Metagenomes from High-Temperature Chemotrophic Systems Reveal Geochemical Controls on Microbial Community Structure and Function

Inskeep, William P.; Rusch, Douglas B.; Jay, Zackary J.; Herrgard, Markus J.; Kozubal, Mark A.; Richardson, Toby H.; Macur, Richard E.; Hamamura, Natsuko; Jennings, Ryan deM.; Fouke, Bruce W.; Reysenbach, Anna-Louise; Roberto, Frank; Young, Mark; Schwartz, Ariel; Boyd, Eric S.; Badger, Jonathan H.; Mathur, Eric J.; Ortmann, Alice C.; Bateson, Mary; Geesey, Gill; Frazier, Marvin

doi:10.1371/journal.pone.0009773

Metagenomes from High-Temperature Chemotrophic Systems Reveal Geochemical Controls on Microbial Community Structure and Function

Journal Article · Fri Mar 19 00:00:00 EDT 2010 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0009773· OSTI ID:1627402

Inskeep, William P. ^[1]; Rusch, Douglas B. ^[2]; Jay, Zackary J. ^[3]; Herrgard, Markus J. ^[4]; Kozubal, Mark A. ^[3]; Richardson, Toby H. ^[4]; Macur, Richard E. ^[3]; Hamamura, Natsuko ^[5]; Jennings, Ryan deM. ^[3]; Fouke, Bruce W. ^[6]; Reysenbach, Anna-Louise ^[5]; Roberto, Frank ^[7]; Young, Mark ^[8]; Schwartz, Ariel ^[4]; Boyd, Eric S. ^[9]; Badger, Jonathan H. ^[2]; Mathur, Eric J. ^[4]; Ortmann, Alice C. ^[10]; Bateson, Mary ^[8]; Geesey, Gill ^[9] more »

Montana State Univ., Bozeman, MT (United States). Thermal Biology Inst. and Dept. of Land Resources and Environmental Sciences; DOE/OSTI
J. Craig Venter Inst., Inc., Rockville, MD (United States)
Montana State Univ., Bozeman, MT (United States). Thermal Biology Inst. and Dept. of Land Resources and Environmental Sciences
Synthetic Genomics Inc., La Jolla, CA (United States)
Ehime Univ., Matsuyama (Japan). Center for Marine Environmental Studies
Univ. of Illinois at Urbana-Champaign, IL (United States)
Idaho National Lab. (INL), Idaho Falls, ID (United States)
Montana State Univ., Bozeman, MT (United States). Thermal Biology Institute and Department of Plant Sciences and Plant Pathology
Montana State Univ., Bozeman, MT (United States). Thermal Biology Institute and Department of Microbiology
Univ. of South Alabama, Mobile, AL (United States). Dept. of Marine Science

The Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host a variety of deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure and function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14–15,000 Sanger reads per site) was obtained for five high-temperature (>65°C) chemotrophic microbial communities sampled from geothermal springs (or pools) in Yellowstone National Park (YNP) that exhibit a wide range in geochemistry including pH, dissolved sulfide, dissolved oxygen and ferrous iron. Metagenome data revealed significant differences in the predominant phyla associated with each of these geochemical environments. Novel members of the Sulfolobales are dominant in low pH environments, while other Crenarchaeota including distantly-related Thermoproteales and Desulfurococcales populations dominate in suboxic sulfidic sediments. Several novel archaeal groups are well represented in an acidic (pH 3) Fe-oxyhydroxide mat, where a higher O₂ influx is accompanied with an increase in archaeal diversity. The presence or absence of genes and pathways important in S oxidation-reduction, H₂-oxidation, and aerobic respiration (terminal oxidation) provide insight regarding the metabolic strategies of indigenous organisms present in geothermal systems. Multiple-pathway and protein-specific functional analysis of metagenome sequence data corroborated results from phylogenetic analyses and clearly demonstrate major differences in metabolic potential across sites. The distribution of functional genes involved in electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, Fe, O₂) control microbial community structure and function in YNP geothermal springs.

View Accepted Manuscript (DOE)

Research Organization:: Idaho National Laboratory (INL), Idaho Falls, ID (United States)

Sponsoring Organization:: Montana Agricultural Experiment Station; National Aeronautics and Space Administration (NASA); National Science Foundation (NSF); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC07-05ID14517

OSTI ID:: 1627402

Journal Information:: PLoS ONE, Journal Name: PLoS ONE Journal Issue: 3 Vol. 5; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

References (62)

Aempyrum pernix K1, a strictly aerobic and hyperthermophilic archaeon, has two terminal oxidases, cytochromeBa 3 and cytochromeaa 3 Ishikawa, Ryuhei; Ishido, Yoko; Tachikawa, Atsuo Archives of Microbiology, Vol. 179, Issue 1 https://doi.org/10.1007/s00203-002-0496-1	journal	January 2002
The NT-26 cytochrome c552 and its role in arsenite oxidation Santini, Joanne M.; Kappler, Ulrike; Ward, Seamus A. Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1767, Issue 2 https://doi.org/10.1016/j.bbabio.2007.01.009	journal	February 2007
Bacterial nitrate reductases: Molecular and biological aspects of nitrate reduction González, P. J.; Correia, C.; Moura, Isabel Journal of Inorganic Biochemistry, Vol. 100, Issue 5-6 https://doi.org/10.1016/j.jinorgbio.2005.11.024	journal	May 2006
Metagenomics – the key to the uncultured microbes Streit, Wolfgang R.; Schmitz, Ruth A. Current Opinion in Microbiology, Vol. 7, Issue 5 https://doi.org/10.1016/j.mib.2004.08.002	journal	October 2004
Prokaryotic sulfur oxidation Friedrich, Cornelius G.; Bardischewsky, Frank; Rother, Dagmar Current Opinion in Microbiology, Vol. 8, Issue 3 https://doi.org/10.1016/j.mib.2005.04.005	journal	June 2005
Bacterial mercury resistance from atoms to ecosystems Barkay, Tamar; Miller, Susan M.; Summers, Anne O. FEMS Microbiology Reviews, Vol. 27, Issue 2-3 https://doi.org/10.1016/s0168-6445(03)00046-9	journal	June 2003
Occurrence, Classification, and Biological Function of Hydrogenases: An Overview Vignais, Paulette M.; Billoud, Bernard Chemical Reviews, Vol. 107, Issue 10, p. 4206-4272 https://doi.org/10.1021/cr050196r	journal	October 2007
Rapid Oxidation of Arsenite in a Hot Spring Ecosystem, Yellowstone National Park Langner, Heiko W.; Jackson, Colin R.; McDermott, Timothy R. Environmental Science & Technology, Vol. 35, Issue 16 https://doi.org/10.1021/es0105562	journal	August 2001
Dissimilatory Oxidation and Reduction of Elemental Sulfur in Thermophilic Archaea Kletzin, Arnulf; Urich, Tim; Müller, Fabian Journal of Bioenergetics and Biomembranes, Vol. 36, Issue 1, p. 77-91 https://doi.org/10.1023/b:jobb.0000019600.36757.8c	journal	February 2004
Isolation of an autotrophic ammonia-oxidizing marine archaeon Könneke, Martin; Bernhard, Anne E.; de la Torre, José R. Nature, Vol. 437, Issue 7058 https://doi.org/10.1038/nature03911	journal	September 2005
The metagenomics of soil Daniel, Rolf Nature Reviews Microbiology, Vol. 3, Issue 6 https://doi.org/10.1038/nrmicro1160	journal	June 2005
Metagenes and molecular pattern discovery using matrix factorization Brunet, J. -P.; Tamayo, P.; Golub, T. R. Proceedings of the National Academy of Sciences, Vol. 101, Issue 12 https://doi.org/10.1073/pnas.0308531101	journal	March 2004
Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment Biddle, J. F.; Fitz-Gibbon, S.; Schuster, S. C. Proceedings of the National Academy of Sciences, Vol. 105, Issue 30 https://doi.org/10.1073/pnas.0709942105	journal	July 2008
The complete genome of the crenarchaeon Sulfolobus solfataricus P2 She, Q.; Singh, R. K.; Confalonieri, F. Proceedings of the National Academy of Sciences, Vol. 98, Issue 14, p. 7835-7840 https://doi.org/10.1073/pnas.141222098	journal	June 2001
Genetic identification of a respiratory arsenate reductase Saltikov, C. W.; Newman, D. K. Proceedings of the National Academy of Sciences, Vol. 100, Issue 19 https://doi.org/10.1073/pnas.1834303100	journal	August 2003
Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum Fitz-Gibbon, S. T.; Ladner, H.; Kim, U. -J. Proceedings of the National Academy of Sciences, Vol. 99, Issue 2 https://doi.org/10.1073/pnas.241636498	journal	January 2002
Identification and Characterization of a Novel Ferric Reductase from the Hyperthermophilic Archaeon Archaeoglobus fulgidus Vadas, Alexander; Monbouquette, Harold G.; Johnson, Eric Journal of Biological Chemistry, Vol. 274, Issue 51 https://doi.org/10.1074/jbc.274.51.36715	journal	December 1999
A Membrane-bound Multienzyme, Hydrogen-oxidizing, and Sulfur-reducing Complex from the Hyperthermophilic Bacterium Aquifex aeolicus Guiral, Marianne; Tron, Pascale; Aubert, Corinne Journal of Biological Chemistry, Vol. 280, Issue 51, p. 42004-42015 https://doi.org/10.1074/jbc.m508034200	journal	October 2005
Identifying bacterial genes and endosymbiont DNA with Glimmer Delcher, Arthur L.; Bratke, Kirsten A.; Powers, Edwin C. Bioinformatics, Vol. 23, Issue 6 https://doi.org/10.1093/bioinformatics/btm009	journal	January 2007
Single Eubacterial Origin of Eukaryotic Sulfide:Quinone Oxidoreductase, a Mitochondrial Enzyme Conserved from the Early Evolution of Eukaryotes During Anoxic and Sulfidic Times Theissen, U. Molecular Biology and Evolution, Vol. 20, Issue 9 https://doi.org/10.1093/molbev/msg174	journal	May 2003
Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus Takami, Hideto; Takaki, Yoshihiro; Chee, Gab-Joo Nucleic Acids Research, Vol. 32, Issue 21 https://doi.org/10.1093/nar/gkh970	journal	January 2004
The Pfam protein families database Finn, R. D.; Tate, J.; Mistry, J. Nucleic Acids Research, Vol. 36, Issue Database https://doi.org/10.1093/nar/gkm960	journal	December 2007
Caldivirga maquilingensis gen. nov., sp. nov., a new genus of rod-shaped crenarchaeote isolated from a hot spring in the Philippines Itoh, Takashi; Suzuki, Ken-ichiro; Sanchez, Priscilla C. International Journal of Systematic and Evolutionary Microbiology, Vol. 49, Issue 3 https://doi.org/10.1099/00207713-49-3-1157	journal	July 1999
Sulfurihydrogenibium yellowstonense sp. nov., an extremely thermophilic, facultatively heterotrophic, sulfur-oxidizing bacterium from Yellowstone National Park, and emended descriptions of the genus Sulfurihydrogenibium, Sulfurihydrogenibium subterraneum and Sulfurihydrogenibium azorense Nakagawa, S.; Shtaih, Z.; Banta, A. International Journal of Systematic and Evolutionary Microbiology, Vol. 55, Issue 6 https://doi.org/10.1099/ijs.0.63708-0	journal	November 2005
Membrane-bound hydrogenase and sulfur reductase of the hyperthermophilic and acidophilic archaeon Acidianus ambivalens Laska, Simone; Lottspeich, Friedrich; Kletzin, Arnulf Microbiology, Vol. 149, Issue 9, p. 2357-2371 https://doi.org/10.1099/mic.0.26455-0	journal	September 2003
The purified SoxABCD quinol oxidase complex ofSulfolobus acidocaldariuscontains a novel haem Lübben, Mathias; Warne, Antony; Albracht, Simon P. J. Molecular Microbiology, Vol. 13, Issue 2 https://doi.org/10.1111/j.1365-2958.1994.tb00426.x	journal	July 1994
Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol de la Torre, José R.; Walker, Christopher B.; Ingalls, Anitra E. Environmental Microbiology, Vol. 10, Issue 3 https://doi.org/10.1111/j.1462-2920.2007.01506.x	journal	March 2008
Linking microbial oxidation of arsenic with detection and phylogenetic analysis of arsenite oxidase genes in diverse geothermal environments Hamamura, N.; Macur, R. E.; Korf, S. Environmental Microbiology, Vol. 11, Issue 2 https://doi.org/10.1111/j.1462-2920.2008.01781.x	journal	February 2009
Methylmercury enters an aquatic food web through acidophilic microbial mats in Yellowstone National Park, Wyoming Boyd, Eric S.; King, Susan; Tomberlin, Jeffery K. Environmental Microbiology, Vol. 11, Issue 4 https://doi.org/10.1111/j.1462-2920.2008.01820.x	journal	April 2009
Archaeal and bacterial communities in geochemically diverse hot springs of Yellowstone National Park, USA Meyer-Dombard, D. R.; Shock, E. L.; Amend, J. P. Geobiology, Vol. 3, Issue 3 https://doi.org/10.1111/j.1472-4669.2005.00052.x	journal	July 2005
Genetic analysis of Carboxydothermus hydrogenoformans carbon monoxide dehydrogenase genes cooF and cooS GonzÃ¡lez, Juan M.; Robb, Frank T. FEMS Microbiology Letters, Vol. 191, Issue 2 https://doi.org/10.1111/j.1574-6968.2000.tb09346.x	journal	October 2000
Enzymology of one-carbon metabolism in methanogenic pathways Ferry, James G. FEMS Microbiology Reviews, Vol. 23, Issue 1 https://doi.org/10.1111/j.1574-6976.1999.tb00390.x	journal	January 1999
Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and Bacteria Amend, Jan P.; Shock, Everett L. FEMS Microbiology Reviews, Vol. 25, Issue 2 https://doi.org/10.1111/j.1574-6976.2001.tb00576.x	journal	April 2001
Microbial arsenic: from geocycles to genes and enzymes Mukhopadhyay, Rita; Rosen, Barry P.; Phung, Le T. FEMS Microbiology Reviews, Vol. 26, Issue 3 https://doi.org/10.1111/j.1574-6976.2002.tb00617.x	journal	August 2002
Geomicrobiology: How Molecular-Scale Interactions Underpin Biogeochemical Systems Newman, D. K. Science, Vol. 296, Issue 5570 https://doi.org/10.1126/science.1010716	journal	May 2002
Comparative Metagenomics of Microbial Communities Tringe, S. G. Science, Vol. 308, Issue 5721 https://doi.org/10.1126/science.1107851	journal	April 2005
The Microbial Engines That Drive Earth's Biogeochemical Cycles Falkowski, P. G.; Fenchel, T.; Delong, E. F. Science, Vol. 320, Issue 5879 https://doi.org/10.1126/science.1153213	journal	May 2008
Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth Chivian, D.; Brodie, E. L.; Alm, E. J. Science, Vol. 322, Issue 5899 https://doi.org/10.1126/science.1155495	journal	October 2008
A Whole-Genome Assembly of Drosophila Myers, E. W. Science, Vol. 287, Issue 5461 https://doi.org/10.1126/science.287.5461.2196	journal	March 2000
Molecular Characterization of the Diversity and Distribution of a Thermal Spring Microbial Community by Using rRNA and Metabolic Genes Hall, Justine R.; Mitchell, Kendra R.; Jackson-Weaver, Olan Applied and Environmental Microbiology, Vol. 74, Issue 15 https://doi.org/10.1128/aem.00233-08	journal	August 2008
Metagenomic and Small-Subunit rRNA Analyses Reveal the Genetic Diversity of Bacteria, Archaea, Fungi, and Viruses in Soil Fierer, N.; Breitbart, M.; Nulton, J. Applied and Environmental Microbiology, Vol. 73, Issue 21 https://doi.org/10.1128/aem.00358-07	journal	September 2007
Hydrogenomics of the Extremely Thermophilic Bacterium Caldicellulosiruptor saccharolyticus van de Werken, H. J. G.; Verhaart, M. R. A.; VanFossen, A. L. Applied and Environmental Microbiology, Vol. 74, Issue 21, p. 6720-6729 https://doi.org/10.1128/aem.00968-08	journal	September 2008
Isolation and Distribution of a Novel Iron-Oxidizing Crenarchaeon from Acidic Geothermal Springs in Yellowstone National Park Kozubal, M.; Macur, R. E.; Korf, S. Applied and Environmental Microbiology, Vol. 74, Issue 4 https://doi.org/10.1128/aem.01200-07	journal	December 2007
Identification of Components of Electron Transport Chains in the Extremely Thermoacidophilic Crenarchaeon Metallosphaera sedula through Iron and Sulfur Compound Oxidation Transcriptomes Auernik, K. S.; Kelly, R. M. Applied and Environmental Microbiology, Vol. 74, Issue 24, p. 7723-7732 https://doi.org/10.1128/aem.01545-08	journal	October 2008
The Genome Sequence of the Metal-Mobilizing, Extremely Thermoacidophilic Archaeon Metallosphaera sedula Provides Insights into Bioleaching-Associated Metabolism Auernik, K. S.; Maezato, Y.; Blum, P. H. Applied and Environmental Microbiology, Vol. 74, Issue 3, p. 682-692 https://doi.org/10.1128/aem.02019-07	journal	December 2007
Ferrous Iron- and Sulfur-Induced Genes in Sulfolobus metallicus Bathe, S.; Norris, P. R. Applied and Environmental Microbiology, Vol. 73, Issue 8, p. 2491-2497 https://doi.org/10.1128/aem.02589-06	journal	February 2007
Assembly of Viral Metagenomes from Yellowstone Hot Springs Schoenfeld, T.; Patterson, M.; Richardson, P. M. Applied and Environmental Microbiology, Vol. 74, Issue 13 https://doi.org/10.1128/aem.02598-07	journal	April 2008
Insights into the Metabolism of Elemental Sulfur by the Hyperthermophilic Archaeon Pyrococcus furiosus: Characterization of a Coenzyme A- Dependent NAD(P)H Sulfur Oxidoreductase Schut, G. J.; Bridger, S. L.; Adams, M. W. W. Journal of Bacteriology, Vol. 189, Issue 12, p. 4431-4441 https://doi.org/10.1128/jb.00031-07	journal	April 2007
Regulation of Mercury Resistance in the Crenarchaeote Sulfolobus solfataricus Schelert, J.; Drozda, M.; Dixit, V. Journal of Bacteriology, Vol. 188, Issue 20, p. 7141-7150 https://doi.org/10.1128/jb.00558-06	journal	October 2006
Transcriptional Map of Respiratory Versatility in the Hyperthermophilic Crenarchaeon Pyrobaculum aerophilum Cozen, Aaron E.; Weirauch, Matthew T.; Pollard, Katherine S. Journal of Bacteriology, Vol. 191, Issue 3 https://doi.org/10.1128/jb.00965-08	journal	December 2008
Complete and Draft Genome Sequences of Six Members of the Aquificales Reysenbach, A. -L.; Hamamura, N.; Podar, M. Journal of Bacteriology, Vol. 191, Issue 6 https://doi.org/10.1128/jb.01645-08	journal	January 2009
The superfamily of heme-copper respiratory oxidases. García-Horsman, J. A.; Barquera, B.; Rumbley, J. Journal of Bacteriology, Vol. 176, Issue 18 https://doi.org/10.1128/jb.176.18.5587-5600.1994	journal	September 1994
The terminal quinol oxidase of the hyperthermophilic archaeon Acidianus ambivalens exhibits a novel subunit structure and gene organization Purschke, W. G.; Schmidt, C. L.; Petersen, A. Journal of Bacteriology, Vol. 179, Issue 4 https://doi.org/10.1128/jb.179.4.1344-1353.1997	journal	February 1997
Phylogeny of Dissimilatory Sulfite Reductases Supports an Early Origin of Sulfate Respiration Wagner, Michael; Roger, Andrew J.; Flax, Jodi L. Journal of Bacteriology, Vol. 180, Issue 11 https://doi.org/10.1128/jb.180.11.2975-2982.1998	journal	June 1998
Novel Genes Coding for Lithotrophic Sulfur Oxidation of Paracoccus pantotrophus GB17 Friedrich, C. G.; Quentmeier, A.; Bardischewsky, F. Journal of Bacteriology, Vol. 182, Issue 17 https://doi.org/10.1128/jb.182.17.4677-4687.2000	journal	September 2000
DNA Microarray Analysis of the Hyperthermophilic Archaeon Pyrococcus furiosus: Evidence for a New Type of Sulfur-Reducing Enzyme Complex Schut, G. J.; Zhou, J.; Adams, M. W. W. Journal of Bacteriology, Vol. 183, Issue 24 https://doi.org/10.1128/jb.183.24.7027-7036.2001	journal	December 2001
Evidence for Autotrophic CO2 Fixation via the Reductive Tricarboxylic Acid Cycle by Members of the Subdivision of Proteobacteria Hugler, M.; Wirsen, C. O.; Fuchs, G. Journal of Bacteriology, Vol. 187, Issue 9 https://doi.org/10.1128/jb.187.9.3020-3027.2005	journal	April 2005
The genome of Hyperthermus butylicus : a sulfur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 °C Brügger, Kim; Chen, Lanming; Stark, Markus Archaea, Vol. 2, Issue 2 https://doi.org/10.1155/2007/745987	journal	January 2007
The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota Anderson, Iain J.; Dharmarajan, Lakshmi; Rodriguez, Jason BMC Genomics, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2164-10-145	journal	January 2009
Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes Eisen, Jonathan A.; Levin, Simon PLoS Biology, Vol. 5, Issue 3, p. e82 https://doi.org/10.1371/journal.pbio.0050082	journal	March 2007
The Archaeal Respiratory Supercomplex SoxM from S.acidocaldarius Combines Features of Quinole and Cytochrome c Oxidases Komorowski, L.; Verheyen, W.; Schäfer, G. Biological Chemistry, Vol. 383, Issue 11 https://doi.org/10.1515/bc.2002.200	journal	January 2002
TM4: A Free, Open-Source System for Microarray Data Management and Analysis Saeed, A. I.; Sharov, V.; White, J. BioTechniques, Vol. 34, Issue 2 https://doi.org/10.2144/03342mt01	journal	February 2003

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Integration of Metagenomic and Stable Carbon Isotope Evidence Reveals the Extent and Mechanisms of Carbon Dioxide Fixation in High-Temperature Microbial Communities Jennings, Ryan de Montmollin; Moran, James J.; Jay, Zackary J. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00088	journal	February 2017
Archaeal Viruses from High-Temperature Environments Munson-McGee, Jacob; Snyder, Jamie; Young, Mark Genes, Vol. 9, Issue 3 https://doi.org/10.3390/genes9030128	journal	February 2018
Correction: Zablocki, O.; et al. Diversity of dsDNA Viruses in a South African Hot Spring Assessed by Metagenomics and Microscopy. Viruses 2017, 9, 348 Zablocki, Olivier; Kirby, Bronwyn; Trindade, Marla Viruses, Vol. 10, Issue 1 https://doi.org/10.3390/v10010017	journal	January 2018
Artifactual pyrosequencing reads in multiple-displacement-amplified sediment metagenomes from the Red Sea Wang, Yong; Lee, On On; Yang, Jiang Ke PeerJ, Vol. 1 https://doi.org/10.7717/peerj.69	journal	April 2013
Temperature and pH controls on glycerol dibiphytanyl glycerol tetraether lipid composition in the hyperthermophilic crenarchaeon Acidilobus sulfurireducens Boyd, Eric S.; Pearson, Ann; Pi, Yundan Extremophiles, Vol. 15, Issue 1 https://doi.org/10.1007/s00792-010-0339-y	journal	December 2010
Detection and analysis of elusive members of a novel and diverse archaeal community within a thermal spring streamer consortium Colman, Daniel R.; Thomas, Raquela; Maas, Kendra R. Extremophiles, Vol. 19, Issue 2 https://doi.org/10.1007/s00792-014-0715-0	journal	December 2014
Microbial community analysis of pH 4 thermal springs in Yellowstone National Park Jiang, Xiaoben; Takacs-Vesbach, Cristina D. Extremophiles, Vol. 21, Issue 1 https://doi.org/10.1007/s00792-016-0889-8	journal	November 2016
Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential Klatt, Christian G.; Wood, Jason M.; Rusch, Douglas B. The ISME Journal, Vol. 5, Issue 8 https://doi.org/10.1038/ismej.2011.73	journal	June 2011
Community genomic analysis of an extremely acidophilic sulfur-oxidizing biofilm Jones, Daniel S.; Albrecht, Heidi L.; Dawson, Katherine S. The ISME Journal, Vol. 6, Issue 1 https://doi.org/10.1038/ismej.2011.75	journal	June 2011
Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park Kozubal, Mark A.; Romine, Margaret; Jennings, Ryan deM The ISME Journal, Vol. 7, Issue 3 https://doi.org/10.1038/ismej.2012.132	journal	November 2012
Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats Jay, Zackary J.; Beam, Jacob P.; Dlakić, Mensur Nature Microbiology, Vol. 3, Issue 6 https://doi.org/10.1038/s41564-018-0163-1	journal	May 2018
Comparative community gene expression analysis of Aquificales-dominated geothermal springs: Metatranscriptomic analysis of Aquificales-dominant springs Hamamura, Natsuko; Meneghin, Jennifer; Reysenbach, Anna-Louise Environmental Microbiology, Vol. 15, Issue 4 https://doi.org/10.1111/1462-2920.12061	journal	January 2013
Archaeal and bacterial diversity in acidic to circumneutral hot springs in the Philippines Huang, Qiuyuan; Jiang, Hongchen; Briggs, Brandon R. FEMS Microbiology Ecology, Vol. 85, Issue 3 https://doi.org/10.1111/1574-6941.12134	journal	May 2013
Hot-spring Systems Geobiology: abiotic and biotic influences on travertine formation at Mammoth Hot Springs, Yellowstone National Park, USA: Hot-spring systems geobiology Fouke, Bruce W. Sedimentology, Vol. 58, Issue 1 https://doi.org/10.1111/j.1365-3091.2010.01209.x	journal	January 2011
Widespread Genetic Switches and Toxicity Resistance Proteins for Fluoride Baker, J. L.; Sudarsan, N.; Weinberg, Z. Science, Vol. 335, Issue 6065 https://doi.org/10.1126/science.1215063	journal	December 2011
Mechanisms of Mineral Substrate Acquisition in a Thermoacidophile Amenabar, Maximiliano J.; Boyd, Eric S. Applied and Environmental Microbiology, Vol. 84, Issue 12 https://doi.org/10.1128/aem.00334-18	journal	April 2018
Involvement of Intermediate Sulfur Species in Biological Reduction of Elemental Sulfur under Acidic, Hydrothermal Conditions Boyd, Eric S.; Druschel, Gregory K. Applied and Environmental Microbiology, Vol. 79, Issue 6 https://doi.org/10.1128/aem.03160-12	journal	January 2013
Comparative Genomic Analysis of Phylogenetically Closely Related Hydrogenobaculum sp. Isolates from Yellowstone National Park Romano, Christine; D'Imperio, Seth; Woyke, Tanja Applied and Environmental Microbiology, Vol. 79, Issue 9 https://doi.org/10.1128/aem.03591-12	journal	February 2013
Metatranscriptomic Analysis of Microbes in an Oceanfront Deep-Subsurface Hot Spring Reveals Novel Small RNAs and Type-Specific tRNA Degradation Murakami, Shinnosuke; Fujishima, Kosuke; Tomita, Masaru Applied and Environmental Microbiology, Vol. 78, Issue 4 https://doi.org/10.1128/aem.06811-11	journal	December 2011
Identification of Novel Positive-Strand RNA Viruses by Metagenomic Analysis of Archaea-Dominated Yellowstone Hot Springs Bolduc, B.; Shaughnessy, D. P.; Wolf, Y. I. Journal of Virology, Vol. 86, Issue 10 https://doi.org/10.1128/jvi.07196-11	journal	February 2012
Microbial evolution in extreme environments: microbial migration, genomic highways, and geochemical barriers in hydrothermal ecosystems Raymond, Jason; Alsop, Eric B. Environmental Systems Research, Vol. 4, Issue 1 https://doi.org/10.1186/s40068-015-0038-x	journal	August 2015
Calculation of the Relative Chemical Stabilities of Proteins as a Function of Temperature and Redox Chemistry in a Hot Spring Dick, Jeffrey M.; Shock, Everett L. PLoS ONE, Vol. 6, Issue 8 https://doi.org/10.1371/journal.pone.0022782	journal	August 2011
Microbial transformations of arsenic: perspectives for biological removal of arsenic from water Cavalca, Lucia; Corsini, Anna; Zaccheo, Patrizia Future Microbiology, Vol. 8, Issue 6 https://doi.org/10.2217/fmb.13.38	journal	June 2013
Novel, Deep-Branching Heterotrophic Bacterial Populations Recovered from Thermal Spring Metagenomes Colman, Daniel R.; Jay, Zackary J.; Inskeep, William P. Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00304	journal	March 2016
Microscale Biosignatures and Abiotic Mineral Authigenesis in Little Hot Creek, California Kraus, Emily A.; Beeler, Scott R.; Mors, R. Agustin Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00997	journal	May 2018

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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
58 GEOSCIENCES
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Metagenomes from High-Temperature Chemotrophic Systems Reveal Geochemical Controls on Microbial Community Structure and Function

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