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

Hug, Laura A.; Thomas, Brian C.; Sharon, Itai; Brown, Christopher T.; Sharma, Ritin; Hettich, Robert L.; Wilkins, Michael J.; Williams, Kenneth H.; Singh, Andrea; Banfield, Jillian F.

doi:10.1111/1462-2920.12930

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

Journal Article · Wed Jul 22 00:00:00 EDT 2015 · Environmental Microbiology

DOI:https://doi.org/10.1111/1462-2920.12930· OSTI ID:1328276

Hug, Laura A. ^[1]; Thomas, Brian C. ^[1]; Sharon, Itai ^[1]; Brown, Christopher T. ^[2]; Sharma, Ritin ^[3]; Hettich, Robert L. ^[3]; Wilkins, Michael J. ^[4]; Williams, Kenneth H. ^[5]; Singh, Andrea ^[1]; Banfield, Jillian F. ^[6]

Univ. of California, Berkeley, CA (United States). Dept. of Earth and Planetary Science
Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
The Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology; The Ohio State Univ., Columbus, OH (United States). School of Earth Sciences
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Dept. of Geophysics, Division of Earth Sciences
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

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. 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. 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 of geochemical resources.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); Natural Sciences and Engineering Research Council of Canada (NSERC); Work for Others (WFO)

Grant/Contract Number:: AC05-00OR22725; AC02-05CH11231

OSTI ID:: 1328276

Alternate ID(s):: OSTI ID: 1470999

Journal Information:: Environmental Microbiology, Vol. 18, Issue 1; ISSN 1462-2912

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 115 works

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