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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. 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

  4. 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...

  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)

    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.

  10. 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.

  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. 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.

  14. 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.

  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. 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: ...

  1. 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 ...

  2. 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...

  3. 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. ; ...

  4. 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.

  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. 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.

  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. 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.

  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. 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.

  18. 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.

  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. 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

  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. 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

  5. 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

  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 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.

  13. 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.

  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. 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.

  19. 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

  20. 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.

  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. 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

  3. 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.

  4. 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.

  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

    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

  10. 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

  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. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  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. 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.

  20. 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.

  1. 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.

  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. 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.

  4. 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

  5. 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.

  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. 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.

  11. 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.

  12. 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

  13. 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/.

  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. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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).

  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. 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.

  6. 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.

  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. 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...

  9. 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...

  10. 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 ...

  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. 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

  8. 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

  9. 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

  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. 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:...

  13. 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 ...

  14. 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...

  15. 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.--.- ...

  16. 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...

  17. 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...

  18. 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

  19. 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, ...

  20. 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

  1. 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 ...

  2. 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...

  3. 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...

  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. 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

  7. 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.

  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. 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...

  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. 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...

  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. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  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. 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.

  16. 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.

  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. 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.

  19. 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

  20. 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

  1. 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

  2. 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.

  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. 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...

  6. 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...

  7. 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...

  8. 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.

  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. 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 ...