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

Abstract

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.

Authors:
 [1];  [1];  [1];  [2];  [3];  [3];  [4];  [5];  [1];  [6]
+ Show Author Affiliations
  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:
Research Org.:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); Natural Sciences and Engineering Research Council of Canada (NSERC); Work for Others (WFO)
OSTI Identifier:
1328276
Alternate Identifier(s):
OSTI ID: 1470999
Grant/Contract Number:  
AC05-00OR22725; AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Environmental Microbiology
Additional Journal Information:
Journal Volume: 18; Journal Issue: 1; Journal ID: ISSN 1462-2912
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES

Citation Formats

Hug, Laura A., Thomas, Brian C., Sharon, Itai, Brown, Christopher T., Sharma, Ritin, Hettich, Robert L., Wilkins, Michael J., Williams, Kenneth H., Singh, Andrea, and Banfield, Jillian F. Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages. United States: N. p., 2015. Web. doi:10.1111/1462-2920.12930.
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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. Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages. United States. https://doi.org/10.1111/1462-2920.12930
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Hug, Laura A., Thomas, Brian C., Sharon, Itai, Brown, Christopher T., Sharma, Ritin, Hettich, Robert L., Wilkins, Michael J., Williams, Kenneth H., Singh, Andrea, and Banfield, Jillian F. Wed . "Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages". United States. https://doi.org/10.1111/1462-2920.12930. https://www.osti.gov/servlets/purl/1328276.
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@article{osti_1328276,
title = {Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages},
author = {Hug, Laura A. and Thomas, Brian C. and Sharon, Itai and Brown, Christopher T. and Sharma, Ritin and Hettich, Robert L. and Wilkins, Michael J. and Williams, Kenneth H. and Singh, Andrea and Banfield, Jillian F.},
abstractNote = {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.},
doi = {10.1111/1462-2920.12930},
journal = {Environmental Microbiology},
number = 1,
volume = 18,
place = {United States},
year = {Wed Jul 22 00:00:00 EDT 2015},
month = {Wed Jul 22 00:00:00 EDT 2015}
}
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https://doi.org/10.1111/1462-2920.12930
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Works referenced in this record:

Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices
journal, April 2013

Autotrophic Carbon Dioxide Fixation via the Calvin-Benson-Bassham Cycle by the Denitrifying Methanotroph “Candidatus Methylomirabilis oxyfera”
journal, February 2014

  • Rasigraf, Olivia; Kool, Dorien M.; Jetten, Mike S. M.
  • Applied and Environmental Microbiology, Vol. 80, Issue 8
  • DOI: 10.1128/AEM.04199-13

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
journal, April 2012

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
journal, May 2012

Denitrifying Bacteria Isolated from Terrestrial Subsurface Sediments Exposed to Mixed-Waste Contamination
journal, March 2010

  • Green, S. J.; Prakash, O.; Gihring, T. M.
  • Applied and Environmental Microbiology, Vol. 76, Issue 10
  • DOI: 10.1128/AEM.03069-09

Enrichment and Molecular Detection of Denitrifying Methanotrophic Bacteria of the NC10 Phylum
journal, March 2009

  • Ettwig, K. F.; van Alen, T.; van de Pas-Schoonen, K. T.
  • Applied and Environmental Microbiology, Vol. 75, Issue 11
  • DOI: 10.1128/AEM.00067-09

Accurate, multi-kb reads resolve complex populations and detect rare microorganisms
journal, February 2015

  • Sharon, Itai; Kertesz, Michael; Hug, Laura A.
  • Genome Research, Vol. 25, Issue 4
  • DOI: 10.1101/gr.183012.114

Acetate Availability and its Influence on Sustainable Bioremediation of Uranium-Contaminated Groundwater
journal, June 2011

Unusual biology across a group comprising more than 15% of domain Bacteria
journal, June 2015

  • Brown, Christopher T.; Hug, Laura A.; Thomas, Brian C.
  • Nature, Vol. 523, Issue 7559
  • DOI: 10.1038/nature14486

Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation
journal, August 2014

  • Qin, W.; Amin, S. A.; Martens-Habbena, W.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 34
  • DOI: 10.1073/pnas.1324115111

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization
journal, August 2012

  • Sharon, I.; Morowitz, M. J.; Thomas, B. C.
  • Genome Research, Vol. 23, Issue 1
  • DOI: 10.1101/gr.142315.112

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
journal, May 2013

  • Albertsen, Mads; Hugenholtz, Philip; Skarshewski, Adam
  • Nature Biotechnology, Vol. 31, Issue 6
  • DOI: 10.1038/nbt.2579

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla
journal, September 2012

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
journal, January 2009

Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria
journal, September 2009

  • Martens-Habbena, Willm; Berube, Paul M.; Urakawa, Hidetoshi
  • Nature, Vol. 461, Issue 7266
  • DOI: 10.1038/nature08465

Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer
journal, March 2014

  • Wrighton, Kelly C.; Castelle, Cindy J.; Wilkins, Michael J.
  • The ISME Journal, Vol. 8, Issue 7
  • DOI: 10.1038/ismej.2013.249

Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers
journal, September 2011

  • Mussmann, M.; Brito, I.; Pitcher, A.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 40
  • DOI: 10.1073/pnas.1106427108

IDPicker 2.0: Improved Protein Assembly with High Discrimination Peptide Identification Filtering
journal, August 2009

  • Ma, Ze-Qiang; Dasari, Surendra; Chambers, Matthew C.
  • Journal of Proteome Research, Vol. 8, Issue 8
  • DOI: 10.1021/pr900360j

The complete genome sequence for putative H 2 - and S-oxidizer C andidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome : Complete genome of
journal, April 2014

  • Handley, Kim M.; Bartels, Daniela; O'Loughlin, Edward J.
  • Environmental Microbiology, Vol. 16, Issue 11
  • DOI: 10.1111/1462-2920.12453

Community-wide analysis of microbial genome sequence signatures
journal, January 2009

  • Dick, Gregory J.; Andersson, Anders F.; Baker, Brett J.
  • Genome Biology, Vol. 10, Issue 8
  • DOI: 10.1186/gb-2009-10-8-r85

Basic local alignment search tool
journal, October 1990

  • Altschul, Stephen F.; Gish, Warren; Miller, Webb
  • Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410
  • DOI: 10.1016/S0022-2836(05)80360-2

Characterization of an Archaeal Medium-Chain Acyl Coenzyme A Synthetase from Methanosarcina acetivorans
journal, September 2010

  • Meng, Y.; Ingram-Smith, C.; Cooper, L. L.
  • Journal of Bacteriology, Vol. 192, Issue 22
  • DOI: 10.1128/JB.00600-10

MUSCLE: a multiple sequence alignment method with reduced time and space complexity
journal, August 2004

Diverse uncultivated ultra-small bacterial cells in groundwater
journal, February 2015

  • Luef, Birgit; Frischkorn, Kyle R.; Wrighton, Kelly C.
  • Nature Communications, Vol. 6, Issue 1
  • DOI: 10.1038/ncomms7372

The changing landscape of microbial biodiversity exploration and its implications for systematics
journal, June 2015

  • Hedlund, Brian P.; Dodsworth, Jeremy A.; Staley, James T.
  • Systematic and Applied Microbiology, Vol. 38, Issue 4
  • DOI: 10.1016/j.syapm.2015.03.003

Minimus: a fast, lightweight genome assembler
journal, January 2007

  • Sommer, Daniel D.; Delcher, Arthur L.; Salzberg, Steven L.
  • BMC Bioinformatics, Vol. 8, Issue 1
  • DOI: 10.1186/1471-2105-8-64

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences
journal, August 2014

  • Yarza, Pablo; Yilmaz, Pelin; Pruesse, Elmar
  • Nature Reviews Microbiology, Vol. 12, Issue 9
  • DOI: 10.1038/nrmicro3330

KEGG for integration and interpretation of large-scale molecular data sets
journal, November 2011

  • Kanehisa, M.; Goto, S.; Sato, Y.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr988

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
journal, July 2012

  • Namiki, Toshiaki; Hachiya, Tsuyoshi; Tanaka, Hideaki
  • Nucleic Acids Research, Vol. 40, Issue 20
  • DOI: 10.1093/nar/gks678

Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea
journal, April 2010

  • Walker, C. B.; de la Torre, J. R.; Klotz, M. G.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 19
  • DOI: 10.1073/pnas.0913533107

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
journal, August 2006

Insights into the phylogeny and coding potential of microbial dark matter
journal, July 2013

  • Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander
  • Nature, Vol. 499, Issue 7459
  • DOI: 10.1038/nature12352

MyriMatch:  Highly Accurate Tandem Mass Spectral Peptide Identification by Multivariate Hypergeometric Analysis
journal, February 2007

  • Tabb, David L.; Fernando, Christopher G.; Chambers, Matthew C.
  • Journal of Proteome Research, Vol. 6, Issue 2
  • DOI: 10.1021/pr0604054

Ray Meta: scalable de novo metagenome assembly and profiling
journal, January 2012

  • Boisvert, Sébastien; Raymond, Frédéric; Godzaridis, Élénie
  • Genome Biology, Vol. 13, Issue 12
  • DOI: 10.1186/gb-2012-13-12-r122

Aquifer environment selects for microbial species cohorts in sediment and groundwater
journal, February 2015

  • Hug, Laura A.; Thomas, Brian C.; Brown, Christopher T.
  • The ISME Journal, Vol. 9, Issue 8
  • DOI: 10.1038/ismej.2015.2

Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment
journal, August 2013

  • Castelle, Cindy J.; Hug, Laura A.; Wrighton, Kelly C.
  • Nature Communications, Vol. 4, Issue 1
  • DOI: 10.1038/ncomms3120

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

Physiology and Diversity of Ammonia-Oxidizing Archaea
journal, October 2012

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008

Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla
journal, October 2013

A sand fly salivary protein acts as a neutrophil chemoattractant
journal, May 2021

  • Guimaraes-Costa, Anderson B.; Shannon, John P.; Waclawiak, Ingrid
  • Nature Communications, Vol. 12, Issue 1
  • DOI: 10.1038/s41467-021-23002-5

SPOCD1 is an essential executor of piRNA-directed de novo DNA methylation
journal, July 2020

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    • Sieber, Christian M. K.; Probst, Alexander J.; Sharrar, Allison
    • Nature Microbiology, Vol. 3, Issue 7
    • DOI: 10.1038/s41564-018-0171-1

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    • Cross, Karissa L.; Campbell, James H.; Balachandran, Manasi
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    Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei
    journal, January 2020

    • Montoliu-Nerin, Merce; Sánchez-García, Marisol; Bergin, Claudia
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    Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes
    journal, January 2018

    • Adam, Panagiotis S.; Borrel, Guillaume; Gribaldo, Simonetta
    • Proceedings of the National Academy of Sciences, Vol. 115, Issue 6
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    journal, January 2019

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    journal, August 2016

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