Thermophilic Archaeal Diversity and Methanogenesis from El Tatio Geyser Field, Chile

References

• Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool (BLAST). J Mol Biol 215:403–410.
   PubMed Web of Science ®Google Scholar
• Ausubel FM, Brent IR, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K. 1990. Current Protocols in Molecular Biology, vol. 1. New York: Green Publishing Associates and Wiley-Interscience.
   Google Scholar
• Baedecker MJ, Cozzarelli IM. 1992. The determination and fate of unstable constituents in contaminated groundwater. In: Lesage S, Jackson RE, editors. Groundwater Contamination and Analysis at Hazardous Waste Sites. New York: Marcel Dekker, p425–461.
   Google Scholar
• Baker GC, Cowan DA. 2004. 16S rDNA primers and the unbiased assessment of thermophile diversity. Biochem Soc Trans 32:218–221.
   PubMed Web of Science ®Google Scholar
• Baker BJ, Sheik CS, Taylor CA, Jain S, Bhasi A, Cavalcoli JD, Dick GJ. 2013. Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling. ISME J 7:1962–1973.
   PubMed Web of Science ®Google Scholar
• Bebout BM, Hoehler TM, Thamdrup B, Albert D, Carpenter SP, Hogan M, Turk K, Des Marais DJ. 2004. Methane production by microbial mats under low sulphate cocentrations. Geobiology 2:87–96.
   Web of Science ®Google Scholar
• Bekins BA, Godsy EM, Warren E. 1999. Distribution of microbial physiologic types in an aquifer contaminated by crude oil. Microb Ecol 37:263–275.
   PubMed Web of Science ®Google Scholar
• Bennett PC, Engel AS, Roberts JA. 2006. Counting and imaging bacteria on mineral surfaces. In: Maurice JPA, Warren LA, editors. Methods of Investigating Microbial-Mineral Interactions, CMS Workshop Lectures Volume 14. Chantilly, Virginia: The Clay Mineral Society, p37–78.
   Google Scholar
• Berg A, Lindblad P, Svensson B. 2014. Cyanobacteria as a source of hydrogen for methane formation. World J Microbiol Biotechnol 30:539–545.
   PubMed Web of Science ®Google Scholar
• Bertrand J, Caumette P, Lebaron P, Matheron R, Normand P, Sime-Ngando T, editors. 2011. Environmental Microbiology: Fundamentals and Applications: Microbial Ecology. New York: Springer.
   Google Scholar
• Bini E. 2010. Archaeal transformation of metals in the environment. FEMS Microbiol Ecol 73:1–16.
   PubMed Web of Science ®Google Scholar
• Bonch-Osmolovskaya EA, Karpov GA. 1987. Microbial methane formation in Uzon Caldera hydrothermal vents. Mikrobiologiya 56:516–518.
   Google Scholar
• Bonch-Osmolovskaya EA, Miroshnichenko ML, Slobodkin Ai, Sokolova TG, Karpov GA, Kostrinkina NA, Zavarzina DG, Prokof'eva MI, Rusanov II, Pimenov NV. 1999. Biodiveristy of anaerobic litrotrophic prokaryotes in terrestrial hot springs of Kamchatka. Microbiology (Moscow) 68:343–352.
   Web of Science ®Google Scholar
• Buckley DH, Baumgartner LK, Visscher PT. 2008. Vertical distribution of methane metabolism in microbial mats of the Great Sippewissett Salt Marsh. Environ Microbiol 10:967–977.
   PubMed Web of Science ®Google Scholar
• Chernyh NA, Mardanov AV, Gumerov VM, Miroshnichenko ML, Lebedinsky AV, Merkel AY, Crowe D, Pimenov NV, Rusanov II, Ravin NV, Moran MA, Bonch-Osmolovskaya EA. 2015. Microbial life in Bourlyashchy, the hottest thermal pool of Uzon Caldera, Kamchatka. Extremophiles 19:1157–1171.
   PubMed Web of Science ®Google Scholar
• Cleverley JS, Benning LG, Mountain BW. 2003. Reaction path modeling in the As-S system; a case study for geothermal As transport. Appl Geochem 18:1325–1345.
   Web of Science ®Google Scholar
• Colwell RK. 2013. EstimateS: statistical estimation of species richness and shared species from samples. Version 9 and earlier. User's Guide and application. Available from: http://viceroy.eeb.uconn.edu/estimates
   Google Scholar
• Cortecci G, Boschetti T, Mussi M, Lameli CH, Mucchino C, Barbieri M. 2005. New chemical and original isotopic data on waters from El Tatio geothermal field, northern Chile. Geochem J 39:547–571.
   Web of Science ®Google Scholar
• Curiale M. 2000. MPN Calculator. Available from: http://www.i2workout.com/mcuriale/mpn/index.html
   Google Scholar
• Dekas AE, Poretsky RS, Orphan VJ. 2009. Deep-sea archaea fix and share nitrogen in methane-consuming microbial consortia. Science 326:422–426.
   PubMed Web of Science ®Google Scholar
• DeSantis TZ, Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, Andersen GL. 2006. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucl Acids Res 34: W394–W399.
   PubMed Web of Science ®Google Scholar
• Dowd SE, Callaway TR, Wolcott RD, Sun Y, McKeehan T, Hagevoort RG, Edrington TS. 2008. Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). BMC Microbol 8:125.
   PubMed Web of Science ®Google Scholar
• Dowd SE, Zaragoza J, Rodriguez JR, Oliver MJ, Payton PR. 2005. Windows .NET network distributed basic local alignment search toolkit (W.ND-BLAST). BMC Bioinformatics 6:93.
   PubMed Web of Science ®Google Scholar
• Engel AS, Johnson LR, Porter ML. 2013. Arsenite oxidase gene diversity among Chloroflexi and Proteobacteria from El Tatio Geyser Field, Chile. FEMS Microbiol Ecol 83:745–756.
   PubMed Web of Science ®Google Scholar
• Escudero LV, Casamayor EO, Chong G, Pedrós-Alió C, Demergasso C. 2013. Distribution of microbial arsenic reduction, oxidation, and extrusion genes along a wide range of environmental arsenic concentrations. PLoS One 10: e78890.
   Google Scholar
• Etiope G, Klusman RW. 2002. Geologic emissions of methane to the atmosphere. Chemosphere 49:777–789.
   PubMed Web of Science ®Google Scholar
• Evans PN, Parks DH, Chadwick GL, Robbins SJ, Orphan VJ, Golding SD, Tyson GW. 2015. Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics. Science 350:434–438.
   PubMed Web of Science ®Google Scholar
• Fuex AN. 1980. Experimental evidence against an appreciable isotopic fractionation of methane during migration. Phys Chem Earth 12:725–988.
   Google Scholar
• Garcia-Valles M, Fernandez-Turiel JL, Gimeno-Torrente D, Saavedra-Alonso J, Martinez-Manent S. 2008. Mineralogical characterization of silica sinters form the El Tatio geothermal field, Chile. Am Min 93:1373–1383.
   Web of Science ®Google Scholar
• Giggenbach WF. 1995. Variations in the chemical and isotopic composition of fluids discharged from the Taupo Volcanic Zone, New Zealand. J Volcanol Geotherm Res 68:89–116.
   Web of Science ®Google Scholar
• Glennon JA, Pfaff RM. 2003. The extraordinary thermal activity of El Tatio geyser field, Antofagasta Region, Chile. The GOSA Trans 8:31–78.
   Google Scholar
• Gontcharova V, Youn E, Wolcott RD, Hollister EB, Gentry TJ, Dowd SE. 2010. Black box chimera check (B2C2): a windows-based software for batch depletion of chimeras from bacterial 16S rRNA gene datasets. Open Microbiol J 11:47–52.
   Google Scholar
• Hine J, Mookerjee PK. 1975. The intrinsic hydrophilic character of organic compounds. Correlations in terms of structural contributions. J Org Chem 40:292–298.
   Web of Science ®Google Scholar
• Holdeman LV, Moore WEC. 1972. Anaerobe Laboratory Manual, 2nd ed. Blacksburg, Virginia: Virginia Polytechnical Institute and State University Press.
   Google Scholar
• Huber T, Faulkner G, Hugenholtz P. 2004. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20:2317–2319.
   PubMed Web of Science ®Google Scholar
• Hur I, Chun J. 2004. A method for comparing multiple bacterial community structures from 16S rDNA clone library sequences. J Microbiol 42:9–13.
   PubMed Web of Science ®Google Scholar
• Jackson CR, Dugas SL. 2003. Phylogenetic analysis of bacterial and archaeal arsC gene sequences suggests an ancient, common origin for arsenate reductase. BMC Evol Biol 3:18.
   PubMed Web of Science ®Google Scholar
• Landrum JT, Bennett PC, Engel AS, Alsina MA, Pastén AP, Milliken K. 2009. Partitioning geochemistry of arsenic and antimony, El Tatio geyser field, Chile. Appl Geochem 24:664–676.
   Web of Science ®Google Scholar
• Lauerer G, Kristjansson JK, Langworthy TA, König H, Stetter KO. 1986. Methanothermus sociabilis sp. nov., a second species within the Methanothermaceae growing at 97°C. Syst Appl Microbiol 8:100–105.
   Web of Science ®Google Scholar
• Lemos LN, Fulthorpe RR, Triplett EW, Roesch LFW. 2011. Rethinking microbial diversity analysis in the high throughput sequencing era. J Microbiol Method 86:42–51.
   PubMed Web of Science ®Google Scholar
• Liu Y, Whitman WB. 2008. Metabolic, phylogenetic and ecological diversity of the methanogenic Archaea. Ann New York Acad Sci 1125:171–189.
   PubMed Web of Science ®Google Scholar
• Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar BA, Lai T, Steppi S, Jobb G, Förster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, König A, Liss T, Lüssman R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer K. 2004. ARB: a software environment for sequence data. Nucl Acids Res 32:1363–1371.
   PubMed Web of Science ®Google Scholar
• Macur RE, Jay ZJ, Taylor WP, Kozubal MA, Kocar BD, Inskeep WP. 2013. Microbial community structure and sulfur biogeochemistry in mildly-acidic sulfidic geothermal springs in Yellowstone National Park. Geobiology 11:86–99.
   PubMed Web of Science ®Google Scholar
• Macy JM, Santini JM, Pauling BV, O'Neill AH, Sly LI. 2000. Two new arsenate/sulfate-reducing bacteria: mechanisms of arsenate reduction. Arch Microbiol 173:49–57.
   PubMed Web of Science ®Google Scholar
• Merkel AY, Podosokorskaya OA, Chernyh NA, Bonch-Osmolovskaya EA. 2015. Occurrence, diversity, and abundance of methanogenic archaea in terrestrial hot springs of Kamchatka and São Miguel Island. Microbiology 84:577–583.
   Web of Science ®Google Scholar
• Meyer-Dombard DR, Amend JP. 2014. Geochemistry and microbial ecology in alkaline hot springs of Ambitle Island, Papua New Guinea. Extremophiles 18:763–778.
   PubMed Web of Science ®Google Scholar
• Nordstrom KD, Ball JW, McCleskey BR. 2005. Ground water to surface water: chemistry of thermal outflows in Yellowstone National Park. In: Innskeep W, McDermott T, editors. Geothermal Biology and Geochemistry in Yellowstone National Park. Bozeman, Montana: Thermal Biology Institute.
   Google Scholar
• Nordstrom KD, McCleskey BR, Ball JW. 2009. Sulfur geochemistry of hydrothermal waters in Yellowstone National Park: IV acid-sulfate waters. Appl Geochem 24:191–207.
   Web of Science ®Google Scholar
• Nozhevnikova AN, Yagodina TG. A thermophilic acetate methane-producing bacterium. Mikrobiologiya 51:534–541.
   Web of Science ®Google Scholar
• Panosyan H, Birkeland N-K. 2014. Microbial diversity in an Armenian geothermal spring assessed by molecular and culture-based methods. J Basic Microbiol 54:1240–1250.
   PubMed Web of Science ®Google Scholar
• Planer-Friedrich B, Lehr C, Matschullat J, Merkel BJ, Nordstrom KD, Sandstrom MW. 2006. Speciation of volatile arsenic at geothermal features in Yellowstone National Park. Geochimica et Cosmochimica Acta 70:2480–2491.
   Web of Science ®Google Scholar
• Reysenbach A-L, Pace NR. 1995. Reliable amplification of hyperthermophilic archaeal 16S rRNA genes by the polymerase chain reaction. In: Robb FT, Place AR, editors. Archaea- A Laboratory Manual: Thermophiles. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press, p101–105.
   Google Scholar
• Saddler GS, Bradbury JF. 2005. Xanthomonadales ord. nov. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM, Boone DR, De Vos P, Goodfellow M, Rainey FA, Schleifer K, editors. Bergey's Manual of Systematic Bacteriology Volume 2. 2nd ed. New York: Springer, p63.
   Google Scholar
• Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541.
   PubMed Web of Science ®Google Scholar
• Singleton GL, Révész K, Coplen TB. 2012. Determination of the δ13C of dissolved inorganic carbon in water; RSIL lab code 1710, chapter 18 of Stable isotope-ratio methods. In: Révész K, Coplen TB, editors. Methods of the Reston Stable Isotope Laboratory: U.S. Geological Survey Techniques and Methods, book 10 section C. Available from: http://pubs.usgs.gov/tm/10c18/
   Google Scholar
• Sjöling S, Cowan DA. 2003. High 16S rDNA bacterial diversity in glacial meltwater lake sediment, Bratina Island, Antarctica. Extremophiles 7:275–282.
   PubMed Web of Science ®Google Scholar
• Spear JR, Walker JJ, McCollom TM, Pace NR. 2005. Hydrogen and bioenergetics in the Yellowstone geothermal ecosystems. Proceedings of the National Academy of Sciences 102:2555–2560.
   PubMed Web of Science ®Google Scholar
• Stetter KO, Thomm M, Winter J, Wildgruber G, Huber H, Zillig W, Janecovic D, König H, Palm P, Wunderl S. 1981. Methanothermus fervidus, sp. nov., a novel extremely thermophilic methanogen isolated from an Icelandic hot spring. Zentralblatt für Bakteriologie Mikrobiologie und Hygiene C2:166–178.
   Google Scholar
• Swingley WD, Meyer-Dombard DR, Shock EL, Alsop EB, Falenski HD, Havig JR, Raymond J. 2012. Coordinating environmental genomics and geochemistry reveals metabolic transitions in a hot spring ecosystem. PLoS One 7: e38108.
   Google Scholar
• Takai K, Nakamura K, Toki T, Tsunogai U, Miyazaki M, Miyazaki J, Hirayama H, Nakagawa S, Nunoura T, Horikoshi K. 2008. Cell proliferation at 122°C and isotopically heavy CH4 production by a hyperthermophilic methanogen under high-pressure cultivation. Proceedings of the National Academy of Sciences 105:10949–10954.
   PubMed Web of Science ®Google Scholar
• Tassi F, Martinez C, Vaselli O, Capaccioni B, Viramonte J. 2005. Light hydrocarbons as redox and temperature indicators in the geothermal field of El Tatio (northern Chile). Appl Geochem 20:2049–2062.
   Web of Science ®Google Scholar
• Tassi F, Aguilera F, Darrah T, Vaselli O, Capaccioni B, Poreda RJ, Huertas AD. 2010. Fluid geochemistry of hydrothermal systems in the Arica-Parinacota, Tarapacá and Antofagasta regions (northern Chile). J Volcanol Geotherm Res 192:1–15.
   Web of Science ®Google Scholar
• Thuring RWJ, Sanders JPM, Borst P. 1975. A freeze-squeeze method for recovering long DNA from agarose gels. Analyt Biochem 66:213–220.
   PubMed Web of Science ®Google Scholar
• Ullrich MK, Pope JG, Seward TM, Wilson N, Planer-Friedrich B. 2013. Sulfur redox chemistry governs diurnal antimony and arsenic cycles at Champagne Pool, Waiotapu, New Zealand. J Volcanol Geotherm Res 262:164–177.
   Web of Science ®Google Scholar
• Ward DM. 1978. Thermophilic methanogenesis in a hot-spring algal-bacterial mat (71 to 30 degrees C). Appl Environ Microbiol 35:1019–1026.
   PubMed Web of Science ®Google Scholar
• Welhan JA 1988. Origins of methane in hydrothermal systems. Chem Geol 71:183–198.
   Web of Science ®Google Scholar
• Wiedemeier T, Swanson M, Moutoux D, Gordon E, Wilson J, Wilson B, Kampbell D, Haas P, Miller R, Hanson J, Chapelle F. 1998. Technical protocol for evaluating natural attenuation of chlorinated solvents in ground water. US Environmental Protection Agency. Epa/600/R-98/129.
   Google Scholar
• Wilde FD, editor. 2008. Field measurements, chapter A6 of National Field Manual for the Collection of Water Quality Data. In: U.S. Geological Survey Techniques of Water-Resources Investigation, book 9. Available from: http://water.usgs.gov/owq/FieldManual/Chapter6/Ch6_contents.html
   Google Scholar
• Zeikus JG, Winfrey MR. 1976. Temperature limitation of methanogenesis in aquatic sediments. Appl Environ Microbiol 31:99–107.
   PubMed Web of Science ®Google Scholar
• Zeikus JG. 1977. The biology of methanogenic bacteria. Bacteriol Rev 41:514–541.
   PubMedGoogle Scholar
• Zeikus JG, Ben-Bassat A, Hegge PW. 1980. Microbiology of methanogenesis in thermal, volcanic environments. J Bacteriol 143:432–440.
   PubMed Web of Science ®Google Scholar
• Zinder SH, Anguish T, Cardwell SC. 1984. Effects of temperature on methanogenesis in a thermophilic (58°C) anaerobic digestor. Appl Environ Microbiol 47:808–813.
   PubMed Web of Science ®Google Scholar
• Zinder SH. 1993. Physiological ecology of methanogens. In: Ferry JG, editor. Methanogenesis: Ecology, Physiology, Biochemistry & Genetics. Dordrecht: Springer, p128–206.
   Google Scholar