western universities before submittal to DOE RFFO in January 1993. The intent of the program is to measure several quantitative variables at different ecological scales in order to characterize the Rocky Flats ecosystem. This information is necessary to document ecological conditions at the Site in impacted and nonimpacted areas to determine if Site practices have had ecological impacts, either positive or negative. This information can be used by managers interested in future use scenarios and CERCLA activities. Others interested in impact analysis may also find the information useful. In addition, these measurements are entered into a database which will serve as a long-term information repository that will document long-term trends and potential future changes to the Site, both natural and anthropogenic.

  4. Ecological Monitoring and Compliance Program Fiscal Year 2000 Report

    SciTech Connect (OSTI)

    Wills, C.A.

    2000-12-01

    The Ecological Monitoring and Compliance program, funded through the U.S. Department of Energy, Nevada Operations Office, monitors the ecosystem of he Nevada Test Site (NTS) and ensures compliance with laws and regulations pertaining to NTS biota. This report summarizes the program's activities conducted by Bechtel Nevada during fiscal year 2000. Program activities included: (1) biological surveys at proposed construction sites, (2) desert tortoise compliance,(3) ecosystem mapping, (4) sensitive species and unique habitat monitoring, and (5) biological monitoring at the HAZMAT Spill Center. Biological surveys for the presence of sensitive species were conducted for 24 NTS projects. Seventeen sites were in desert tortoise habitat, and six acres of tortoise habitat were documented as being disturbed this year. No tortoises were found in or displaced from project areas, and no tortoises were accidentally injured or killed. A topical report describing the classification of habitat types o n the NTS was completed. The report is the culmination of three years of field vegetation mapping and the analysis of vegetation data from over 1,500 ecological landform units. A long-term monitoring plan for important plant species that occur on the NTS was completed. Sitewide inventories were conducted for the western burrowing owl, bat species of concern, wild horses, raptor nests, and mule deer. Fifty-nine of 69 known owl burrows were monitored. Forty-four of the known burrows are in disturbed habitat. As in previous years, some owls were present year round on the NTS. An overall decrease in active owl burrows was observed within all three ecoregions (Mojave Desert, Transition, Great Basin Desert) from October through January. An increase in active owl burrows was observed from mid-March to early April. A total of 45 juvenile owls was detected from eight breeding pairs. One nest burrow was detected in the Mojave Desert,one in the Great Basin Desert, and six in the Transition

  5. Ecological Monitoring and Compliance Program Fiscal Year 2001

    SciTech Connect (OSTI)

    C. A. Wills

    2001-12-01

    The Ecological Monitoring and Compliance program, funded through the U.S. Department of Energy, National Nuclear Security Administration Nevada Operations Office, monitors the ecosystem of the Nevada Test Site (NTS) and ensures compliance with laws and regulations pertaining to NTS biota. This report summarizes the program's activities conducted by Bechtel Nevada during fiscal year 2001. Program activities included: (1) biological surveys at proposed construction sites, (2) desert tortoise compliance, (3) ecosystem mapping and data management, (4) sensitive species and unique habitat monitoring, and (5) biological monitoring at the HAZMAT Spill Center. Biological surveys for the presence of sensitive species were conducted for 23 NTS projects. Eleven sites were in desert tortoise habitat. These projects have the potential to disturb a total of 588 acres, where 568 acres of disturbance would be off-road driving. No tortoises were found in or displaced from project areas, and no tortoise s were accidentally injured or killed at project areas. One tortoise was crushed by a vehicle on a paved road. A topical report describing the classification of habitat types on the NTS was completed and distributed. The report is the culmination of three years of field vegetation mapping and the analysis of vegetation data from over 1,500 ecological landform units. Compilation of historical wildlife data was initiated. A long-term monitoring plan for important plant species that occur on the NTS was completed. Site-wide monitoring was conducted for the western burrowing owl, bat species of concern, wild horses, and raptor nests. Sixty-nine of 77 known owl burrows were monitored. As in previous years, some owls were present year round on the NTS. An overall decrease in active owl burrows was observed within all three ecoregions (Mojave Desert, Transition, Great Basin Desert) from October through January. An increase in active owl burrows was observed from mid March to early April. A

  6. A Strategic Project Appraisal framework for ecologically sustainable urban infrastructure

    SciTech Connect (OSTI)

    Morrissey, John; Iyer-Raniga, Usha; McLaughlin, Patricia; Mills, Anthony

    2012-02-15

    Actors in the built environment are progressively considering environmental and social issues alongside functional and economic aspects of development projects. Infrastructure projects represent major investment and construction initiatives with attendant environmental, economic and societal impacts across multiple scales. To date, while sustainability strategies and frameworks have focused on wider national aspirations and strategic objectives, they are noticeably weak in addressing micro-level integrated decision making in the built environment, particularly for infrastructure projects. The proposed approach of this paper is based on the principal that early intervention is the most cost-effective and efficient means of mitigating the environmental effects of development projects, particularly macro infrastructure developments. A strategic overview of the various project alternatives, taking account for stakeholder and expert input, could effectively reduce project impacts/risks at low cost to the project developers but provide significant benefit to wider communities, including communities of future stakeholders. This paper is the first exploratory step in developing a more systematic framework for evaluating strategic alternatives for major metropolitan infrastructure projects, based on key sustainability principles. The developed Strategic Project Appraisal (SPA) framework, grounded in the theory of Strategic Environmental Assessment (SEA), provides a means of practically appraising project impacts and alternatives in terms of quantified ecological limits; addresses the neglected topic of metropolitan infrastructure as a means of delivering sustainability outcomes in the urban context and more broadly, seeks to open a debate on the potential for SEA methodology to be more extensively applied to address sustainability challenges in the built environment. Practically applied and timed appropriately, the SPA framework can enable better decision-making and more

  7. Tri Party Agreement Administrative Record Presentation for Dennis A. Faulk, EPA Jane A. Hedges, Ecology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    TPA) and Milestone Tutorial John Price, Ecology What is it? Hanford Federal Facility Agreement and Consent Order (HFFACO) * Legal Agreement, Parts One - Five - Federal Facility Agreement between US Department of Energy and US Environmental Protection Agency (US DOE and US EPA) - Consent Order between US DOE and Washington Department of Ecology - A 3-party agreement [TPA] on how to integrate the Federal Facility Agreement with the Consent Order Why is there an EPA-DOE Federal Facility Agreement?

  8. Ecological risk assessment guidance for preparation of remedial investigation/feasibility study work plans

    SciTech Connect (OSTI)

    Pentecost, E.D.; Vinikour, W.S.

    1993-08-01

    This guidance document (1) provides instructions on preparing the components of an ecological work plan to complement the overall site remedial assessment investigation/feasibility study (RI/FS) work plan and (2) directs the user on how to implement ecological tasks identified in the plan. Under the Comprehensive Environmental Response, Compensation, and Liability Act of 1980 (CERCLA), as amended by the Superfired Amendments and Reauthorization Act of 1986 (SARA), an RI/FS work plan win have to be developed as part of the site-remediation scoping the process. Specific guidance on the RI/FS process and the preparation of work plans has been developed by the US Environmental Protection Agency (EPA 1988a). This document provides guidance to US Department of Energy (DOE) staff and contractor personnel for incorporation of ecological information into environmental remediation planning and decision making at CERCLA sites. An overview analysis of early ecological risk assessment methods (i.e., in the 1980s) at Superfund sites was conducted by the EPA (1989a). That review provided a perspective of attention given to ecological issues in some of the first RI/FS studies. By itself, that reference is of somewhat limited value; it does, however, establish a basis for comparison of past practices in ecological risk with current, more refined methods.

  9. Selecting indicators of soil, microbial, and plant conditions to understand ecological changes in Georgia pine forests

    SciTech Connect (OSTI)

    Dale, Virginia H; Garten Jr, Charles T; Wolfe, Amy K; Sobek, Edward A

    2008-11-01

    Characterizing how resource use and management activities affect ecological conditions is necessary to document and understand anthropogenic changes in ecological systems. Resource managers on military installations have the delicate task of balancing the training needs of soldiers effectively with the need to maintain a high quality of ecological conditions. This study considers ways that ecological indicators can provide information on impacts that training has on environmental characteristics that occur at different scales and in different sectors of the environment. The characteristics examined include soil chemistry, soil microbes, and vegetation. A discriminant function analysis was conducted to determine whether ecological indicators could differentiate among different levels of military use. A combination of 10 indicators explained 90% of the variation among plots from five different military use levels. Results indicated that an appropriate suite of ecological indicators for military resource managers includes soil, microbial, and vegetation characteristics. Since many of these indicators are related, managers at this location potentially have freedom to choose indicators that are relatively easy to measure, without sacrificing information.

  10. A Carbon Flux Super Site. New Insights and Innovative Atmosphere-Terrestrial Carbon Exchange Measurements and Modeling

    SciTech Connect (OSTI)

    Leclerc, Monique Y.

    2014-11-17

    This final report presents the main activities and results of the project “A Carbon Flux Super Site: New Insights and Innovative Atmosphere-Terrestrial Carbon Exchange Measurements and Modeling” from 10/1/2006 to 9/30/2014. It describes the new AmeriFlux tower site (Aiken) at Savanna River Site (SC) and instrumentation, long term eddy-covariance, sodar, microbarograph, soil and other measurements at the site, and intensive field campaigns of tracer experiment at the Carbon Flux Super Site, SC, in 2009 and at ARM-CF site, Lamont, OK, and experiments in Plains, GA. The main results on tracer experiment and modeling, on low-level jet characteristics and their impact on fluxes, on gravity waves and their influence on eddy fluxes, and other results are briefly described in the report.

  11. Shape of the terrestrial plasma sheet in the near-Earth magnetospheric tail as imaged by the Interstellar Boundary Explorer

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Dayeh, M. A.; Fuselier, S. A.; Funsten, H. O.; McComas, D. J.; Ogasawara, K.; Petrinec, S. M.; Schwadron, N. A.; Valek, P.

    2015-04-11

    We present remote, continuous observations from the Interstellar Boundary Explorer of the terrestrial plasma sheet location back to -16 Earth radii (RE) in the magnetospheric tail using energetic neutral atom emissions. The time period studied includes two orbits near the winter and summer solstices, thus associated with large negative and positive dipole tilt, respectively. Continuous side-view images reveal a complex shape that is dominated mainly by large-scale warping due to the diurnal motion of the dipole axis. Superposed on the global warped geometry are short-time fluctuations in plasma sheet location that appear to be consistent with plasma sheet flapping andmore » possibly twisting due to changes in the interplanetary conditions. We conclude that the plasma sheet warping due to the diurnal motion dominates the average shape of the plasma sheet. Over short times, the position of the plasma sheet can be dominated by twisting and flapping.« less

  12. Shape of the terrestrial plasma sheet in the near-Earth magnetospheric tail as imaged by the Interstellar Boundary Explorer

    SciTech Connect (OSTI)

    Dayeh, M. A.; Fuselier, S. A.; Funsten, H. O.; McComas, D. J.; Ogasawara, K.; Petrinec, S. M.; Schwadron, N. A.; Valek, P.

    2015-04-11

    We present remote, continuous observations from the Interstellar Boundary Explorer of the terrestrial plasma sheet location back to -16 Earth radii (RE) in the magnetospheric tail using energetic neutral atom emissions. The time period studied includes two orbits near the winter and summer solstices, thus associated with large negative and positive dipole tilt, respectively. Continuous side-view images reveal a complex shape that is dominated mainly by large-scale warping due to the diurnal motion of the dipole axis. Superposed on the global warped geometry are short-time fluctuations in plasma sheet location that appear to be consistent with plasma sheet flapping and possibly twisting due to changes in the interplanetary conditions. We conclude that the plasma sheet warping due to the diurnal motion dominates the average shape of the plasma sheet. Over short times, the position of the plasma sheet can be dominated by twisting and flapping.

  13. [Climate implications of terrestrial paleoclimate]. Quaternary Sciences Center, Desert Research Institute annual report, fiscal year 1994/1995

    SciTech Connect (OSTI)

    Wigand, P.E.

    1995-12-31

    The objective of this study is to collect terrestrial climate indicators for paleoclimate synthesis. The paleobiotic and geomorphic records are being examined for the local and regional impact of past climates to assess Yucca Mountain`s suitability as a high-level nuclear waste repository. In particular these data are being used to provide estimates of the timing, duration and extremes of past periods of moister climate for use in hydrological models of local and regional recharge that are being formulated by USGS and other hydrologists for the Yucca Mountain area. The project includes botanical, faunal, and geomorphic components that will be integrated to accomplish this goal. To this end personnel at the Quaternary Sciences Center of the Desert Research Institute in Reno, Nevada are conducting the following activities: Analyses of packrat middens; Analysis of pollen samples; and Determination of vegetation climate relationships.

  14. Predicting ecological roles in the rhizosphere using metabolome and transportome modeling

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Larsen, Peter E.; Collart, Frank R.; Dai, Yang; Blanchard, Jeffrey L.

    2015-09-02

    The ability to obtain complete genome sequences from bacteria in environmental samples, such as soil samples from the rhizosphere, has highlighted the microbial diversity and complexity of environmental communities. New algorithms to analyze genome sequence information in the context of community structure are needed to enhance our understanding of the specific ecological roles of these organisms in soil environments. We present a machine learning approach using sequenced Pseudomonad genomes coupled with outputs of metabolic and transportomic computational models for identifying the most predictive molecular mechanisms indicative of a Pseudomonad’s ecological role in the rhizosphere: a biofilm, biocontrol agent, promoter ofmore » plant growth, or plant pathogen. Computational predictions of ecological niche were highly accurate overall with models trained on transportomic model output being the most accurate (Leave One Out Validation F-scores between 0.82 and 0.89). The strongest predictive molecular mechanism features for rhizosphere ecological niche overlap with many previously reported analyses of Pseudomonad interactions in the rhizosphere, suggesting that this approach successfully informs a system-scale level understanding of how Pseudomonads sense and interact with their environments. The observation that an organism’s transportome is highly predictive of its ecological niche is a novel discovery and may have implications in our understanding microbial ecology. The framework developed here can be generalized to the analysis of any bacteria across a wide range of environments and ecological niches making this approach a powerful tool for providing insights into functional predictions from bacterial genomic data.« less

  15. Multi-level effects of low dose rate ionizing radiation on southern toad, Anaxyrus [Bufo] terrestris

    SciTech Connect (OSTI)

    Stark, Karolina; Scott, David E.; Tsyusko, Olga; Coughlin, Daniel P.; Hinton, Thomas G.; Amendola, Roberto

    2015-04-30

    Despite their potential vulnerability to contaminants from exposure at multiple life stages, amphibians are one of the least studied groups of vertebrates in ecotoxicology, and research on radiation effects in amphibians is scarce. We used multiple endpoints to assess the radiosensitivity of the southern toad (Anaxyrus [Bufo] terrestris) during its pre-terrestrial stages of development –embryonic, larval, and metamorphic. Toads were exposed, from several hours after oviposition through metamorphosis (up to 77 days later), to four low dose rates of ¹³⁷Cs at 0.13, 2.4, 21, and 222 mGy d⁻¹, resulting in total doses up to 15.8 Gy. Radiation treatments did not affect hatching success of embryos, larval survival, or the length of the larval period. The individual family variation in hatching success of embryos was larger than the radiation response. In contrast, newly metamorphosed individuals from the higher dose-rate treatments had higher mass and mass/length body indices, a measure which may relate to higher post-metamorphic survival. The increased mass and index at higher dose rates may indicate that the chronic, low dose rate radiation exposures triggered secondary responses. Additionally, the increases in growth were linked to a decrease in DNA damage (as measured by the Comet Assay) in red blood cells at a dose rate of 21mGy d⁻¹ and a total dose of 1.1 Gy. In conclusion, the complex effects of low dose rates of ionizing radiation may trigger growth and cellular repair mechanisms in amphibian larvae.

  16. The North American Carbon Program Multi-scale synthesis and Terrestrial Model Intercomparison Project Part 1: Overview and experimental design

    SciTech Connect (OSTI)

    Huntzinger, D.N.; Schwalm, C.; Michalak, A.M; Schaefer, K.; King, A.W.; Wei, Y.; Jacobson, A.; Liu, S.; Cook, R.; Post, W.M.; Berthier, G.; Hayes, D.; Huang, M.; Ito, A.; Lei, H.; Lu, C.; Mao, J.; Peng, C.H.; Peng, S.; Poulter, B.; Riccuito, D.; Shi, X.; Tian, H.; Wang, W.; Zeng, N.; Zhao, F.; Zhu, Q.

    2013-01-01

    Terrestrial biosphere models (TBMs) have become an integral tool for extrapolating local observations and understanding of land-atmosphere carbon exchange to larger regions. The North American Carbon Program (NACP) Multi-scale synthesis and Terrestrial Model Intercomparison Project (MsTMIP) is a formal model intercomparison and evaluation effort focused on improving the diagnosis and attribution of carbon exchange at regional and global scales. MsTMIP builds upon current and past synthesis activities, and has a unique framework designed to isolate, interpret, and inform understanding of how model structural differences impact estimates of carbon uptake and release. Here we provide an overview of the MsTMIP effort and describe how the MsTMIP experimental design enables the assessment and quantification of TBM structural uncertainty. Model structure refers to the types of processes considered (e.g. nutrient cycling, disturbance, lateral transport of carbon), and how these processes are represented (e.g. photosynthetic formulation, temperature sensitivity, respiration) in the models. By prescribing a common experimental protocol with standard spin-up procedures and driver data sets, we isolate any biases and variability in TBM estimates of regional and global carbon budgets resulting from differences in the models themselves (i.e. model structure) and model-specific parameter values. An initial intercomparison of model structural differences is represented using hierarchical cluster diagrams (a.k.a. dendrograms), which highlight similarities and differences in how models account for carbon cycle, vegetation, energy, and nitrogen cycle dynamics. We show that, despite the standardized protocol used to derive initial conditions, models show a high degree of variation for GPP, total living biomass, and total soil carbon, underscoring the influence of differences in model structure and parameterization on model estimates.

  17. A framework for assessing ecological risks of petroleum-derived materials in soil

    SciTech Connect (OSTI)

    Suter, G.W. II

    1997-05-01

    Ecological risk assessment estimates the nature and likelihood of effects of human actions on nonhuman organisms, populations, and ecosystems. It is intended to be clearer and more rigorous in its approach to estimation of effects and uncertainties than previously employed methods of ecological assessment. Ecological risk assessment is characterized by a standard paradigm that includes problem formulation, analysis of exposure and effects, risk characterization, and communication with a risk manager. This report provides a framework that applies the paradigm to the specific problem of assessing the ecological risks of petroleum in soil. This type of approach requires that assessments be performed in phases: (1) a scoping assessment to determine whether there is a potential route of exposure for potentially significant ecological receptors; (2) a screening assessment to determine whether exposures could potentially reach toxic levels; and (3) a definitive assessment to estimate the nature, magnitude, and extent of risks. The principal technical issue addressed is the chemically complex nature of petroleum--a complexity that may be dealt with by assessing risks on the basis of properties of the whole material, properties of individual chemicals that are representative of chemical classes, distributions of properties of the constituents of chemical classes, properties of chemicals detected in the soil, and properties of indicator chemicals. The advantages and feasibility of these alternatives are discussed. The report concludes with research recommendations for improving each stage in the assessment process.

  18. Ecology Information Request HgC2H6 for 241-AW Tank Farm, 01/13/2015

    SciTech Connect (OSTI)

    Dyekman, Dale L.; Greene, Michael R.

    2015-01-15

    This information was requested by Phil Gent of Ecology on 12/18/2014 and confirmed on 01/13/2015 to Dale Dyekman.

  19. Quantifying the role of fire in the Earth system - Part 2: Impact on the net carbon balance of global terrestrial ecosystems for the 20th century

    SciTech Connect (OSTI)

    Li, Fang; Bond-Lamberty, Benjamin; Levis, Samuel

    2014-03-07

    Fire is the primary terrestrial ecosystem disturbance agent on a global scale. It affects carbon balance of global terrestrial ecosystems by emitting carbon to atmosphere directly and immediately from biomass burning (i.e., fire direct effect), and by changing net ecosystem productivity and land-use carbon loss in post-fire regions due to biomass burning and fire-induced vegetation mortality (i.e., fire indirect effect). Here, we provide the first quantitative assessment about the impact of fire on the net carbon balance of global terrestrial ecosystems for the 20th century, and investigate the roles of fire direct and indirect effects. This study is done by quantifying the difference between the 20th century fire-on and fire-off simulations with NCAR community land model CLM4.5 as the model platform. Results show that fire decreases net carbon gain of the global terrestrial ecosystems by 1.0 Pg C yr-1 average across the 20th century, as a results of fire direct effect (1.9 Pg C yr-1) partly offset by indirect effect (-0.9 Pg C yr-1). Fire generally decreases the average carbon gains of terrestrial ecosystems in post-fire regions, which are significant over tropical savannas and part of forests in North America and the east of Asia. The general decrease of carbon gains in post-fire regions is because fire direct and indirect effects have similar spatial patterns and the former (to decrease carbon gain) is generally stronger. Moreover, the effect of fire on net carbon balance significantly declines prior to ~1970 with trend of 8 Tg C yr-1 due to increasing fire indirect effect and increases afterward with trend of 18 Tg C yr-1 due to increasing fire direct effect.

  20. Landscape ecological planning: Integrating land use and wildlife conservation for biomass crops

    SciTech Connect (OSTI)

    Schiller, A.

    1995-12-31

    What do a mussel shoat, a zoo, and a biomass plantation have in common? Each can benefit from ecology-based landscape planning. This paper provides examples of landscape ecological planning from some diverse projects the author has worked on, and discusses how processes employed and lessons learned from these projects are being used to help answer questions about the effects of biomass plantings (hardwood tree crops and native grasses) on wildlife habitat. Biomass environmental research is being designed to assess how plantings of different acreage, composition and landscape context affect wildlife habitat value, and is addressing the cumulative effect on wildlife habitat of establishing multiple biomass plantations across the landscape. Through landscape ecological planning, answers gleaned from research can also help guide biomass planting site selection and harvest strategies to improve habitat for native wildlife species within the context of economically viable plantation management - thereby integrating the needs of people with those of the environment.

  1. 2001 Gordon Research Conference on Archaea: Ecology [sic], Metabolism. Final progress report [agenda and attendee list

    SciTech Connect (OSTI)

    Daniels, Charles

    2001-08-10

    The Gordon Research Conference on Archaea: Ecology, Metabolism [and Molecular Biology] was held at Proctor Academy, Andover, New Hampshire, August 5-10, 2001. The conference was attended by 135 participants. The attendees represented the spectrum of endeavor in this field, coming from academia, industry, and government laboratories, and included US and foreign scientists, senior researchers, young investigators, and students. Emphasis was placed on current unpublished research and discussion of the future target areas in this field. There was a conscious effort to stimulate discussion about the key issues in the field today. Session topics included the following: Ecology and genetic elements; Genomics and evolution; Ecology, genomes and gene regulation; Replication and recombination; Chromatin and transcription; Gene regulation; Post-transcription processing; Biochemistry and metabolism; Proteomics and protein structure; Metabolism and physiology. The featured speaker addressed the topic: ''Archaeal viruses, witnesses of prebiotic evolution?''

  2. Incorporating ecological risk assessment into remedial investigation/feasibility study work plans

    SciTech Connect (OSTI)

    Not Available

    1994-06-01

    This guidance document (1) provides instructions on preparing the components of an ecological work plan to complement the overall site remedial investigation/feasibility study (RI/FS) work plan and (2) directs the user on how to implement ecological tasks identified in the plan. Under the Comprehensive Environmental Response, Compensation, and Liability Act of 1980 (CERCLA), as amended by the Superfund Amendments and Reauthorization Act of 1986 (SARA), and RI/FS work plan will have to be developed as part of the site-remediation scoping process. Specific guidance on the RI/FS process and the preparation of work plans has been developed by the US Environmental Protection Agency (EPA 1988a). This document provides guidance to US Department of Energy (DOE) staff and contractor personnel for incorporation of ecological information into environmental remediation planning and decision making at CERCLA sites.

  3. Envisioning an Ecologically Sustainable Campus At New England College

    SciTech Connect (OSTI)

    Paula Amato; Gregory Palmer

    2010-09-30

    Appropriation funding for our project Ecologically Sustainable Campus - New England College (NH). 67.09. supported five environmental initiatives: (1) a wood pellet boiler for our Science Building, (2) solar hot water panels and systems for five campus buildings, (3) campus-wide energy lighting efficiency project, (4) new efficiency boiler system in Colby Residence Hall, and (5) energy efficient lighting system for the new artificial athletic turf field. (1) New England College purchased and installed a new wood pellet boiler in the Science Building. This new boiler serves as the primary heating source for this building. Our boiler was purchased through New England Wood Pellet, LLC, located in Jaffrey, New Hampshire. The boiler selected was a Swebo, P500. 300KW wood pellet boiler. The primary goals, objectives, and outcomes of this initiative include the installation of a wood pellet boiler system that is environmentally friendly, highly efficient, and represents a sustainable and renewable resource for New England College. This project was completed on December 15, 2010. (2) New England College purchased and installed solar hot water panels and systems for the Science Building, the Simon Center (student center), the H. Raymond Danforth Library, Gilmore Dining Hall, and Bridges Gymnasium. The College worked with Granite State Plumbing & Heating, LLC, located in Weare, New Hampshire on this project. The solar panels are manufactured by Heat Transfer; the product is Heat Transfer 30-tube collector panels (Evacuated Tube Type) with stainless steel hardware. The interior equipment includes Super Stor Ultra stainless steel super insulated storage tank, Taco 009 Bronze circulator pump, Solar Relay Control Pack, and a Taco Thermal Expansion Tank. The primary goals, objectives, and outcomes of this initiative will allow the College to utilize the sun as an energy resource. These solar hot water panels and systems will alleviate our dependency on fossil fuel as our primary

  4. Plutonium Isotopes in the Terrestrial Environment at the Savannah River Site, USA. A Long-Term Study

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Armstrong, Christopher R.; Nuessle, Patterson R.; Brant, Heather A.; Hall, Gregory; Halverson, Justin E.; Cadieux, James R.

    2015-01-16

    This work presents the findings of a long term plutonium study at Savannah River Site (SRS) conducted between 2003 and 2013. Terrestrial environmental samples were obtained at Savannah River National Laboratory (SRNL) in A-area. Plutonium content and isotopic abundances were measured over this time period by alpha spectrometry and three stage thermal ionization mass spectrometry (3STIMS). Here we detail the complete sample collection, radiochemical separation, and measurement procedure specifically targeted to trace plutonium in bulk environmental samples. Total plutonium activities were determined to be not significantly above atmospheric global fallout. However, the 238Pu/239+240Pu activity ratios attributed to SRS are abovemore » atmospheric global fallout ranges. The 240Pu/239Pu atom ratios are reasonably consistent from year to year and are lower than fallout, while the 242Pu/239Pu atom ratios are higher than fallout values. Overall, the plutonium signatures obtained in this study reflect a mixture of weapons-grade, higher burn-up, and fallout material. This study provides a blue print for long term low level monitoring of plutonium in the environment.« less

  5. Frontiers in Assessing the Role of Chemical Speciation And Natural Attenuation on the Bioavailability of Contaminants in the Terrestrial Environment

    SciTech Connect (OSTI)

    Gerson, A.R.; Anastasio, C.; Crowe, S.; Fowle, D.; Guo, B.; Kennedy, I.; Lombi, E.; Nico, P.S.; Marcus, M.A.; Martin, R.R.; Naftel, S.J.; Nelson, A.J.; Paktunc, D.; Roberts, J.A.; Weisener, C.G.; Werner, M.L.

    2009-05-28

    It has long been recognized that contaminants interact with the solid soil phase via a series of sorption-desorption (all chemicals) and precipitation-dissolution (polar and ionic compounds) reactions including physical migration into micropores and diffusion into the solid phase (see Chapter 2). Until recently the extent of such interactions and the binding with different solid pools was established via a series of chemical extractions (see Chapter 20) and a combination of instrumental techniques. However, none of these techniques provide a true indication of the speciation of contaminants on or in solid minerals and organics. The last decade has witnessed the emergence of tools that provide an assessment of the speciation and attenuation of chemicals at molecular level. In this chapter we provide an overview of the current state-of-the-art for assessing speciation and attenuation of contaminants in the terrestrial environment. Given that speciation and attenuation influence chemical bioavailability, we devote part of this chapter to the application of isotopic dilution techniques to bioavailability assessment. We have not attempted to be exhaustive but rather to highlight a number of studies in sufficient detail so that the reader will be provided with an insight as to whether such approaches are applicable to their field of endeavor and what the realistic outcomes might be.

  6. DOE Final Report on Collaborative Research. Quantifying Climate Feedbacks of the Terrestrial Biosphere under Thawing Permafrost Conditions in the Arctic

    SciTech Connect (OSTI)

    Zhuang, Qianlai; Schlosser, C. Adam; Melillo, Jerry M.; Anthony, Katey Walter; Kicklighter, David; Gao, Xiang

    2015-11-03

    Our overall goal is to quantify the potential for threshold changes in natural emission rates of trace gases, particularly methane and carbon dioxide, from pan-arctic terrestrial systems under the spectrum of anthropogenically-forced climate warming, and the conditions under which these emissions provide a strong feedback mechanism to global climate warming. This goal is motivated under the premise that polar amplification of global climate warming will induce widespread thaw and degradation of the permafrost, and would thus cause substantial changes to the landscape of wetlands and lakes, especially thermokarst (thaw) lakes, across the Arctic. Through a suite of numerical experiments that encapsulate the fundamental processes governing methane emissions and carbon exchanges – as well as their coupling to the global climate system - we intend to test the following hypothesis in the proposed research: There exists a climate warming threshold beyond which permafrost degradation becomes widespread and stimulates large increases in methane emissions (via thermokarst lakes and poorly-drained wetland areas upon thawing permafrost along with microbial metabolic responses to higher temperatures) and increases in carbon dioxide emissions from well-drained areas. Besides changes in biogeochemistry, this threshold will also influence global energy dynamics through effects on surface albedo, evapotranspiration and water vapor. These changes would outweigh any increased uptake of carbon (e.g. from peatlands and higher plant photosynthesis) and would result in a strong, positive feedback to global climate warming.

  7. A study of the terrestrial thermosphere by remote sensing of OI dayglow in the far and extreme ultraviolet

    SciTech Connect (OSTI)

    Cotton, D.M.

    1991-01-01

    The upper region of the Earth's atmosphere, the thermosphere, is a key part of the coupled solar-terrestrial system. An important method of obtaining information in the this region is through analysis of radiation excited through the interactions of the thermosphere with solar ionizing, extreme and far ultraviolet radiation. This dissertation presents one such study by the remote sensing of OI in the far and extreme ultraviolet dayglow. The research program included the development construction, and flight of a sounding rocket spectrometer to test this current understanding of the excitation and transport mechanisms of the OI 1356, 1304, 1027, and 989 {angstrom} emissions. This data set was analyzed using current electron and radiative transport models with the purpose of checking the viability of OI remote sensing; that is, whether existing models and input parameters are adequate to predict these detailed measurements. From discrepancies between modeled and measured emissions, inferences about these input parameters were made. Among other things, the data supports a 40% optically thick cascade contribution to the 1304 {angstrom} emission. From upper lying states corresponding to 1040, 1027 and 989 {angstrom} about half of this cascade has been accounted for in this study. There is also evidence that the Lyman {beta} airglow from the geo-corona contributes a significant proportion (30-50%) to the OI 1027 {angstrom} feature. Furthermore, the photoelectron contribution to the 1027 {angstrom} feature appears to be underestimated in the current models by a factor of 20.

  8. Survey of ecological resources at selected US Department of Energy sites

    SciTech Connect (OSTI)

    McAllister, C.; Beckert, H.; Abrams, C.

    1996-09-01

    The U.S. Department of Energy (DOE) owns and manages a wide range of ecological resources. During the next 30 years, DOE Headquarters and Field Offices will make land-use planning decisions and conduct environmental remediation and restoration activities in response to federal and state statutes. This document fulfills, in part, DOE`s need to know what types of ecological resources it currently owns and manages by synthesizing information on the types and locations of ecological resources at 10 DOE sites: Hanford Site, Idaho National Engineering Laboratory, Lawrence Livermore National Laboratory, Sandia National Laboratory, Rocky Flats Plant, Los Alamos National Laboratory, savannah River Site, Oak Ridge National Laboratory, Argonne National Laboratory, and Fernald Environmental Management Project. This report summarizes information on ecosystems, habitats, and federally listed threatened, endangered, and candidate species that could be stressed by contaminants or physical activity during the restoration process, or by the natural or anthropogenic transport of contaminants from presently contaminated areas into presently uncontaminated areas. This report also provides summary information on the ecosystems, habitats, and threatened and endangered species that exist on each of the 10 sites. Each site chapter contains a general description of the site, including information on size, location, history, geology, hydrology, and climate. Descriptions of the major vegetation and animal communities and of aquatic resources are also provided, with discussions of the treatened or endangered plant or animal species present. Site-specific ecological issues are also discussed in each site chapter. 106 refs., 11 figs., 1 tab.

  9. The Promise and Challenge of Producing Biofuel Feedstocks: An Ecological Perspective (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    DeLucia, Evan

    2011-04-26

    Evan DeLucia of the University of Illinois at Urbana-Champaign and the Energy Biosciences Institute talks about "The Promise and Challenge of Producing Biofuel Feedstocks: An Ecological Perspective" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

  10. Idaho National Engineering Laboratory radioecology and ecology programs. 1983 progress report

    SciTech Connect (OSTI)

    Markham, O. D.

    1983-06-01

    Progress is reported in research on: the baseline ecology of the Idaho National Engineering Laboratory (INEL), the effects of disturbance on animal and plant communities, and the behavior of radionuclides in the environment surrounding radioactive waste sites. Separate abstracts have been prepared for individual reports. (ACR)

  11. A proposal to improve ecological compensation practice in road and railway projects in Spain

    SciTech Connect (OSTI)

    Villarroya, Ana Puig, Jordi

    2013-09-15

    To reduce ecological impacts caused by development projects, avoidance, minimization and compensation techniques have to be taken together into consideration along Environmental Impact Assessment (EIA) procedures. This paper explores the particular role that ecological compensation has had in recent road and railway EIA procedures in Spain, as seen through the review of a set of recent EIA Records of Decision (RODs) that confirms precedent findings. Noticing that residual impacts are not paid much attention, and that there is no evidence of a solid public participation in ecological impact evaluation, it proposes to increase the awareness on residual impacts, as a way to make easier public access to the allegedly most sensitive moment of EIA implementation: (residual) impact evaluation. -- Highlights: ► Ecological compensation practice in Spain is much lower than avoidance or mitigation. ► Residual impacts are overlooked in EIA processes and public participation is low. ► An increased awareness of residual impacts may also promote public participation. ► Current context needs these small steps to move towards better compensation practice.

  12. Summary of the Nevada Applied Ecology Group and correlative programs. Version 1

    SciTech Connect (OSTI)

    Friesen, H.N.

    1992-10-01

    This summary document presents results in a broad context; it is not limited to findings of the Nevada Applied Ecology Group. This book is organized to present the findings of the Nevada Applied Ecology Group and correlative programs in accordance with the originally stated objectives of the Nevada Applied Ecology Group. This plan, in essence, traces plutonium from its injection into the environment to movement in the ecosystem to development of cleanup techniques. Information on other radionuclides was also obtained and will be presented briefly. Chapter 1 presents a brief description of the ecological setting of the Test Range Complex. The results of investigations for plutonium distribution are presented in Chapter 2 for the area surrounding the Test Range Complex and in Chapter 3 for on-site locations. Chapters 4 and 5 present the results of investigations concerned with concentrations and movement, respectively, of plutonium in the ecosystem of the Test Range Complex, and Chapter 6 summarizes the potential hazard from this plutonium. Development of techniques for cleanup and treatment is presented in Chapter 7, and the inventory of radionuclides other than plutonium is presented briefly in Chapter 8.

  13. A Study of the Abundance and 13C/12C Ratio of Atmospheric Carbon Dioxide to Advance the Scientific Understanding of Terrestrial Processes Regulating the Global Carbon Cycle

    SciTech Connect (OSTI)

    Stephen C. Piper

    2005-10-15

    The primary goal of our research program, consistent with the goals of the U.S. Climate Change Science Program and funded by the terrestrial carbon processes (TCP) program of DOE, has been to improve understanding of changes in the distribution and cycling of carbon among the active land, ocean and atmosphere reservoirs, with particular emphasis on terrestrial ecosystems. Our approach is to systematically measure atmospheric CO2 to produce time series data essential to reveal temporal and spatial patterns. Additional measurements of the 13C/12C isotopic ratio of CO2 provide a basis for distinguishing organic and inorganic processes. To pursue the significance of these patterns further, our research also involved interpretations of the observations by models, measurements of inorganic carbon in sea water, and of CO2 in air near growing land plants.

  14. Economic and Physical Modeling of Land Use in GCAM 3.0 and an Application to Agricultural Productivity, Land, and Terrestrial Carbon

    SciTech Connect (OSTI)

    Wise, Marshall A.; Calvin, Katherine V.; Kyle, G. Page; Luckow, Patrick; Edmonds, James A.

    2014-09-01

    We explore the impact of changes in agricultural productivity on global land use and terrestrial carbon using the new agriculture and land use modeling approach developed for Global Change Assessment Model (GCAM) version 3.0. This approach models economic land use decisions with regional, physical, and technological specificity while maintaining economic and physical integration with the rest of the GCAM model. Physical land characteristics and quantities are tracked explicitly, and crop production practices are modeled discretely to facilitate coupling with physical models. Economic land allocation is modeled with non-linear functions in a market equilibrium rather than through a constrained optimization. In this paper, we explore three scenarios of future agriculture productivity in all regions of the globe over this century, ranging from a high growth to a zero growth level. The higher productivity growth scenario leads to lower crop prices, increased production of crops in developing nations, preservation of global forested lands and lower terrestrial carbon emissions. The scenario with no productivity improvement results in higher crop prices, an expansion of crop production in the developed world, loss of forested lands globally, and higher terrestrial carbon emissions.

  15. Produced water discharges to the Gulf of Mexico: Background information for ecological risk assessments

    SciTech Connect (OSTI)

    Meinhold, A.F.; Holtzman, S.; DePhillips, M.P.

    1996-06-01

    This report reviews ecological risk assessment concepts and methods; describes important biological resources in the Gulf of Mexico of potential concern for produced water impacts; and summarizes data available to estimate exposure and effects of produced water discharges. The emphasis is on data relating to produced water discharges in the central and western Gulf of Mexico, especially in Louisiana. Much of the summarized data and cited literature are relevant to assessments of impacts in other regions. Data describing effects on marine and estuarine fishes, mollusks, crustaceans and benthic invertebrates are emphasized. This review is part of a series of studies of the health and ecological risks from discharges of produced water to the Gulf of Mexico. These assessments will provide input to regulators in the development of guidelines and permits, and to industry in the use of appropriate discharge practices.

  16. Over-winter ecology of Oncorhynchus nerka in the Sawtooth Valley Lakes

    SciTech Connect (OSTI)

    Steinhart, G.B.; Wurtsbaugh, W.A.

    1996-05-01

    Included in this section of the report on limnology of Lakes in the Snake River Plain are descriptions of winter limnological conditions and kokanee growth characteristics from 1993 to 1995. The winter is usually a very harsh period for animals, and little is know about the over-winter ecology os sockeye salmon. They are active a temperatures below 4 F. The chapter discusses methods and results. 14 figs, 4 tabs.

  17. The ecological relevance of transport in waste disposal systems in Western Europe

    SciTech Connect (OSTI)

    Salhofer, Stefan Schneider, Felicitas; Obersteiner, Gudrun

    2007-07-01

    With the development of modern waste management systems in Western Europe, a remarkable increase in the distances for waste transportation has been observed. The question thus arises whether recycling with longer transport distances is ecologically advantageous or whether disposal without recycling is to be preferred. This situation was analysed using selected product and waste streams. This included refrigerators, paper, polyethylene films and expanded polystyrene. For each of these streams, a life cycle analysis was conducted with an emphasis on waste transport. The system boundaries were set in terms of the generation of waste to recycling or landfilling. The comparison included several scenarios with recycling and different transport distances. Landfilling was used as the reference scenario. The results obtained demonstrated how transport distances influence the ecological benefit of recycling. In the case of expanded polystyrene, the ecological boundaries are reached in practical situations, while with other materials these boundaries are far from being attained. In these cases, more complex and elaborate collection schemes, such as kerbside collection, which is economically convenient and shows the highest collection rates, can also be recommended.

  18. Determination of ecologically vital groundwaters at selected sites in the Formerly Utilized Sites Remedial Action Program

    SciTech Connect (OSTI)

    Vinikour, W.S.; Yin, S.C.L.

    1989-08-01

    The US Department of Energy is classifying groundwaters at sites in its Formerly Utilized Sites Remedial Action Program (FUSRAP). Of particular concern is the potential presence of groundwaters that are highly vulnerable to contamination and that are either (1) irreplaceable sources of drinking water or (2) ecologically vital. Conditions at nine FUSRAP sites were evaluated to determine if ecologically vital groundwaters are present. The sites evaluated were Wayne Interim Storage Site, Maywood Interim Storage Site, and Middlesex Sampling Plant in New Jersey; Ashland 2 Site, Seaway Industrial Park, Colonie Interim storage Site, and Niagara Falls Storage Site in New York; and the St. Louis Airport Site and Hazelwood Interim Storage Site in Missouri. The analyses indicated that groundwaters are vulnerable to contamination at all but two of the sites -- the Ashland 2 and Seaway Industrial Park sites in New York. Groundwater discharge points were identified within a 2-mile radius (i.e., the classification review area) of all of the sites. No ecologically vital groundwater areas exist in the vicinities of any of the nine FUSRAP sites evaluated. 35 refs., 17 figs.

  19. Ecological compensation: From general guidance and expertise to specific proposals for road developments

    SciTech Connect (OSTI)

    Villarroya, Ana; Puig, Jordi

    2014-02-15

    The main scientific bibliography addressing the rationale behind ecological compensation is reviewed in order to examine general guidelines. This contains interesting general guidance on how to implement compensation, and provides the basis for future developments in compensation practice. On this basis, we propose a further step in compensation practice, advancing compensation proposals or rules for specific kinds of projects and contexts, focusing on road projects in the Spanish Environmental Impact Assessment (EIA). Three main residual impacts of roads are identified which usually remain uncompensated for: the loss of natural and semi-natural land use, the increase in emissions resulting from any new road, and the fragmentation, severance or barrier effect on the landscape and its wildlife. To counteract these, four proposals, or “rules”, are advanced: conservation of natural and semi-natural land use area, conservation of dominant plant species physiognomy, compensation for emissions, and the rule of positive defragmentation. -- Highlights: • Ecological compensation theory does not specify guidelines for types of projects. • EIA practitioners lack valuable specific guidance on how to implement compensation. • Specific guidance for road project ecological compensation is proposed. • Compensation proposals should have in mind present-day compensation practice level. • Specific ways to compensate for habitat loss, emissions, and fragmentation are shown.

  20. Unlocking Short Read Sequencing for Metagenomics

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Rodrigue, Sébastien; Materna, Arne C.; Timberlake, Sonia C.; Blackburn, Matthew C.; Malmstrom, Rex R.; Alm, Eric J.; Chisholm, Sallie W.; Gilbert, Jack Anthony

    2010-07-28

    We describe an experimental and computational pipeline yielding millions of reads that can exceed 200 bp with quality scores approaching that of traditional Sanger sequencing. The method combines an automatable gel-less library construction step with paired-end sequencing on a short-read instrument. With appropriately sized library inserts, mate-pair sequences can overlap, and we describe the SHERA software package that joins them to form a longer composite read.

  1. Metagenomic Profiling Reveals Lignocellulose Degrading System...

    Office of Scientific and Technical Information (OSTI)

    Language: English Subject: 99 GENERAL AND MISCELLANEOUS; WOOD; HEMICELLULOSE; FUNCTIONALS Asian longhorned beetle; wood; hemicellulose; nutrient-acquisition; insect gut; microbial; ...

  2. MOWII Webinar: The ECO TLP, an Economical and Ecologically Sound Tension Leg Platform for Deep Water Wind Farms

    Broader source: Energy.gov [DOE]

    Join the Maine Ocean and Wind industry Initiative (MOWII) for a free webinar that describes the components and installation process of economical and ecologically sound tension leg platforms for...

  3. Ecological risk assessment of elemental pollution in sediment from Tunku Abdul Rahman National Park, Sabah

    SciTech Connect (OSTI)

    Elias, Md Suhaimi; Hamzah, Mohd Suhaimi; Rahman, Shamsiah Ab; Salim, Nazaratul Ashifa Abdullah; Siong, Wee Boon; Sanuri, Ezwiza

    2014-02-12

    Eleven (11) surface sediment samples were collected from Tunku Abdul Rahman National Park, Sabah. The neutron activation analysis (NAA) and inductively coupled plasma-mass spectrometry (ICP-MS) techniques were applied for the determinations metal contents and their distributions in sediment samples. The results shown that Arsenic (As) concentrations are enriched at all sampling stations except for station TAR 09, with enrichment factor (EF) values ranged from 1.1 to 7.2. The elements such as Cd, Cr, Sb and U showed enrichment at a few stations and other elements (Cr, Cu, Pb, Th, Zn) shown as background levels in all stations. Degrees of contamination in this study were calculated base on concentrations of six elements (As, Cd, Cr, Cu, Pb, and Zn). TAR 11 station can be categorized as very high degree of contamination with degree of contamination value of 43.2. TAR 07 station can be categorized as a considerable degree of contamination (contamination value of 16.9). Six stations (TAR 01, 03, 04, 05, 06, 08, 10) showed moderate degree of contamination, with contamination values ranging from 8.0 to 16.0. TAR 02 and TAR 09 stations showed low degree of contaminations (< 8.0). TAR 11 showed very high ecological risk index (R{sub I}) with RI value is 916. TAR 07 and TAR 10 showed moderate ecological risk index with R{sub I} value 263 and 213, respectively. Other stations showed low ecological risk with RI values ranging from 42.3 to 117 (< 150). Very high ecological risk index could give an adverse effect to the benthic organism. The data obtained from the enrichment factor, degree of contamination and ecological risk index provided vital information, which can be used for future comparison. Information from the present study will be useful to the relevant government agencies and authorities in preparing preventive action to control direct discharge of heavy metals from industries, agro-base activities and domestic waste to the rivers and the sea.

  4. Ecological Studies

    Office of Legacy Management (LM)

    Studies Book 1 Rulison Animal (and Fish) Printout . . Results g4-..* 9%- mc,-y----T. . , ... RULISON COLORADO ANIMAL RESULTS COLO FI-1-FISH 54024604505860075438 04 26 70. 0.170 KG ...

  5. Ecology's OUO

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The information contained in this e-mail message may be privileged, confidential and ... please limlt dissemination in order to preserve its privilege and confidential nature. ...

  6. Ecological economizer

    SciTech Connect (OSTI)

    Peterson, E.M.

    1992-06-16

    This patent describes an engine economizer system adapted to supply an internal combustion engine with a heated air and water vapor mixture. It comprises a containment vessel, the vessel having: water level control means, an engine coolant fluid circuit, an engine lubricant circuit, an elongated air passage, air disbursement means, a water reservoir, air filter means, a vacuum aspiration port, and engine induction means associated with one of the carburetor and intake manifold and adapted to draw in the heated air and water vapor mixture by means of a hose connection to the aspiration port.

  7. Global patterns and controls of soil organic carbon dynamics as simulated by multiple terrestrial biosphere models. Current status and future directions

    SciTech Connect (OSTI)

    Tian, Hanqin; Lu, Chaoqun; Yang, Jia; Banger, Kamaljit; Huntzinger, Deborah N.; Schwalm, Christopher R.; Michalak, A. M.; Cook, Robert B.; Ciais, Philippe; Hayes, Daniel J.; Huang, Maoyi; Ito, Akihiko; Jain, Atul K.; Lei, Huimin; Mao, Jiafu; Pan, Shufen; Post, W. M.; Peng, Shushi; Poulter, Benjamin; Ren, Wei; Ricciuto, Daniel M.; Schaefer, Kevin; Shi, Xiaoying; Tao, Bo; Wang, Weile; Wei, Yaxing; Yang, Qichun; Zhang, Bowen; Zeng, Ning

    2015-06-05

    Soil is the largest organic carbon (C) pool of terrestrial ecosystems, and loss from soil accounts for a large pro portion of land-atmosphere C exchange. Due to large pool size and variable residence time from years to millennia, even small changes in soil organic C(SOC) have substantial effects on the terrestrial C budget, thereby affecting atmospheric carbon dioxide (CO2)concentration and climate change. In the past decades, a wide variety of studies have been conducted to quantify global SOC stocks and soil exchange with the atmosphere through site measurements, inventories, and empirical/process-based modeling. However, these estimates are highly uncertain and identifying major driving forces controlling soil C storage and fluxes remains a key research challenge his study has compiled century-long (1901-2010)estimates of SOC storage and heterotrophic respiration (Rh) from ten terrestrial biosphere models (TBMs) in the Multi-scale Synthesis and Terrestrial Model Intercomparison Project (MsTMIP) and two observation based datasets. The ten-TBM ensemble shows that global SOC estimate range from 4 to 2111 Pg C (1 Pg = 1015g) with a median value of 1158 Pg C33 in 2010. Modeling approach estimates a broad range of Rh from 35 to 69 Pg C yr-1 with a median value of 51Pg C yr-1 during 200–2010. The largest uncertainty in SOC stocks exists in the 40–65°N latitude band while Rh differences are the largest in the tropics. All the models agreed that climate and land use changes have decreased SOC stocks while elevated CO2 and atmospheric nitrogen deposition have increased SOC stocks though the response varied significantly among models. Model representations of temperature and moisture sensitivity,nutrient limitation and land use partially explain the divergent estimates of global SOC stocks and soil fluxes in this study. In addition, major sources of uncertainty from model estimation include exclusion of SOC storage in

  8. Global patterns and controls of soil organic carbon dynamics as simulated by multiple terrestrial biosphere models: Current status and future directions

    SciTech Connect (OSTI)

    Tian, Hanqin; Lu, Chaoqun; Yang, Jia; Banger, Kamaljit; Huntzinger, Deborah N.; Schwalm, Christopher R.; Michalak, Anna M.; Cook, Robert; Ciais, Philippe; Hayes, Daniel; Huang, Maoyi; Ito, Akihiko; Jain, Atul K.; Lei, Huimin; Mao, Jiafu; Pan, Shufen; Post, Wilfred M.; Peng, Shushi; Poulter, Benjamin; Ren, Wei; Ricciuto, Daniel; Schaefer, Kevin; Shi, Xiaoying; Tao, Bo; Wang, Weile; Wei, Yaxing; Yang, Qichun; Zhang, Bowen; Zeng, Ning

    2015-06-05

    Soil is the largest organic carbon (C) pool of terrestrial ecosystems, and C loss from soil accounts for a large proportion of land-atmosphere C exchange. Therefore, a small change in soil organic C (SOC) can affect atmospheric carbon dioxide (CO₂) concentration and climate change. In the past decades, a wide variety of studies have been conducted to quantify global SOC stocks and soil C exchange with the atmosphere through site measurements, inventories, and empirical/process-based modeling. However, these estimates are highly uncertain, and identifying major driving forces controlling soil C dynamics remains a key research challenge. This study has compiled century-long (1901–2010) estimates of SOC storage and heterotrophic respiration (Rh) from 10 terrestrial biosphere models (TBMs) in the Multi-scale Synthesis and Terrestrial Model Intercomparison Project and two observation-based data sets. The 10 TBM ensemble shows that global SOC estimate ranges from 425 to 2111 Pg C (1 Pg = 10¹⁵ g) with a median value of 1158 Pg C in 2010. The models estimate a broad range of Rh from 35 to 69 Pg C yr⁻¹ with a median value of 51 Pg C yr⁻¹ during 2001–2010. The largest uncertainty in SOC stocks exists in the 40–65°N latitude whereas the largest cross-model divergence in Rh are in the tropics. The modeled SOC change during 1901–2010 ranges from –70 Pg C to 86 Pg C, but in some models the SOC change has a different sign from the change of total C stock, implying very different contribution of vegetation and soil pools in determining the terrestrial C budget among models. The model ensemble-estimated mean residence time of SOC shows a reduction of 3.4 years over the past century, which accelerate C cycling through the land biosphere. All the models agreed that climate and land use changes decreased SOC stocks, while elevated atmospheric CO₂ and nitrogen deposition over intact ecosystems increased SOC stocks—even though the responses varied significantly

  9. Global patterns and controls of soil organic carbon dynamics as simulated by multiple terrestrial biosphere models: Current status and future directions

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Tian, Hanqin; Lu, Chaoqun; Yang, Jia; Banger, Kamaljit; Huntzinger, Deborah N.; Schwalm, Christopher R.; Michalak, Anna M.; Cook, Robert; Ciais, Philippe; Hayes, Daniel; et al

    2015-06-05

    Soil is the largest organic carbon (C) pool of terrestrial ecosystems, and C loss from soil accounts for a large proportion of land-atmosphere C exchange. Therefore, a small change in soil organic C (SOC) can affect atmospheric carbon dioxide (CO₂) concentration and climate change. In the past decades, a wide variety of studies have been conducted to quantify global SOC stocks and soil C exchange with the atmosphere through site measurements, inventories, and empirical/process-based modeling. However, these estimates are highly uncertain, and identifying major driving forces controlling soil C dynamics remains a key research challenge. This study has compiled century-longmore » (1901–2010) estimates of SOC storage and heterotrophic respiration (Rh) from 10 terrestrial biosphere models (TBMs) in the Multi-scale Synthesis and Terrestrial Model Intercomparison Project and two observation-based data sets. The 10 TBM ensemble shows that global SOC estimate ranges from 425 to 2111 Pg C (1 Pg = 10¹⁵ g) with a median value of 1158 Pg C in 2010. The models estimate a broad range of Rh from 35 to 69 Pg C yr⁻¹ with a median value of 51 Pg C yr⁻¹ during 2001–2010. The largest uncertainty in SOC stocks exists in the 40–65°N latitude whereas the largest cross-model divergence in Rh are in the tropics. The modeled SOC change during 1901–2010 ranges from –70 Pg C to 86 Pg C, but in some models the SOC change has a different sign from the change of total C stock, implying very different contribution of vegetation and soil pools in determining the terrestrial C budget among models. The model ensemble-estimated mean residence time of SOC shows a reduction of 3.4 years over the past century, which accelerate C cycling through the land biosphere. All the models agreed that climate and land use changes decreased SOC stocks, while elevated atmospheric CO₂ and nitrogen deposition over intact ecosystems increased SOC stocks—even though the responses varied

  10. The ecological evaluation of surface water outfalls at a manufacturing plant in New Jersey

    SciTech Connect (OSTI)

    Harman, C.R.; Gilchrist, W.

    1995-12-31

    Historic metal machining operations at a manufacturing plant in northern New Jersey had resulted in the contamination of three surface water outfalls leading from the plant to a second-order stream used for trout fishing. The outfalls were fed by a combination of non-contact cooling water, stormwater runoff and groundwater infiltration. The outfalls ranged in length from 180 meters to 600 meters. All three of the outfalls pass through forested wetland areas and contained emergent wetland pockets. The ecological evaluation consisted of the collection of sediment samples to evaluate the extent of chemical contamination and the evaluation of the biological integrity of a portion of the surface water outfalls. Additionally, an ecological characterization of the surrounding habitat was prepared. Sediment sampling indicated elevated concentrations of antimony, cadmium, chromium, copper, lead, mercury, nickel, silver, and zinc. Nickel concentrations were the most significant, with concentrations ranging up to 9,850 mg/kg. PCB concentrations ranged between 0.45 mg/kg and 6.4 mg/kg. Elevated concentrations of metals and PCBs were detected to a sediment depth of 45 centimeters. To evaluate the potential for biological impacts from the metals in the sediments, a modified Rapid Bioassessment Protocol 1 evaluation was conducted on the macroinvertebrate population. The results of the evaluation indicated a very sparse macroinvertebrate community. Those organisms that were identified were typical of highly contaminated surface water system. The surrounding wetland systems appeared to be unaffected by the outfall contamination. Based on the results of the first phase of the ecological evaluation, a program of additional sediment sampling and further biological evaluation was prepared.

  11. Nano-Scale Secondary Ion Mass Spectrometry - A new analytical tool in biogeochemistry and soil ecology

    SciTech Connect (OSTI)

    Herrmann, A M; Ritz, K; Nunan, N; Clode, P L; Pett-Ridge, J; Kilburn, M R; Murphy, D V; O'Donnell, A G; Stockdale, E A

    2006-10-18

    Soils are structurally heterogeneous across a wide range of spatio-temporal scales. Consequently, external environmental conditions do not have a uniform effect throughout the soil, resulting in a large diversity of micro-habitats. It has been suggested that soil function can be studied without explicit consideration of such fine detail, but recent research has indicated that the micro-scale distribution of organisms may be of importance for a mechanistic understanding of many soil functions. Due to a lack of techniques with adequate sensitivity for data collection at appropriate scales, the question 'How important are various soil processes acting at different scales for ecological function?' is challenging to answer. The nano-scale secondary ion mass spectrometer (NanoSIMS) represents the latest generation of ion microprobes which link high-resolution microscopy with isotopic analysis. The main advantage of NanoSIMS over other secondary ion mass spectrometers is the ability to operate at high mass resolution, whilst maintaining both excellent signal transmission and spatial resolution ({approx}50 nm). NanoSIMS has been used previously in studies focusing on presolar materials from meteorites, in material science, biology, geology and mineralogy. Recently, the potential of NanoSIMS as a new tool in the study of biophysical interfaces in soils has been demonstrated. This paper describes the principles of NanoSIMS and discusses the potential of this tool to contribute to the field of biogeochemistry and soil ecology. Practical considerations (sample size and preparation, simultaneous collection of isotopes, mass resolution, isobaric interference and quantification of the isotopes of interest) are discussed. Adequate sample preparation avoiding biases in the interpretation of NanoSIMS data due to artifacts and identification of regions-of interest are of most concerns in using NanoSIMS as a new tool in biogeochemistry and soil ecology. Finally, we review the areas of

  12. Implementation of basic studies in the ecological restoration of surface-mined land

    SciTech Connect (OSTI)

    Tischew, S.; Kirmer, A.

    2007-06-15

    This paper focuses on attempts to encourage a new state of the art in the ecological restoration of surface-mined land in Germany. On most of these sites, the application of traditional recultivation methods often destroys valuable ecological potential by leveling of the surface, ameliorating of nutrient-poor substrates, and seeding or planting of species not suited to the present habitat conditions. Many studies have shown that even highly disturbed ecosystems, such as large mining areas, can regenerate spontaneously over long-term periods. Colonization processes were influenced by the availability of diaspore sources as well as the suitability of sites for establishment. The predictability of succession could be improved by the identification of switch points in successional pathways depending on age and conditions of the sites. Based on the developmental potential, orientation by nature and biodiversity are selected as main targets for priority areas for nature conservation in mining sites. On priority areas restoration measures must be restricted to the use of near-natural methods (e.g., application of fresh, diaspore-rich plant clipping material, dumping of overburden with seed bank and vegetative propagules, seeding of site-specific, local seed mixtures) that are very successful in preventing erosion and accelerating vegetation development. Despite the success of these methods, the transfer of knowledge between scientists, practitioners, and administrative organizations has proved to be insufficient. Therefore, one of the main tasks in ecological restoration must be the inclusion of all stakeholders involved in decision-making processes and the establishment of a network of excellence to enhance the exchange of knowledge.

  13. Literature Review on the Effects of Prescription Fire on theEcology of Site 300

    SciTech Connect (OSTI)

    Preston, R

    2011-03-14

    Lawrence Livermore National Laboratory has historically conducted prescription burns across approximately 2,000 acres of Site 300 on an annual basis to safeguard test facilities and operations from the risk of wildfire encroachment. Prescription burns began in 1960, and although fire frequency varies among the designated burn areas, all have been burned at least once. A patchwork of native perennial grassland communities and associated special-status plant and animal populations occur onsite in many areas that have been receiving these treatments. Because the size and locations of prescription burns may shift in coming years, an evaluation is warranted to determine how these shifts may affect listed biota, including rare plants, and the distinct ecological conditions present on the site. This report presents the results of a literature review conducted by ICF International (ICF) to collect basic information on native perennial grasslands in California, the influence of fire on these grasslands, and management tools for restoring and maintaining them. The objective of this study was to review the scientific literature on California native grasslands and summarize the current state of knowledge pertaining to the possible effects -- both beneficial and detrimental -- of prescribed fire on the ecology of Site 300. The results of this review are intended to inform future management practices that may be carried out at Site 300 to maintain the plant and wildlife communities and to ensure that the ecological conditions benefit the special-status species that inhabit the Site. This review is also intended to identify a study approach to investigate changes over the next 10 years in the burned areas and in areas where burning will be discontinued.

  14. Study of the Role of Terrestrial Processes in the Carbon Cycle Based on Measurements of the Abundance and Isotopic Composition of Atmospheric CO2

    SciTech Connect (OSTI)

    Piper, Stephen C; Keeling, Ralph F

    2012-01-03

    The main objective of this project was to continue research to develop carbon cycle relationships related to the land biosphere based on remote measurements of atmospheric CO2 concentration and its isotopic ratios 13C/12C, 18O/16O, and 14C/12C. The project continued time-series observations of atmospheric carbon dioxide and isotopic composition begun by Charles D. Keeling at remote sites, including Mauna Loa, the South Pole, and eight other sites. Using models of varying complexity, the concentration and isotopic measurements were used to study long-term change in the interhemispheric gradients in CO2 and 13C/12C to assess the magnitude and evolution of the northern terrestrial carbon sink, to study the increase in amplitude of the seasonal cycle of CO2, to use isotopic data to refine constraints on large scale changes in isotopic fractionation which may be related to changes in stomatal conductance, and to motivate improvements in terrestrial carbon cycle models. The original proposal called for a continuation of the new time series of 14C measurements but subsequent descoping to meet budgetary constraints required termination of measurements in 2007.

  15. RADIATION DOSE ASSESSMENT FOR THE BIOTA OF TERRESTRIAL ECOSYSTEMS IN THE SHORELINE ZONE OF THE CHERNOBYL NUCLEAR POWER PLANT COOLING POND

    SciTech Connect (OSTI)

    Farfan, E.; Jannik, T.

    2011-10-01

    Radiation exposure of the biota in the shoreline area of the Chernobyl Nuclear Power Plant Cooling Pond was assessed to evaluate radiological consequences from the decommissioning of the Cooling Pond. The article addresses studies of radioactive contamination of the terrestrial faunal complex and radionuclide concentration ratios in bodies of small birds, small mammals, amphibians, and reptiles living in the area. The data were used to calculate doses to biota using the ERICA Tool software. Doses from {sup 90}Sr and {sup 137}Cs were calculated using the default parameters of the ERICA Tool and were shown to be consistent with biota doses calculated from the field data. However, the ERICA dose calculations for plutonium isotopes were much higher (2-5 times for small mammals and 10-14 times for birds) than the doses calculated using the experimental data. Currently, the total doses for the terrestrial biota do not exceed maximum recommended levels. However, if the Cooling Pond is allowed to drawdown naturally and the contaminants of the bottom sediments are exposed and enter the biological cycle, the calculated doses to biota may exceed the maximum recommended values. The study is important in establishing the current exposure conditions such that a baseline exists from which changes can be documented following the lowering of the reservoir water. Additionally, the study provided useful radioecological data on biota concentration ratios for some species that are poorly represented in the literature.

  16. U.S. Regional Association of the International Association for Landscape Ecology Annual Meeting

    Broader source: Energy.gov [DOE]

    The U.S. Regional Association of the International Association for Landscape Ecology Annual Meeting will be held April 3–7, 2016 in Asheville, North Carolina. The theme of the meeting is “Landscape Change,” and it will gather landscape ecologists to discuss the interactions between humans and the environment. Bioenergy Technologies Office (BETO) Sustainability Technology Manager Kristen Johnson will be giving presentations on BETO activities as part of two symposia, “Reshaping Landscapes: Bioenergy and Biodiversity II” and “Opportunities and Barriers for Sustainable Bioenergy.”

  17. Ecological evaluation of proposed dredged material from Winyah Bay, South Carolina

    SciTech Connect (OSTI)

    Ward, J.A.; Gardiner, W.W.; Pinza, M.R.; Word, J.Q.

    1993-10-01

    The navigational channels of Winyah Bay, Georgetown Harbor, South Carolina require dredging to enable normal shipping traffic to use these areas. Before dredging, environmental assessments must be conducted to determine the suitability of this dredged sediment for unconfined, open-water disposal. The Charleston, South Carolina District Office of the US Army Corps of Engineers (USACE) requested that the Battelle/Marine Science Laboratory (MSL) collect sediment samples and conduct the required physical/chemical, toxicological, and bioaccumulation evaluations as required in the 1991 Implementation Manual. This report is intended to provide information required to address potential ecological effects of the Entrance Channel and Inner Harbor sediments proposed disposal in the ocean.

  18. Radionuclide Concentrations in Terrestrial Vegetation and Soil Samples On and Around the Hanford Site, 1971 Through 2008

    SciTech Connect (OSTI)

    Simmons, Mary Ann; Poston, Ted M.; Fritz, Brad G.; Bisping, Lynn E.

    2011-07-29

    utilized onsite, but as one moves to unindustrialized areas on the site, surrounding buffer areas and perimeter location into the more distant sites, concentrations of these radionuclides approach background and cannot be distinguished from fallout activity. More importantly, concentrations in soil and vegetation samples did not exceed environmental benchmark concentrations, and associated exposure to human and ecological receptors were well below levels that are demonstratively hazardous to human health and the environment.

  19. Risk assessment for the Waste Technologies Industries (WTI) hazardous waste incineration facility (East Liverpool, Ohio). Volume 6. Screening ecological risk assessment

    SciTech Connect (OSTI)

    1997-05-01

    The Screening Ecological Risk Assessment (SERA) includes an evaluation of available biotic information from the site vicinity to provide a preliminary description of potential ecological receptors (e.g., rare, threatened and endangered species; migratory birds; and important game species), and important ecological habitats (e.g., wetland areas). A conceptual site model is developed that describe show stressors associated with the WTI facility might affect the ecological components in the surrounding environment through the development and evaluation of specific ecological endpoints. Finally, an estimate of the potential for current and/or future adverse impacts to the biotic component of the environment is provided, based on the integration of potential exposures of ecological receptors to WTI emissions and toxicological threshold values.

  20. Data Archive of the Harvard Forest, a Long Term Ecological Research (LTER) Site

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Since 1907 research and education have been the mission of the Harvard Forest is one of the oldest and most intensively studied forests in North America. Located in Petersham, Massachusetts, its 3000 acres of land have been a center of research and education since 1907. The Long Term Ecological Research (LTER) program, established in 1988 and funded by the National Science Foundation, provides a framework for much of this activity. An understanding of forest responses to natural and human disturbance and environmental change over broad spatial and temporal scales pulls together research topics including biodiversity studies, the effects of invasive organisms, large experiments and permanent plot studies, historical and retrospective studies, soil nutrient dynamics, and plant population and community ecological interactions. Major research in forest-atmosphere exchange, hydrology, and regional studies places the work in regional and global context, aided by modeling tools. Conservation and management research and linkages to policy have been part of the Forest since its beginning, and the approaches used in New England can often apply to international studies. [Copied from http://harvardforest.fas.harvard.edu/research.html] In addition to more than 150 datasets, the Visual Information Access system at Harvard University Library makes nearly 900 images pertaining to Harvard Forest research available online to the public.

  1. The Gut Microbiota of Rural Papua New Guineans: Composition, Diversity Patterns, and Ecological Processes

    SciTech Connect (OSTI)

    Martínez, Inés; Stegen, James C.; Maldonado-Gómez, Maria X.; Eren, A. Murat; Siba, Peter M.; Greenhill, Andrew R.; Walter, Jens

    2015-04-01

    Comparisons between the fecal microbiota of humans from industrialized and non-industrialized communities indicate a pronounced impact of westernization on the diversity and composition of the human gut microbiota. However, the exact consequences of westernization on community characteristics are still insufficiently understood, and the ecological processes that drive differences have not been elucidated. Here we have compared the fecal microbiota of adults from two non-industrialized regions in Papua New Guinea (PNG) with that of United States (US) residents. Papua New Guineans harbor communities with greater bacterial diversity but lower inter-individual variation. Although the fecal microbiota in PNG and US was largely dominated by shared bacterial lineages, the relative abundance of 25 families, 45 genera, and 230 species-level OTUs differed, and 47 core OTUs in PNG were undetectable in US residents. To gain insight into the ecological mechanisms that cause the observed differences, we quantified community assembly processes in PNG and US microbiomes using a null modeling approach. This analysis demonstrated a significant higher rate of bacterial dispersal in PNG and divergent selective environments in the US. Interestingly, equivalent findings were obtained for other datasets comparing industrialized and non-industrialized microbiomes. Overall, the findings demonstrate a dominant role for microbial dispersal in shaping the human gut microbiota in non-industrialized societies, and point to differential selection pressures across individuals as a major factor shaping microbiomes associated with modern lifestyle.

  2. Ecological distribution and population physiology defined by proteomics in a natural microbial community

    SciTech Connect (OSTI)

    Muller, R; Denef, Vincent; Kalnejals, Linda; Suttle, K Blake; Thomas, Brian; Wilmes, P; Smith, Richard L.; Nordstrom, D Kirk; McCleskey, R Blaine; Shah, Manesh B; Verberkmoes, Nathan C; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2010-01-01

    An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems.We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism s metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ

  3. Ecological survey of M-Field, Edgewood Area Aberdeen Proving Ground, Maryland

    SciTech Connect (OSTI)

    Downs, J.L.; Eberhardt, L.E.; Fitzner, R.E.; Rogers, L.E.

    1991-12-01

    An ecological survey was conducted on M-Field, at the Edgewood Area, Aberdeen Proving Ground, Maryland. M-Field is used routinely to test army smokes and obscurants, including brass flakes, carbon fibers, and fog oils. The field has been used for testing purposes for the past 40 years, but little documented history is available. Under current environmental regulations, the test field must be assessed periodically to document the presence or potential use of the area by threatened and endangered species. The M-Field area is approximately 370 acres and is part of the US Army's Edgewood Area at Aberdeen Proving Ground in Harford County, Maryland. The grass-covered field is primarily lowlands with elevations from about 1.0 to 8 m above sea level, and several buildings and structures are present on the field. The ecological assessment of M-Field was conducted in three stages, beginning with a preliminary site visit in May to assess sampling requirements. Two field site visits were made June 3--7, and August 12--15, 1991, to identify the biota existing on the site. Data were gathered on vegetation, small mammals, invertebrates, birds, large mammals, amphibians, and reptiles.

  4. Ecological survey of M-Field, Edgewood Area Aberdeen Proving Ground, Maryland

    SciTech Connect (OSTI)

    Downs, J.L.; Eberhardt, L.E.; Fitzner, R.E.; Rogers, L.E.

    1991-12-01

    An ecological survey was conducted on M-Field, at the Edgewood Area, Aberdeen Proving Ground, Maryland. M-Field is used routinely to test army smokes and obscurants, including brass flakes, carbon fibers, and fog oils. The field has been used for testing purposes for the past 40 years, but little documented history is available. Under current environmental regulations, the test field must be assessed periodically to document the presence or potential use of the area by threatened and endangered species. The M-Field area is approximately 370 acres and is part of the US Army`s Edgewood Area at Aberdeen Proving Ground in Harford County, Maryland. The grass-covered field is primarily lowlands with elevations from about 1.0 to 8 m above sea level, and several buildings and structures are present on the field. The ecological assessment of M-Field was conducted in three stages, beginning with a preliminary site visit in May to assess sampling requirements. Two field site visits were made June 3--7, and August 12--15, 1991, to identify the biota existing on the site. Data were gathered on vegetation, small mammals, invertebrates, birds, large mammals, amphibians, and reptiles.

  5. USDOE study: Human health and ecological risk assessment for produced water discharges

    SciTech Connect (OSTI)

    Meinhold, A.F.; Holtzman, S.; DePhillips, M.; Hamilton, L.D.

    1994-12-31

    Produced water generated during the production of oil and gas can contain high concentrations of radionuclides, organics and heavy metals. There are concerns about potential human health and ecological impacts from the discharge of these contaminants to the Gulf of Mexico. Data collected in the United States Department of Energy (USDOE) field study are being used in a series of human health and ecological risk assessments. These assessments will support scientifically-based regulation and risk management. This presentation: summarizes risk assessments performed for produced water discharges; describes how uncertainties in these assessments are guiding data collection efforts in the USDOE field study; and outlines ongoing risk assessment studies. In these studies, risk assessment is treated as an iterative process. An initial screening-level assessment is performed to identify important contaminants, transport and exposure pathways, and parameters. These intermediate results are used to guide data collection efforts and refinements to the analysis. At this stage in the analysis, risk is described in terms of probabilities; the uncertainties in each measured or modeled parameter are considered explicitly.

  6. The Gut Microbiota of Rural Papua New Guineans: Composition, Diversity Patterns, and Ecological Processes

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Martínez, Inés; Stegen, James C.; Maldonado-Gómez, Maria X.; Eren, A. Murat; Siba, Peter M.; Greenhill, Andrew R.; Walter, Jens

    2015-04-01

    Comparisons between the fecal microbiota of humans from industrialized and non-industrialized communities indicate a pronounced impact of westernization on the diversity and composition of the human gut microbiota. However, the exact consequences of westernization on community characteristics are still insufficiently understood, and the ecological processes that drive differences have not been elucidated. Here we have compared the fecal microbiota of adults from two non-industrialized regions in Papua New Guinea (PNG) with that of United States (US) residents. Papua New Guineans harbor communities with greater bacterial diversity but lower inter-individual variation. Although the fecal microbiota in PNG and US was largelymore » dominated by shared bacterial lineages, the relative abundance of 25 families, 45 genera, and 230 species-level OTUs differed, and 47 core OTUs in PNG were undetectable in US residents. To gain insight into the ecological mechanisms that cause the observed differences, we quantified community assembly processes in PNG and US microbiomes using a null modeling approach. This analysis demonstrated a significant higher rate of bacterial dispersal in PNG and divergent selective environments in the US. Interestingly, equivalent findings were obtained for other datasets comparing industrialized and non-industrialized microbiomes. Overall, the findings demonstrate a dominant role for microbial dispersal in shaping the human gut microbiota in non-industrialized societies, and point to differential selection pressures across individuals as a major factor shaping microbiomes associated with modern lifestyle.« less

  7. Ecological Forecasting in Chesapeake Bay: Using a Mechanistic-Empirical Modelling Approach

    SciTech Connect (OSTI)

    Brown, C. W.; Hood, Raleigh R.; Long, Wen; Jacobs, John M.; Ramers, D. L.; Wazniak, C.; Wiggert, J. D.; Wood, R.; Xu, J.

    2013-09-01

    The Chesapeake Bay Ecological Prediction System (CBEPS) automatically generates daily nowcasts and three-day forecasts of several environmental variables, such as sea-surface temperature and salinity, the concentrations of chlorophyll, nitrate, and dissolved oxygen, and the likelihood of encountering several noxious species, including harmful algal blooms and water-borne pathogens, for the purpose of monitoring the Bay's ecosystem. While the physical and biogeochemical variables are forecast mechanistically using the Regional Ocean Modeling System configured for the Chesapeake Bay, the species predictions are generated using a novel mechanistic empirical approach, whereby real-time output from the coupled physical biogeochemical model drives multivariate empirical habitat models of the target species. The predictions, in the form of digital images, are available via the World Wide Web to interested groups to guide recreational, management, and research activities. Though full validation of the integrated forecasts for all species is still a work in progress, we argue that the mechanisticempirical approach can be used to generate a wide variety of short-term ecological forecasts, and that it can be applied in any marine system where sufficient data exist to develop empirical habitat models. This paper provides an overview of this system, its predictions, and the approach taken.

  8. GIS Framework for Large River Geomorphic Classification to Aid in the Evaluation of Flow-Ecology Relationships

    SciTech Connect (OSTI)

    Vernon, Christopher R.; Arntzen, Evan V.; Richmond, Marshall C.; McManamay, R. A.; Hanrahan, Timothy P.; Rakowski, Cynthia L.

    2013-02-01

    Assessing the environmental benefits of proposed flow modification to large rivers provides invaluable insight into future hydropower project operations and relicensing activities. Providing a means to quantitatively define flow-ecology relationships is integral in establishing flow regimes that are mutually beneficial to power production and ecological needs. To compliment this effort an opportunity to create versatile tools that can be applied to broad geographic areas has been presented. In particular, integration with efforts standardized within the ecological limits of hydrologic alteration (ELOHA) is highly advantageous (Poff et al. 2010). This paper presents a geographic information system (GIS) framework for large river classification that houses a base geomorphic classification that is both flexible and accurate, allowing for full integration with other hydrologic models focused on addressing ELOHA efforts. A case study is also provided that integrates publically available National Hydrography Dataset Plus Version 2 (NHDPlusV2) data, Modular Aquatic Simulation System two-dimensional (MASS2) hydraulic data, and field collected data into the framework to produce a suite of flow-ecology related outputs. The case study objective was to establish areas of optimal juvenile salmonid rearing habitat under varying flow regimes throughout an impounded portion of the lower Snake River, USA (Figure 1) as an indicator to determine sites where the potential exists to create additional shallow water habitat. Additionally, an alternative hydrologic classification useable throughout the contiguous United States which can be coupled with the geomorphic aspect of this framework is also presented. This framework provides the user with the ability to integrate hydrologic and ecologic data into the base geomorphic aspect of this framework within a geographic information system (GIS) to output spatiotemporally variable flow-ecology relationship scenarios.

  9. GIS Framework for Large River Geomorphic Classification to Aid in the Evaluation of Flow-Ecology Relationships

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    2296 Prepared for the U.S. Department of Energy under Contract DE-AC05-76RL01830 GIS Framework for Large River Geomorphic Classification to Aid in the Evaluation of Flow-Ecology Relationships CR Vernon EV Arntzen MC Richmond RA McManamay 1 TP Hanrahan CL Rakowski February 2013 PNNL-22296 GIS Framework for Large River Geomorphic Classification to Aid in the Evaluation of Flow-Ecology Relationships CR Vernon EV Arntzen MC Richmond RA McManamay 1 TP Hanrahan CL Rakwoski February 2013 Prepared for

  10. U.S. Department of Energy - Washington State Department of Ecology - U.S. Environmental Protection Agency

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Washington State Department of Ecology - U.S. Environmental Protection Agency 300 Area 100-B,C 100-KW & KE 100-N 100-D & DR 100-H 100-F 400 Area (FFTF) 200 West Area 200 East Area Changes Proposed to the Schedule for Cleaning Up Hanford's Plutonium Finishing Plant U.S. Department of Energy * U.S. Environmental Protection Agency * Washington State Department of Ecology Fact Sheet of its buildings over the next 14 years. There are 15 additional actions being proposed. Some of these actions

  11. Giving Back: Collaborations with Others in Ecological Studies on the Nevada National Security Site

    SciTech Connect (OSTI)

    Scott A. Wade; Kathryn S. Knapp; Cathy A. Wills

    2013-02-24

    Formerly named the Nevada Test Site, the Nevada National Security Site (NNSS) was the historical site for nuclear weapons testing from the 1950s to the early 1990s. The site was renamed in 2010 to reflect the diversity of nuclear, energy, and homeland security activities now conducted at the site. Biological and ecological programs and research have been conducted on the site for decades to address the impacts of radiation and to take advantage of the relatively undisturbed and isolated lands for gathering basic information on the occurrence and distribution of native plants and animals. Currently, the Office of the Assistant Manager for Environmental Management of the U.S. Department of Energy (DOE), National Nuclear Security Administration Nevada Site Office (NNSA/NSO) oversees the radiological biota monitoring and ecological compliance programs on the NNSS. The top priority of these programs are compliance with federal and state regulations. They focus on performing radiological dose assessments for the public who reside near the NNSS and for populations of plants and animals on the NNSS and in protecting important species and habitat from direct impacts of mission activities. The NNSS serves as an invaluable outdoor laboratory. The geographic and ecological diversity of the site offers researchers many opportunities to study human influences on ecosystems. NNSA/NSO has pursued collaborations with outside agencies and organizations to be able to conduct programs and studies that enhance radiological biota monitoring and ecosystem preservation when budgets are restrictive, as well as to provide valuable scientific information to the human health and natural resource communities at large. NNSA/NSO is using one current collaborative study to better assess the potential dose to the off-site public from the ingestion of game animals, the most realistic pathway for off-site public exposure at this time from radionuclide contamination on the NNSS. A second

  12. ON THE EFFECT OF GIANT PLANETS ON THE SCATTERING OF PARENT BODIES OF IRON METEORITE FROM THE TERRESTRIAL PLANET REGION INTO THE ASTEROID BELT: A CONCEPT STUDY

    SciTech Connect (OSTI)

    Haghighipour, Nader; Scott, Edward R. D.

    2012-04-20

    In their model for the origin of the parent bodies of iron meteorites, Bottke et al. proposed differentiated planetesimals, formed in 1-2 AU during the first 1.5 Myr, as the parent bodies, and suggested that these objects and their fragments were scattered into the asteroid belt as a result of interactions with planetary embryos. Although viable, this model does not include the effect of a giant planet that might have existed or been growing in the outer regions. We present the results of a concept study where we have examined the effect of a planetary body in the orbit of Jupiter on the early scattering of planetesimals from the terrestrial region into the asteroid belt. We integrated the orbits of a large battery of planetesimals in a disk of planetary embryos and studied their evolutions for different values of the mass of the planet. Results indicate that when the mass of the planet is smaller than 10 M{sub Circled-Plus }, its effects on the interactions among planetesimals and planetary embryos are negligible. However, when the planet mass is between 10 and 50 M{sub Circled-Plus }, simulations point to a transitional regime with {approx}50 M{sub Circled-Plus} being the value for which the perturbing effect of the planet can no longer be ignored. Simulations also show that further increase of the mass of the planet strongly reduces the efficiency of the scattering of planetesimals from the terrestrial planet region into the asteroid belt. We present the results of our simulations and discuss their possible implications for the time of giant planet formation.

  13. Ecological Monitoring and Compliance Program Fiscal/Calendar Year 2004 Report

    SciTech Connect (OSTI)

    Bechtel Nevada

    2005-03-01

    The Ecological Monitoring and Compliance program, funded through the U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office, monitors the ecosystem of the Nevada Test Site and ensures compliance with laws and regulations pertaining to Nevada Test Site biota. This report summarizes the program's activities conducted by Bechtel Nevada during the Fiscal Year 2004 and the additional months of October, November, and December 2004, reflecting a change in the monitoring period to a calendar year rather than a fiscal year as reported in the past. This change in the monitoring period was made to better accommodate information required for the Nevada Test Site Environmental Report, which reports on a calendar year rather than a fiscal year. Program activities included: (1) biological surveys at proposed construction sites, (2) desert tortoise compliance, (3) ecosystem mapping and data management, (4) sensitive species and unique habitat monitoring, (5) habitat restoration monitoring, and (6) biological monitoring at the Hazardous Materials Spill Center.

  14. A Theoretical Reassessment of Microbial Maintenance and Implications for Microbial Ecology Modeling

    SciTech Connect (OSTI)

    Wang, Gangsheng; Post, Wilfred M

    2012-01-01

    We attempted to reconcile three microbial maintenance models (Herbert, Pirt, and Compromise) through a critical reassessment. We provided a rigorous proof that the true growth yield coefficient (YG) is the ratio of the specific maintenance rate (a in Herbert) to the maintenance coefficient (m in Pirt). Other findings from this study include: (1) the Compromise model is identical to the Herbert for computing microbial growth and substrate consumption, but it expresses the dependence of maintenance on both microbial biomass and substrate; (2) the maximum specific growth rate in the Herbert ( max,H) is higher than those in the other two models ( max,P and max,C), and the difference is the physiological maintenance factor (mq = a); and (3) the overall maintenance coefficient (mT) is more sensitive to mq than to the specific growth rate ( G) and YG. Our critical reassessment of microbial maintenance provides a new approach for quantifying some important components in soil microbial ecology models.

  15. Ecological effects of a major oil spill on Panamanian coastal marine communities

    SciTech Connect (OSTI)

    Jackson, J.B.C.; Cubit, J.D.; Keller, B.D.; Batista, V.; Burns, K.; Caffey, H.M.; Caldwell, R.L.; Garrity, S.D.; Getter, C.D.; Gonzalez, C.; Guzman, H.M.; Kaufmann, K.W.; Knap, A.H.; Levings, S.C.; Marshall, M.J.; Steger, R.; Thompson, R.C.; Weil, E. )

    1989-01-06

    In 1986 more than 8 million liters of crude oil spilled into a complex region of mangroves, seagrasses, and coral reefs just east of the Caribbean entrance to the Panama Canal. This was the largest recorded spill into coastal habitats in the tropical Americas. Many populations of plants and animals in both oiled and unoiled sites had been studied previously, thereby providing an unprecedented measure of ecological variation before the spill. Documentation of the spread of oil and its biological effects begun immediately. Intertidal mangroves, seagrasses, algae, and associated invertebrates were covered by oil and died soon after. More surprisingly, there was also extensive mortality of shallow subtidal reef corals and infauna of seagrass beds. After 1.5 years only some organisms in areas exposed to the open sea have recovered.

  16. Potential Ecological Effects of Contaminants in the Exposed Par Pond Sediments

    SciTech Connect (OSTI)

    Paller, M.H.; Wike, L.D.

    1996-08-01

    Sediment and small mammal samples were collected from the exposed sediments of Par Pond in early 1995, shortly before the reservoir was refilled after a 4-year drawdown. Sampling was confined to elevations between 58 and 61 meters (190 and 200 feet) above mean sea level, which includes the sediments likely to be exposed if the Par Pond water level is permitted to fluctuate naturally. Both soil and small mammal samples were analyzed for a number of radionuclides and metals. Some of the soil samples were also analyzed for organic contaminants. The objective of the study was to determine if contaminant levels in the Par Pond sediments were high enough to cause deleterious ecological effects.

  17. Ecological and biomedical effects of effluents from near-term electric vehicle storage battery cycles

    SciTech Connect (OSTI)

    Not Available

    1980-05-01

    An assessment of the ecological and biomedical effects due to commercialization of storage batteries for electric and hybrid vehicles is given. It deals only with the near-term batteries, namely Pb/acid, Ni/Zn, and Ni/Fe, but the complete battery cycle is considered, i.e., mining and milling of raw materials, manufacture of the batteries, cases and covers; use of the batteries in electric vehicles, including the charge-discharge cycles; recycling of spent batteries; and disposal of nonrecyclable components. The gaseous, liquid, and solid emissions from various phases of the battery cycle are identified. The effluent dispersal in the environment is modeled and ecological effects are assessed in terms of biogeochemical cycles. The metabolic and toxic responses by humans and laboratory animals to constituents of the effluents are discussed. Pertinent environmental and health regulations related to the battery industry are summarized and regulatory implications for large-scale storage battery commercialization are discussed. Each of the seven sections were abstracted and indexed individually for EDB/ERA. Additional information is presented in the seven appendixes entitled; growth rate scenario for lead/acid battery development; changes in battery composition during discharge; dispersion of stack and fugitive emissions from battery-related operations; methodology for estimating population exposure to total suspended particulates and SO/sub 2/ resulting from central power station emissions for the daily battery charging demand of 10,000 electric vehicles; determination of As air emissions from Zn smelting; health effects: research related to EV battery technologies. (JGB)

  18. Pacific Northwest Laboratory annual report for 1983 to the DOE Office of Energy Research. Part 2. Ecological sciences

    SciTech Connect (OSTI)

    Vaughan, B.E.

    1984-02-01

    The 1983 annual report highlights research in five areas funded by the Ecological Sciences Division of the Office of Energy Research. The five areas include: western semi-arid ecosystems; marine sciences; mobilization fate and effects of chemical wastes; radionuclide fate and effects; and statistical and quantitative research. The work was accomplished under 19 individual projects. Individual projects are indexed separately.

  19. Lawrence Livermore National Laboratory interests and capabilities for research on the ecological effects of global climatic and atmospheric change

    SciTech Connect (OSTI)

    Amthor, J.S.; Houpis, J.L.; Kercher, J.R.; Ledebuhr, A.; Miller, N.L.; Penner, J.E.; Robison, W.L.; Taylor, K.E.

    1994-09-01

    The Lawrence Livermore National Laboratory (LLNL) has interests and capabilities in all three types of research that must be conducted in order to understand and predict effects of global atmospheric and climatic (i.e., environmental) changes on ecological systems and their functions (ecosystem function is perhaps most conveniently defined as mass and energy exchange and storage). These three types of research are: (1) manipulative experiments with plants and ecosystems; (2) monitoring of present ecosystem, landscape, and global exchanges and pools of energy, elements, and compounds that play important roles in ecosystem function or the physical climate system, and (3) mechanistic (i.e., hierarchic and explanatory) modeling of plant and ecosystem responses to global environmental change. Specific experimental programs, monitoring plans, and modeling activities related to evaluation of ecological effects of global environmental change that are of interest to, and that can be carried out by LLNL scientists are outlined. Several projects have the distinction of integrating modeling with empirical studies resulting in an Integrated Product (a model or set of models) that DOE or any federal policy maker could use to assess ecological effects. The authors note that any scheme for evaluating ecological effects of atmospheric and climatic change should take into account exceptional or sensitive species, in particular, rare, threatened, or endangered species.

  20. DOE responses to Ecology review comments for ``Sampling and analysis plans for the 100-D Ponds voluntary remediation project``

    SciTech Connect (OSTI)

    NONE

    1996-12-31

    The Sampling and Analysis Plan describes the sampling and analytical activities which will be performed to support closure of the 100-D Ponds at the Hanford Reservation. This report contains responses by the US Department of Energy to Ecology review for ``Sampling and Analysis Plan for the 100-D Ponds Voluntary Remediation Project.``