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Title: The Study of Microbial Environmental Processes Related to the Natural Attenuation of Uranium at the Rifle Site using Systems-level Biology

Abstract

Microbes exist in communities in the environment where they are fundamental drivers of global carbon, nutrient and metal cycles. In subsurface environments, they possess significant metabolic potential to affect these global cycles including the transformation of radionuclides. This study examined the influence of microbial communities in sediment zones undergoing biogeochemical cycling of carbon, nutrients and metals including natural attenuation of uranium. This study examined the relationship of both the microbiota (taxonomy) and their metabolic capacity (function) in driving carbon, nutrient and metal cycles including uranium reduction at the Department of Energy (DOE) Rifle Integrated Field Research Challenge (RIFRC). Objectives of this project were: 1) to apply systems-level biology through application of ‘metaomics’ approaches (collective analyses of whole microbial community DNA, RNA and protein) to the study of microbial environmental processes and their relationship to C, N and metals including the influence of microbial communities on uranium contaminant mobility in subsurface settings undergoing natural attenuation, 2) improve methodologies for data generation using metaomics (collectively metagenomics, metatranscriptomics and proteomics) technologies and analysis and interpretation of that data and 3) use the data generated from these studies towards microbial community-scale metabolic modeling. The strategy for examining these subsurface microbial communities was to generatemore » sequence reads from microbial community DNA (metagenomics or whole genome shotgun sequencing (WGS)) and RNA (metatranscriptomcs or RNAseq) and protein information using proteomics. Results were analyzed independently and through computational modeling. Overall, the community model generated information on the microbial community structure that was observed using metaomic approaches at RIFRC sites and thus provides an important framework for continued community modeling development. The model as created is capable of predicting the response of the community structure in changing environments such as anoxic/oxic conditions or limitations by carbon or nutrients. The ability to more accurately model these responses is critical to understanding carbon and energy flows in an ecosystem is critical towards improving our ability to make predictions that can be used to design more efficient remediation and management strategies, and better understand the implications of environmental perturbations on these ecosystems.« less

Authors:
 [1];  [2];  [3]
  1. J. Craig Venter Inst. (JCVI), Rockville, MD (United States)
  2. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
  3. Univ. of Toronto, ON (Canada)
Publication Date:
Research Org.:
J. Craig Venter Inst., Rockville, MD (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1358080
Report Number(s):
FinalreportDOE-JCVI-SC-0006837
DOE Contract Number:
SC0006837
Resource Type:
Technical Report
Resource Relation:
Related Information: Conferences, Publications and Products2013 Genomic Science Annual Contractor-Grantee Meeting2014 Genomic Science Annual Contractor-Grantee Meeting2015 Genomic Science Annual Contractor-Grantee Meeting2016 Genomic Science Annual Contractor-Grantee MeetingCell Factories & Biosustainability Technologies for Cell Factory Construction Conference, Copenhagen, Denmark, 2015Department of Plant and Environmental Sciences (PLEN), University of Copenhagen, Denmark 2015International Environmental Omics Synthesis Conference (iEOS), St. Andrews, Scotland, 2015Phytobiomes 2015, Washington DC 2015EU-US Working Group on Environmental Biotechnology Short-CourseMethé BA, Li K, Zhao J, Lipton M, Mahadevan R. The Application of Ecosystem Modeling atSubsurface Sites to Study Carbon, Nutrient and Metal Cycling in Microbial Communities. In prep.Li K, Shrivastava S, Stockwell TB. (2015). "Degenerate Primer Design for Highly Variable Genomes". PCR Primer Design, 103-115.Goll J, Rusch DB, Tanenbaum DM, Thiagarajan M, Li K, Methé BA and Yooseph S (2010). "METAREP: JCVI metagenomics reports: an open source tool for high-performance comparative metagenomics". Bioinformatics. 26(20):2631-2.Improvements to Corbata software tools at Github
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Methe, Barbara, Lipton, Mary, and Mahadevan, Krishna. The Study of Microbial Environmental Processes Related to the Natural Attenuation of Uranium at the Rifle Site using Systems-level Biology. United States: N. p., 2016. Web. doi:10.2172/1358080.
Methe, Barbara, Lipton, Mary, & Mahadevan, Krishna. The Study of Microbial Environmental Processes Related to the Natural Attenuation of Uranium at the Rifle Site using Systems-level Biology. United States. doi:10.2172/1358080.
Methe, Barbara, Lipton, Mary, and Mahadevan, Krishna. 2016. "The Study of Microbial Environmental Processes Related to the Natural Attenuation of Uranium at the Rifle Site using Systems-level Biology". United States. doi:10.2172/1358080. https://www.osti.gov/servlets/purl/1358080.
@article{osti_1358080,
title = {The Study of Microbial Environmental Processes Related to the Natural Attenuation of Uranium at the Rifle Site using Systems-level Biology},
author = {Methe, Barbara and Lipton, Mary and Mahadevan, Krishna},
abstractNote = {Microbes exist in communities in the environment where they are fundamental drivers of global carbon, nutrient and metal cycles. In subsurface environments, they possess significant metabolic potential to affect these global cycles including the transformation of radionuclides. This study examined the influence of microbial communities in sediment zones undergoing biogeochemical cycling of carbon, nutrients and metals including natural attenuation of uranium. This study examined the relationship of both the microbiota (taxonomy) and their metabolic capacity (function) in driving carbon, nutrient and metal cycles including uranium reduction at the Department of Energy (DOE) Rifle Integrated Field Research Challenge (RIFRC). Objectives of this project were: 1) to apply systems-level biology through application of ‘metaomics’ approaches (collective analyses of whole microbial community DNA, RNA and protein) to the study of microbial environmental processes and their relationship to C, N and metals including the influence of microbial communities on uranium contaminant mobility in subsurface settings undergoing natural attenuation, 2) improve methodologies for data generation using metaomics (collectively metagenomics, metatranscriptomics and proteomics) technologies and analysis and interpretation of that data and 3) use the data generated from these studies towards microbial community-scale metabolic modeling. The strategy for examining these subsurface microbial communities was to generate sequence reads from microbial community DNA (metagenomics or whole genome shotgun sequencing (WGS)) and RNA (metatranscriptomcs or RNAseq) and protein information using proteomics. Results were analyzed independently and through computational modeling. Overall, the community model generated information on the microbial community structure that was observed using metaomic approaches at RIFRC sites and thus provides an important framework for continued community modeling development. The model as created is capable of predicting the response of the community structure in changing environments such as anoxic/oxic conditions or limitations by carbon or nutrients. The ability to more accurately model these responses is critical to understanding carbon and energy flows in an ecosystem is critical towards improving our ability to make predictions that can be used to design more efficient remediation and management strategies, and better understand the implications of environmental perturbations on these ecosystems.},
doi = {10.2172/1358080},
journal = {},
number = ,
volume = ,
place = {United States},
year = 2016,
month = 8
}

Technical Report:

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  • The U.S. Department of Energy (DOE) is cleaning up and/or monitoring large, dilute plumes contaminated by metals, such as uranium and chromium, whose mobility and solubility change with redox status. Field-scale experiments with acetate as the electron donor have stimulated metal-reducing bacteria to effectively remove uranium [U(VI)] from groundwater at the Uranium Mill Tailings Site in Rifle, Colorado. The Pacific Northwest National Laboratory and a multidisciplinary team of national laboratory and academic collaborators has embarked on a research proposed for the Rifle site, the object of which is to gain a comprehensive and mechanistic understanding of the microbial factors andmore » associated geochemistry controlling uranium mobility so that DOE can confidently remediate uranium plumes as well as support stewardship of uranium-contaminated sites. This Quality Assurance Project Plan provides the quality assurance requirements and processes that will be followed by the Rifle Integrated Field-Scale Subsurface Research Challenge Project.« less
  • The Rifle IFRC continued to make excellent progress during the last 12 months. As noted above, a key field experiment (Best Western) was performed during 2011 as a logical follow-on to the Super 8 field experiment preformed in 2010. In the Super 8 experiment, we successfully combined desorption and bioreduction and deployed a number of novel tracer techniques to enhance our ability to interpret the biogeochemistry of the experiment. In the Best Western experiment, we used the same experimental plot (Plot C) as was used for Super 8. The overarching objective of the Best Western field experiment was to comparedmore » the impacts of abiotic vs. biotic increases in alkalinity and to assess the mass of the sorbed pool of U(VI) at Rifle at the field scale. Both of these objectives were met. Preliminary analysis of the data indicate that the underlying biogeochemical data sets were obtained that will support a mechanistic understanding of the underlying processes, including remarkable insight into previously unrecognized microbial processes taking place during acetate amendment of the subsurface for a second time.« less
  • Mountain States Research and Development was contracted on March 1, 1981 to make an economic evaluation study at each of 12 abandoned uranium mill tailings sites in the western states. The objective of this work was to obtain the data necessary at each site to determine the possible revenue that could be derived from reprocessing the tailings. To accomplish this objective a drilling and sampling program was established for each site to determine the total amount of tailings and subbase material available for treatment and the amount of recoverable uranium, vanadium and molybdenum. These three metals were selected due tomore » their common occurrence in uranium ores and common extractability in the leaching process. Laboratory leaching was then conducted on the samples obtained to determine the extractability of each of these metals and the optimum plant process to be applied. As the metal contents were generally low and represented mineral that had not been leached during previous processing, the economic evaluation is limited to consideration of the direct capital and operating costs required in connection with processing of each respective site material. Excavating, transportation and disposal of the material from each site in an environmentally acceptable location and manner was not within the scope of this project. This report contains the results of the investigations of the New Rifle Site in Colorado.« less
  • Ford, Bacon and Davis Utah Inc. has performed an engineering assessment of the problems resulting from the existence of radioactive uranium mill tailings at Rifle, Colorado. The Phase II - Title I services include the preparation of topographic maps, the performance of core drillings and radiometric measurements sufficient to determine areas and volumes of tailings and other radium-contaminated materials, the evaluation of resulting radiation exposures of individuals and nearby populations, the investigation of site hydrology and meteorology and the evaluation and costing of alternative corrective actions. Radon gas release from the 3.1 million tons of tailings at the two Riflemore » sites, constitutes the most significant environmental impact. Windblown tailings, external gamma radiation and localized contamination of surface waters are other environmental effects. The 15 alternative remedial action options presented range from millsite decomtamination and off-site remedial action (Options I and IV), to adding various depths of stabilization cover material (Options II, V, VI, and VII), to removal of the tailings to long-term storage sites and decontamination of the present sites (Options III and VIII through XV). Cost estimates for the first 14 options range from $224,000 to $20,300,000. Option XV, estimated at $32,200,000, includes the cost for moving both Rifle tailings piles and the Grand Junction tailings pile to DeBeque for long-term storage and site decontamination after removal of the piles. Reprocessing of the tailings for uranium appears to be economically attractive at present.« less
  • Ford, Bacon and Davis Utah Inc. has performed an engineering assessment of the problems resulting from the existence of radioactive uranium mill tailings at Rifle, Colorado. The Phase II--Title I services include the preparation of topographic maps, the performance of core drillings and radiometric measurements sufficient to determine areas and volumes of tailings and other radium-contaminated materials, the evaluation of resulting radiation exposures of individuals and nearby populations, the investigation of site hydrology and meteorology and the evaluation and costing of alternative corrective actions. Radon gas release from the 3.1 million tons of tailings at the two Rifle sites, constitutesmore » the most significant environmental impact. Windblown tailings, external gamma radiation and localized contamination of surface waters are other environmental effects. The 15 alternative remedial action options presented range from millsite decontamination and off-site remedial action (Options I and IV), to adding various depths of stabilization cover material (Options II, V, VI and VII), to removal of the tailings to long-term storage sites and decontamination of the present sites (Options III and VIII through XV). Cost estimates for the first 14 options range from $224,000 to $20,300,000. Option XV, estimated at $32,200,000, includes the cost for moving both Rifle tailings piles and the Grand Junction tailings pile to DeBeque for long-term storage and site decontamination after removal of the piles. Reprocessing of the tailings for uranium appears to be economically attractive at present.« less