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Title: Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO 2 concentrations

Abstract

As in many deep underground environments, the microbial communities in subsurface high-CO 2 ecosystems remain relatively unexplored. Recent investigations based on single-gene assays revealed a remarkable variety of organisms from little studied phyla in Crystal Geyser (Utah, USA), a site where deeply sourced CO 2-saturated fluids are erupted at the surface. To provide genomic resolution of the metabolisms of these organisms, we used a novel metagenomic approach to recover 227 high-quality genomes from 150 microbial species affiliated with 46 different phylum-level lineages. Bacteria from two novel phylum-level lineages have the capacity for CO 2 fixation. Analyses of carbon fixation pathways in all studied organisms revealed that the Wood-Ljungdahl pathway and the Calvin-Benson-Bassham Cycle occurred with the highest frequency, whereas the reverse TCA cycle was little used. We infer that this, and selection for form II RuBisCOs, are adaptions to high CO 2-concentrations. However, many autotrophs can also grow mixotrophically, a strategy that confers metabolic versatility. The assignment of 156 hydrogenases to 90 different organisms suggests that H 2 is an important inter-species energy currency even under gaseous CO 2-saturation. Overall, metabolic analyses at the organism level provided insight into the biochemical cycles that support subsurface life under the extreme conditionmore » of CO 2 saturation.« less

Authors:
 [1];  [1];  [1];  [2];  [1];  [1];  [1];  [1];  [1];  [1];  [3]
  1. Department of Earth and Planetary Sciences, University of California, Berkeley 307 McCone Hall CA 94720 USA
  2. Department of Plant and Microbial Biology, University of California, Berkeley CA 94720 USA
  3. Department of Earth and Planetary Sciences, University of California, Berkeley 307 McCone Hall CA 94720 USA; Department of Environmental Science, Policy, and Management, University of California, Berkeley CA USA; Earth Science Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road Berkeley CA USA
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1567074
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Environmental Microbiology
Additional Journal Information:
Journal Volume: 19; Journal Issue: 2; Journal ID: ISSN 1462-2912
Publisher:
Wiley
Country of Publication:
United States
Language:
English

Citation Formats

Probst, Alexander J., Castelle, Cindy J., Singh, Andrea, Brown, Christopher T., Anantharaman, Karthik, Sharon, Itai, Hug, Laura A., Burstein, David, Emerson, Joanne B., Thomas, Brian C., and Banfield, Jillian F. Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations. United States: N. p., 2016. Web. doi:10.1111/1462-2920.13362.
Probst, Alexander J., Castelle, Cindy J., Singh, Andrea, Brown, Christopher T., Anantharaman, Karthik, Sharon, Itai, Hug, Laura A., Burstein, David, Emerson, Joanne B., Thomas, Brian C., & Banfield, Jillian F. Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations. United States. doi:10.1111/1462-2920.13362.
Probst, Alexander J., Castelle, Cindy J., Singh, Andrea, Brown, Christopher T., Anantharaman, Karthik, Sharon, Itai, Hug, Laura A., Burstein, David, Emerson, Joanne B., Thomas, Brian C., and Banfield, Jillian F. Thu . "Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations". United States. doi:10.1111/1462-2920.13362. https://www.osti.gov/servlets/purl/1567074.
@article{osti_1567074,
title = {Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations},
author = {Probst, Alexander J. and Castelle, Cindy J. and Singh, Andrea and Brown, Christopher T. and Anantharaman, Karthik and Sharon, Itai and Hug, Laura A. and Burstein, David and Emerson, Joanne B. and Thomas, Brian C. and Banfield, Jillian F.},
abstractNote = {As in many deep underground environments, the microbial communities in subsurface high-CO2 ecosystems remain relatively unexplored. Recent investigations based on single-gene assays revealed a remarkable variety of organisms from little studied phyla in Crystal Geyser (Utah, USA), a site where deeply sourced CO2-saturated fluids are erupted at the surface. To provide genomic resolution of the metabolisms of these organisms, we used a novel metagenomic approach to recover 227 high-quality genomes from 150 microbial species affiliated with 46 different phylum-level lineages. Bacteria from two novel phylum-level lineages have the capacity for CO2 fixation. Analyses of carbon fixation pathways in all studied organisms revealed that the Wood-Ljungdahl pathway and the Calvin-Benson-Bassham Cycle occurred with the highest frequency, whereas the reverse TCA cycle was little used. We infer that this, and selection for form II RuBisCOs, are adaptions to high CO2-concentrations. However, many autotrophs can also grow mixotrophically, a strategy that confers metabolic versatility. The assignment of 156 hydrogenases to 90 different organisms suggests that H2 is an important inter-species energy currency even under gaseous CO2-saturation. Overall, metabolic analyses at the organism level provided insight into the biochemical cycles that support subsurface life under the extreme condition of CO2 saturation.},
doi = {10.1111/1462-2920.13362},
journal = {Environmental Microbiology},
number = 2,
volume = 19,
place = {United States},
year = {2016},
month = {7}
}

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Works referenced in this record:

Autotrophic carbon fixation in archaea
journal, May 2010

  • Berg, Ivan A.; Kockelkorn, Daniel; Ramos-Vera, W. Hugo
  • Nature Reviews Microbiology, Vol. 8, Issue 6, p. 447-460
  • DOI: 10.1038/nrmicro2365

MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004

  • Edgar, R. C.
  • Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
  • DOI: 10.1093/nar/gkh340

Search and clustering orders of magnitude faster than BLAST
journal, August 2010


KEGG: Kyoto Encyclopedia of Genes and Genomes
journal, January 2000

  • Kanehisa, Minoru; Goto, Susumu
  • Nucleic Acids Research, Vol. 28, Issue 1, p. 27-30
  • DOI: 10.1093/nar/28.1.27