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Title: Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth's biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics to aquifer sediments and groundwater, and reconstruct 2,540 draft-quality, near-complete and complete strain-resolved genomes that represent the majority of known bacterial phyla as well as 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity and representing up to 36% of organisms detected in the system are used to document the distribution of pathways in coexisting organisms. Consistent with prior findings indicating metabolic handoffs in simple consortia, we find that few organisms within the community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages of organisms are selected for, altering linkages among the major biogeochemical cycles.
Authors:
 [1] ; ORCiD logo [1] ;  [1] ;  [1] ;  [1] ;  [1] ;  [1] ;  [1] ;  [2] ;  [3] ;  [3] ;  [3] ;  [3] ;  [1]
  1. Univ. of California, Berkeley, CA (United States)
  2. The Ohio State Univ., Columbus, OH (United States)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Publication Date:
Grant/Contract Number:
AC02-05CH11231
Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 7; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 58 GEOSCIENCES; element cycles; metagenomics; microbial ecology
OSTI Identifier:
1377548

Anantharaman, Karthik, Brown, Christopher T., Hug, Laura A., Sharon, Itai, Castelle, Cindy J., Probst, Alexander J., Thomas, Brian C., Singh, Andrea, Wilkins, Michael J., Karaoz, Ulas, Brodie, Eoin L., Williams, Kenneth H., Hubbard, Susan S., and Banfield, Jillian F.. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. United States: N. p., Web. doi:10.1038/ncomms13219.
Anantharaman, Karthik, Brown, Christopher T., Hug, Laura A., Sharon, Itai, Castelle, Cindy J., Probst, Alexander J., Thomas, Brian C., Singh, Andrea, Wilkins, Michael J., Karaoz, Ulas, Brodie, Eoin L., Williams, Kenneth H., Hubbard, Susan S., & Banfield, Jillian F.. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. United States. doi:10.1038/ncomms13219.
Anantharaman, Karthik, Brown, Christopher T., Hug, Laura A., Sharon, Itai, Castelle, Cindy J., Probst, Alexander J., Thomas, Brian C., Singh, Andrea, Wilkins, Michael J., Karaoz, Ulas, Brodie, Eoin L., Williams, Kenneth H., Hubbard, Susan S., and Banfield, Jillian F.. 2016. "Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system". United States. doi:10.1038/ncomms13219. https://www.osti.gov/servlets/purl/1377548.
@article{osti_1377548,
title = {Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system},
author = {Anantharaman, Karthik and Brown, Christopher T. and Hug, Laura A. and Sharon, Itai and Castelle, Cindy J. and Probst, Alexander J. and Thomas, Brian C. and Singh, Andrea and Wilkins, Michael J. and Karaoz, Ulas and Brodie, Eoin L. and Williams, Kenneth H. and Hubbard, Susan S. and Banfield, Jillian F.},
abstractNote = {The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth's biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics to aquifer sediments and groundwater, and reconstruct 2,540 draft-quality, near-complete and complete strain-resolved genomes that represent the majority of known bacterial phyla as well as 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity and representing up to 36% of organisms detected in the system are used to document the distribution of pathways in coexisting organisms. Consistent with prior findings indicating metabolic handoffs in simple consortia, we find that few organisms within the community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages of organisms are selected for, altering linkages among the major biogeochemical cycles.},
doi = {10.1038/ncomms13219},
journal = {Nature Communications},
number = ,
volume = 7,
place = {United States},
year = {2016},
month = {10}
}

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