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Title: Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages

Nitrogen, sulfur and carbon fluxes in the terrestrial subsurface are determined by the intersecting activities of microbial community members, yet the organisms responsible are largely unknown. Metagenomic methods can identify organisms and functions, but genome recovery is often precluded by data complexity. To address this limitation, we developed subsampling assembly methods to re-construct high-quality draft genomes from complex samples. Here, we applied these methods to evaluate the interlinked roles of the most abundant organisms in biogeochemical cycling in the aquifer sediment. Community proteomics confirmed these activities. The eight most abundant organisms belong to novel lineages, and two represent phyla with no previously sequenced genome. Four organisms are predicted to fix carbon via the Calvin Benson Bassham, Wood Ljungdahl or 3-hydroxyproprionate/4-hydroxybutarate pathways. The profiled organisms are involved in the network of denitrification, dissimilatory nitrate reduction to ammonia, ammonia oxidation and sulfate reduction/oxidation, and require substrates supplied by other community members. An ammonium-oxidizing Thaumarchaeote is the most abundant community member, despite low ammonium concentrations in the groundwater. Finally, this organism likely benefits from two other relatively abundant organisms capable of producing ammonium from nitrate, which is abundant in the groundwater. Overall, dominant members of the microbial community are interconnected through exchange ofmore » geochemical resources.« less
 [1] ;  [1] ;  [1] ;  [2] ;  [3] ;  [3] ;  [4] ;  [5] ;  [1] ;  [6]
  1. Univ. of California, Berkeley, CA (United States). Dept. of Earth and Planetary Science
  2. Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  4. The Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology; The Ohio State Univ., Columbus, OH (United States). School of Earth Sciences
  5. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Dept. of Geophysics, Division of Earth Sciences
  6. Univ. of California, Berkeley, CA (United States). Dept. of Earth and Planetary Science; Univ. of California, Berkeley, CA (United States). Dept. of Environmental Science, Policy, and Management
Publication Date:
OSTI Identifier:
Grant/Contract Number:
AC05-00OR22725; AC02-05CH11231
Accepted Manuscript
Journal Name:
Environmental Microbiology
Additional Journal Information:
Journal Volume: 18; Journal Issue: 1; Journal ID: ISSN 1462-2912
Research Org:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); NSERC; ORNL work for others
Country of Publication:
United States