Comparison of multiple ecogenomics methods for determining ecosystem function in uranium-contaminated environments Metadata

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  • Main Title Comparison of multiple ecogenomics methods for determining ecosystem function in uranium-contaminated environments


  • Author: Hazen, T.C.
    Creator Type: Personal
  • Author: Dehal, P.
    Creator Type: Personal
  • Author: Arkin, A.P.
    Creator Type: Personal
  • Author: Fields, M.W.
    Creator Type: Personal
  • Author: Keller, M.
    Creator Type: Personal
  • Author: Zhou, J.
    Creator Type: Personal
  • Author: Andersen, G.L.
    Creator Type: Personal
  • Author: Brodie, E.L.
    Creator Type: Personal
  • Author: Wyborski, D.L.
    Creator Type: Personal
  • Author: Abulencia, C.B.
    Creator Type: Personal
  • Author: Hemme, ChrisL.
    Creator Type: Personal
  • Author: Gentry, T.
    Creator Type: Personal
  • Author: Watson, D.B.
    Creator Type: Personal
  • Author: Richardson, P.
    Creator Type: Personal


  • Sponsor: United States. Department of Energy. Office of Biological and Environmental Research.
    Contributor Type: Organization
    Contributor Info: USDOE Director. Office of Science. Office of Biological and Environmental Research


  • Name: Lawrence Berkeley National Laboratory
    Place of Publication: Berkeley, California
    Additional Info: Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA (United States)


  • Creation: 2007-01-10


  • English


  • Content Description: Background: Bioremediation may offer the only feasiblestrategy for the nearly intractable problem of metal and radionuclidecontamination of soil and groundwater. To understand bioremediation incontaminated environments, it is critical to determine the organismspresent in these environments, analyze their responses to stressconditions, and elucidate functional position in the environment.Methods: We used multiple molecular techniques on both sediment andgroundwater to develop a better understanding of the functionalcapability and stress level within the microbial community inrelationship to over one hundred geochemical parameters. Due to the lowpH (3.5-4.5) and high contaminant levels (e.g., uranium) microbialdensities and activities were low. We used a phage polymeraseamplification system to construct large and small insert DNA libraries,performed metagenome sequencing, constructed clonal libraries of selectfunctional genes (SSU rRNA gene, nirK, nirS, amoA, pmoA, and dsrAB), useda SSU rDNA Phylochip microarray (9,000 taxa), and a functional gene array(23K genes). A complete comparison for community differences andsimilarities between the different techniques was assessed using severalbioinformatics techniques. Results: SSU rDNA analysis revealed thepresence of distinct bacterial phyla, including proteobacteria,acidobacteria, and planctomycetes along the contaminant gradient.Metagenome analysis identified many of the same organisms, and diversitywas lower in water than sediment. Analysis with functional gene arrays,phylochip, and specific probes for genes and organisms involved inbiogeochemical cycling of C, N, and S, metal resistance, stress response,and contaminant degradation suggested that the dominant species could bebiostimulated during in situ uranium reduction. Several other findings ofdifference and similarities between methods are presented. Conclusion:These systems biology field studies could be enabling for strategies toattenuate nletal and radionuclide contamination.


  • Keyword: Amplification
  • Keyword: Dna
  • Keyword: Water
  • Keyword: Sediments
  • Keyword: Genes
  • STI Subject Categories: 54
  • Keyword: Bioremediation
  • Keyword: Biology
  • Keyword: Polymerases
  • Keyword: Radioisotopes
  • Keyword: Soils
  • Keyword: Uranium
  • Keyword: Contamination
  • Keyword: Ecosystems
  • Keyword: Functionals
  • Keyword: Probes


  • Conference: Annual Meeting of the American Society forMicrobiology, Toronto, Canada, 20-24 May 2007


  • Name: Office of Scientific & Technical Information Technical Reports
    Code: OSTI


  • Name: UNT Libraries Government Documents Department
    Code: UNTGD

Resource Type

  • Article


  • Text


  • Report No.: LBNL--62430-Ext.-Abs.
  • Grant Number: DE-AC02-05CH11231
  • Office of Scientific & Technical Information Report Number: 922722
  • Archival Resource Key: ark:/67531/metadc901196