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Title: Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry

Abstract

Geothermal habitats in Yellowstone National Park (YNP) provide an unparalleled opportunity to understand the environmental factors that control the distribution of archaea in thermal habitats. Here we describe, analyze, and synthesize metagenomic and geochemical data collected from seven high-temperature sites that contain microbial communities dominated by archaea relative to bacteria. The specific objectives of the study were to use metagenome sequencing to determine the structure and functional capacity of thermophilic archaeal-dominated microbial communities across a pH range from 2.5 to 6.4 and to discuss specific examples where the metabolic potential correlated with measured environmental parameters and geochemical processes occurring in situ. Random shotgun metagenome sequence (~40–45 Mb Sanger sequencing per site) was obtained from environmental DNA extracted from high-temperature sediments and/or microbial mats and subjected to numerous phylogenetic and functional analyses. Analysis of individual sequences (e.g., MEGAN and G + C content) and assemblies from each habitat type revealed the presence of dominant archaeal populations in all environments, 10 of whose genomes were largely reconstructed from the sequence data. Analysis of protein family occurrence, particularly of those involved in energy conservation, electron transport, and autotrophic metabolism, revealed significant differences in metabolic strategies across sites consistent with differences in major geochemicalmore » attributes (e.g., sulfide, oxygen, pH). These observations provide an ecological basis for understanding the distribution of indigenous archaeal lineages across high-temperature systems of YNP.« less

Authors:
 [1];  [2];  [3];  [2];  [4];  [5];  [2];  [2];  [6];  [7];  [8]
+ Show Author Affiliations
  1. Montana State Univ., Bozeman, MT (United States). Dept. of Land Resources and Environmental Sciences; Montana State Univ., Bozeman, MT (United States). Thermal Biology Inst.
  2. Montana State Univ., Bozeman, MT (United States). Dept. of Land Resources and Environmental Sciences
  3. Technical Univ. of Denmark, Hørsholm (Denmark). Novo Nordisk Foundation Center for Biosustainability
  4. Indiana Univ., Bloomington, IN (United States). Center for Genomics and Bioinformatics
  5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  6. Montana State Univ., Bozeman, MT (United States). Thermal Biology Inst.; Montana State Univ., Bozeman, MT (United States). Dept. of Chemistry and Biochemistry
  7. Colorado School of Mines, Golden, CO (United States). Dept. of Civil and Environmental Engineering
  8. Newmont Mining Corporation, Englewood, CO (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Earth and Environmental Systems Science Division
OSTI Identifier:
1628087
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 4; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; Microbiology; archaea; thermophilic archaea and bacteria; geochemistry; phylogeny; functional genomics

Citation Formats

Inskeep, William P., Jay, Zackary J., Herrgard, Markus J., Kozubal, Mark A., Rusch, Douglas B., Tringe, Susannah G., Macur, Richard E., Jennings, Ryan deM., Boyd, Eric S., Spear, John R., and Roberto, Francisco F. Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry. United States: N. p., 2013. Web. doi:10.3389/fmicb.2013.00095.
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Inskeep, William P., Jay, Zackary J., Herrgard, Markus J., Kozubal, Mark A., Rusch, Douglas B., Tringe, Susannah G., Macur, Richard E., Jennings, Ryan deM., Boyd, Eric S., Spear, John R., & Roberto, Francisco F. Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry. United States. https://doi.org/10.3389/fmicb.2013.00095
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Inskeep, William P., Jay, Zackary J., Herrgard, Markus J., Kozubal, Mark A., Rusch, Douglas B., Tringe, Susannah G., Macur, Richard E., Jennings, Ryan deM., Boyd, Eric S., Spear, John R., and Roberto, Francisco F. Tue . "Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry". United States. https://doi.org/10.3389/fmicb.2013.00095. https://www.osti.gov/servlets/purl/1628087.
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@article{osti_1628087,
title = {Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry},
author = {Inskeep, William P. and Jay, Zackary J. and Herrgard, Markus J. and Kozubal, Mark A. and Rusch, Douglas B. and Tringe, Susannah G. and Macur, Richard E. and Jennings, Ryan deM. and Boyd, Eric S. and Spear, John R. and Roberto, Francisco F.},
abstractNote = {Geothermal habitats in Yellowstone National Park (YNP) provide an unparalleled opportunity to understand the environmental factors that control the distribution of archaea in thermal habitats. Here we describe, analyze, and synthesize metagenomic and geochemical data collected from seven high-temperature sites that contain microbial communities dominated by archaea relative to bacteria. The specific objectives of the study were to use metagenome sequencing to determine the structure and functional capacity of thermophilic archaeal-dominated microbial communities across a pH range from 2.5 to 6.4 and to discuss specific examples where the metabolic potential correlated with measured environmental parameters and geochemical processes occurring in situ. Random shotgun metagenome sequence (~40–45 Mb Sanger sequencing per site) was obtained from environmental DNA extracted from high-temperature sediments and/or microbial mats and subjected to numerous phylogenetic and functional analyses. Analysis of individual sequences (e.g., MEGAN and G + C content) and assemblies from each habitat type revealed the presence of dominant archaeal populations in all environments, 10 of whose genomes were largely reconstructed from the sequence data. Analysis of protein family occurrence, particularly of those involved in energy conservation, electron transport, and autotrophic metabolism, revealed significant differences in metabolic strategies across sites consistent with differences in major geochemical attributes (e.g., sulfide, oxygen, pH). These observations provide an ecological basis for understanding the distribution of indigenous archaeal lineages across high-temperature systems of YNP.},
doi = {10.3389/fmicb.2013.00095},
journal = {Frontiers in Microbiology},
number = ,
volume = 4,
place = {United States},
year = {Tue Jan 01 00:00:00 EST 2013},
month = {Tue Jan 01 00:00:00 EST 2013}
}
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https://doi.org/10.3389/fmicb.2013.00095
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