Archaeal and bacterial communities in geochemically diverse hot springs of Yellowstone National Park, USA

Geobiology

Volumn 3, Issue 3, 2005, Pages 211-227

  Meyer Dombard, D R ^a,c   Shock, E L ^b   Amend, J P ^a  

^a WASHINGTON UNIVERSITY   (United States)

^b ARIZONA STATE UNIVERSITY   (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIUM; BIOLOGICAL SURVEY; GEOCHEMICAL SURVEY; MICROBIAL COMMUNITY; POLYMERASE CHAIN REACTION; THERMAL SPRING;

NORTH AMERICA; UNITED STATES; WYOMING; YELLOWSTONE NATIONAL PARK;

AQUIFICALES; ARCHAEA; BACTERIA (MICROORGANISMS); BISON; CRENARCHAEOTA; EURYARCHAEOTA; THERMODESULFOBACTERIALES; THERMOPROTEALES;

EID: 33644829921     PISSN: 14724677     EISSN: 14724669     Source Type: Journal    
DOI: 10.1111/j.1472-4669.2005.00052.x     Document Type: Article

References (78)

1. Allen ET Day AL ( 1935) Hot Springs of the Yellowstone National Park. Waverly Press, Inc, Baltimore, MD.
2. Altschul S Madden T Schaffer A Zhang J Zhang Z Miller W Lipman D ( 1997) Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Research 25, 3389 3402.
3. Amend JP Rogers KL Meyer-Dombard DR ( 2004) Microbially mediated sulfur-redox: Energetics in marine hydrothermal vent systems. In Sulfur Biogeochemistry - Past and Present (eds Amend JP Edwards KJ, Lyons TW). GSA Special Paper 379, pp. 17 34.
4. Amend JP Rogers KL Shock EL Inguaggiato S Gurrieri S ( 2003) Energetics of chemolithoautotrophy in the hydrothermal system of Vulcano Island, southern Italy. Geobiology 1, 37 58.
5. Amend JP Shock EL ( 2001) Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and Bacteria. FEMS Microbiology Reviews 25, 175 243.
6. Bach W Edwards KJ ( 2003) Iron and sulfide oxidation within the basaltic ocean crust-extent, processes, timing, and implications for chemolithoautotrophic primary biomass production. Geochimica et Cosmochimica Acta 67, 3871 3887.
7. Ball JW Nordstrom DK Jenne EA Vivit DV ( 1998) Chemical Analyses of Hot Springs, Pools, Geysers, and Surface Waters from Yellowstone National Park, Wyoming, and Vicinity, 1974-75. US Geological Survey, US Department of the Interior, Boulder, CO, p. 45.
8. Ball JW Nordstrom DK McCleskey RB Schoonen MAA Xu Y ( 2001) Water Chemistry and On-Site Sulfur-Speciation Data for Selected Springs in Yellowstone National Park, Wyoming, 1996-98. US Geological Survey, US Department of the Interior, Boulder, CO, p. 41.
9. Barns SM Delwiche CF Palmer JD Pace NR ( 1996) Perspectives on Archaeal diversity, thermophily and monophily from environmental rRNA sequences. Proceedings of the National Academy of Sciences, USA 93, 9188 9193.
10. Barns SM Fundyga RE Jeffries MW Pace NR ( 1994) Remarkable Archaeal diversity detected in a Yellowstone National Park hot spring environment. Proceedings of the National Academy of Sciences, USA 91, 1609 1613.
11. Baross JA ( 1995) Isolation, Growth, and Maintenance of Hyperthermophiles. In Archaea, A Laboratory Manual: Thermophiles (eds Robb FT Place AR). Cold Spring Harbor Press, New York, pp. 15 23.
12. Ben-Bassat A Zeikus JG ( 1981) Thermobacteroides acetoethylicus gen. nov. and sp. nov., a new chemoorganotrophic, anaerobic, thermophilic bacterium. Archives of Microbiology 128, 365 370.
13. Blank CE Cady SL Pace NR ( 2002) Microbial composition of near-boiling silica-depositing thermal springs throughout Yellowstone National Park. Applied and Environmental Microbiology 68, 5123 5135.
14. Bond PL Smriga SP Banfield JF ( 2000) Phylogeny of microorganisms populating a thick, subaerial, predominantly lithotrophic biofilm at an extreme acid mine drainage site. Applied and Environmental Microbiology 66, 3842 3849.
15. Boomer SM Lodge DP Dutton BE Pierson B ( 2002) Molecular characterization of novel red green nonsulfur bacteria from five distinct hot spring communities in Yellowstone National Park. Applied and Environmental Microbiology 68, 346 355.
16. Bridge TAM Johnson DB ( 1998) Reduction of soluble iron and reductive dissolution of ferric iron-containing minerals by moderately thermophilic iron-oxidizing Bacteria. Applied and Environmental Microbiology 64, 2181 2186.
17. Brock TD ( 1978) Thermophilic Microorganisms and Life at High Temperatures. Springer-Verlag, New York.
18. Brock TD Brock KM Belly RT Weiss RL ( 1972) Sulfolobus: a new genus of sulfur-oxidizing bacteria living at low pH and high temperature. Archives of Microbiology 84, 54 68.
19. Brock TD Freeze H ( 1969) Thermus aquaticus gen. n. and sp. n., a nonsporulating extreme thermophile. Journal of Bacteriology 98, 289 297.
20. Cole JR Chai B Marsh TL Farris RJ Wang Q Kulam SA Chandra S McGarrell DM Schmidt TM Garrity GM Tiedje JM ( 2003) The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Research 31, 442 443.
21. Eder W Huber R ( 2002) New isolates and physiological properties of the Aquificales and description of Thermocrinus albus sp. nov. Extremophiles 6, 309 318.
22. Ellis AJ Mahon WAJ ( 1964) Natural hydrothermal systems and experimental hot-water/rock interactions (Pt I.). Geochimica et Cosmochimica Acta 28, 1323 1357.
23. Ellis AJ Mahon WAJ ( 1967) Natural hydrothermal systems and experimental hot-water/rock interactions (Pt II.). Geochimica et Cosmochimica Acta 31, 519 538.
24. Engle M Li Y Woese CR Wiegel J ( 1995) Isolation and characterization of a novel alkalitolerant thermophile, Anaerobranca horikoshii gen. nov., sp. nov. International Journal of Systematic and Evolutionary Microbiology 45, 454 461.
25. Felsenstein J ( 1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783 791.
26. Fouke BW Bonheyo GT Sanzenbacher E Frias-Lopez J ( 2003) Partitioning of bacterial communities between travertine depositional facies at Mammoth Hot Springs, Yellowstone National Park, USA. Canadian Journal of Earth Sciences 40, 1531 1548.
27. Fournier RO ( 1989) Geochemistry and dynamics of the Yellowstone National Park hydrothermal system. Annual Reviews of Earth and Planetary Sciences 17, 13 53.
28. Fournier RO Pitt AM ( 1985) The Yellowstone magmatic- hydrothermal system, U.S.A. In Transactions of the Geothermal Council's International Symposium on Geothermal Energy, International Volume (ed. Stone C). Geothermal Resources Council, Davis, CA, pp. 319 327.
29. Fournier R Thompson J Hutchinson R ( 1994) The geochemistry of hot spring waters at Norris Geyser Basin, Yellowstone National Park. Geothermal Resources Council Transactions 18, 177 179.
30. Giggenbach WF ( 1975) A simple method for the collection and analysis of volcanic gas samples. Bulletin of Volcanology 39, 132 145.
31. Giggenbach WF Goguel RL ( 1989) Collection and Analysis of Geothermal and Volcanic Water and Gas Discharges. Chemical Division of Department of Scientific and Industrial Research, Petone, New Zealand Report CD 2401, p. 81.
32. Giggenbach WF Tedesco D Sulistiyo Y Caprai A Cioni R Favara R Fischer TP Hirabayashi J-I Korzhinsky M Martini M Menyailov I Shinohara H ( 2001) Evaluation of results from the fourth and fifth IAVCEI field workshop on volcanic gases, Vulcano Island, Italy, and Java, Indonesia. Journal of Volcanology and Geothermal Research 108, 157 172.
33. Graber JR Kirshtein J Speck M Reysenbach AL ( 2001) Community structure along a thermal gradient in a stream near Obsidian Pool, Yellowstone National Park. In Thermophiles: Biodiversity, Ecology and Evolution (eds Reysenbach AL Voytek M, Mancinelli R). Klewer Academic / Plenum Publishers, New York, pp. 81 89.
34. Henry EA Devereux R Maki JS Gilmour CC Woese CR Mandelco L Schauder R Remsen CC Mitchell R ( 1994) Characterization of a new thermophilic sulfate-reducing bacterium Thermodesulfovibrio yellowstonii, gen. nov. and sp. nov. its phylogenetic relationship to Thermodesulfobacterium commune and their origins deep within the bacterial domain. Archives of Microbiology 161, 62 69.
35. Hoehler TM Alperin MJ Albert DB Martens CS ( 2001) Apparent minimum free energy requirements for methanogenic and sulfate-bacteria in an anoxic marine sediment. FEMS Microbiology Ecology 38, 33 41.
36. Huber R Eder W Heldwein S Wanner G Huber H Rachel R Stetter KO ( 1998) Thermocrinis ruber gen. nov., sp. nov., a pink-filament forming hyperthermophilic Bacterium isolated from Yellowstone National Park. Applied and Environmental Microbiology 64, 3576 3583.
37. Huber T Faulkner G Hugenholtz P ( 2004) Bellerophon; a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20, 2317 2319.
38. Huelsenbeck J Rannala B ( 1997) Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science 276, 227 232.
39. Hugenholtz P Pitulle C Hershberger KL Pace NR ( 1998) Novel division level bacterial diversity in a Yellowstone hot spring. Journal of Bacteriology 180, 366 376.
40. Hurt RA Qiu X Wu L Palumbo AV Tiedje JM Zhou J ( 2001) Simultaneous recovery of RNA and DNA from soils and sediments. Applied and Environmental Microbiology 67, 4495 4503.
41. Inskeep WP Macur RE Harrison G Bostick BJ Fendorf S ( 2004) Biomineralization of As(V)-hydrous ferric oxyhydroxide in microbial mats of an acid-sulfate-chloride geothermal spring, Yellowstone National Park. Geochimica et Cosmochimica Acta 68, 3141 3155.
42. Jackson CR Langner HW Donahoe-Christiansen J Inskeep WP McDermott TR ( 2001) Molecular analysis of microbial community structure in an arsenite-oxidizing acidic thermal spring. Environmental Microbiology 3, 532 542.
43. Jackson TJ Ramaley RF Meinschein WG ( 1973) Thermomicrobium, a new genus of extremely thermophilic bacteria. International Journal of Systematic Bacteriology 23, 28 36.
44. Jahnke L Eder W Huber R Hope JM Hinrichs K-U Hayes JM Des Marais DJ Cady SL Summons RE ( 2001) Signature lipids and stable carbon isotope analyses of Octopus Spring hyperthermophilic communities compared with those of Aquificales representatives. Applied and Environmental Microbiology 67, 5179 5189.
45. Jahnke L Embaye T Hope J Turk KA Van Zuilen M Des Marais DJ Farmer JD Summons RE ( 2004) Lipid biomarker and carbon isotopic signatures for stromatolite-forming, microbial mat communities and Phormidium cultures from Yellowstone National Park. Geobiology 2, 31 47.
46. Johnson DB Body DA Bridge TAM Bruhn DF Roberto FF ( 2001) Biodiversity of acidophilic moderate thermophiles isolated from two sites in Yellowstone National Park and their roles in the dissimilatory oxio-reduction of iron. In Thermophiles: Biodiversity, Ecology and Evolution (eds Reysenbach AL Voytek M Mancinelli R). Kluwer Academic / Plenum Publishers, New York, NY, pp. 23 39.
47. Johnson DB Okibe N Roberto FF ( 2003) Novel thermo-acidophilic bacteria isolated from geothermal sites in Yellowstone National Park: physiological and phylogenetic characteristics. Archives of Microbiology 180, 60 68.
48. Kashefi K Holmes DE Reysenbach AL Lovley DR ( 2002) Use of Fe(III) as an electron acceptor to recover previously uncultured hyperthermophile: isolation and characterization of Geothermobacterium ferrireducens gen. nov., sp. nov. Applied and Environmental Microbiology 68, 1735 1742.
49. Kato K Kobayashi T Yamamoto H Nakagawa T Maki Y Hoaki T ( 2004) Microbial mat boundaries between chemolithotrophs and phototrophs in geothermal hot spring effluents. Geomicrobiology Journal 21, 91 98.
50. Kennedy BM Lynch MA Reynolds JH Smith SP ( 1985) Intensive sampling of noble gases in fluids at Yellowstone: I. Early overview of data; regional patterns. Geochimica et Cosmochimica Acta 49, 1251 1261.
51. Krauskopf KB ( 1964) The possible role of volatile metal compounds in ore genesis. Economic Geology 59, 22 45.
52. Lane DJ ( 1991) 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics (eds Stackebrandt E Goodfellow M). John Wiley and Sons, Chichester, UK, pp. 115 175.
53. Langner HW Inskeep WP ( 2000) Microbial reduction of arsenate in the presence of ferrihydrite. Environmental Science and Technology 34, 3131 3136.
54. Langner HW Jackson CR McDermott TR Inskeep WP ( 2001) Rapid oxidation of arsenite in a hot spring ecosystem, Yellowstone National Park. Environmental Science and Technology 35, 3302 3309.
55. Macur RE Langner HW Kocar BD Inskeep WP ( 2004) Linking geochemical processes with microbial community analysis: successional dynamics in an arsenic-rich, acid-sulphate geothermal spring. Geobiology 2, 163 177.
56. Marteinsson VT Hauksdottir S Hobel CFV Kristmannsdottir H Hreggvidsson GO Kristjansson JK ( 2001) Phylogenetic diversity analysis of subterranean hot springs in Iceland. Applied and Environmental Microbiology 67, 4242 4248.
57. McCollom T Shock EL ( 1997) Geochemical constraints on chemolithoautotrophic metabolism by microorganisms in seafloor hydrothermal systems. Geochimica et Cosmochimica Acta 61, 4375 4391.
58. Meyer-Dombard DR ( 2004) Geochemical constraints on microbial diversity in Yellowstone National Park, Thesis, Doctor of Philosophy. Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, p. 210.
59. Miller DN Bryant JE Madsen EL Ghiorse WC ( 1999) Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Applied and Environmental Microbiology 65, 4715 4724.
60. Nakagawa S Shtaih Z Banta A Beveridge TJ Sako Y Reysenbach A-L ( 2005) Sulfurihydrogenibium yellowstonense sp. nov., an extremely thermophillic, facultatively heterotrophic, sulfur- oxidizing bacterium from Yellowstone National Park, and emended descriptions of the genus Sulfurihydrogenibium, Sulfurihyrogenibium subterraneum, and Sulfurihydrogenibium azorense. Geobiology 55, 2263 2268.
61. Papke RT Ramsing NB Bateson MM Ward DM ( 2003) Geographical isolation in hot spring cyanobacteria. Environmental Microbiology 5, 650 659.
62. Pierson BK Parenteau MN Griffin BM ( 1999) Phototrophs in high-iron-concentration microbial mats: physiological ecology of phototrophs in an iron-depositing hot spring. Applied and Environmental Microbiology 65, 5474 5483.
63. Reed DW Fujita Y Delwiche ME Blackwelder DB Sheridan PP Uchida T Colwell FS ( 2002) Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin. Applied and Environmental Microbiology 68, 3759 3770.
64. Reysenbach AL Ehringer M Hershberger K ( 2000) Microbial diversity at 83 °C in Calcite Springs, Yellowstone National Park: another environment where the Aquificales and 'Korarchaeota' coexist. Extremophiles 4, 61 67.
65. Schrenk MO Kelly DS Delaney JR Baross JA ( 2003) Incidence and diversity of microorganisms within the walls of an active deep-sea sulfide chimney. Applied and Environmental Microbiology 69, 3580 3592.
66. Shock EL Holland M Meyer-Dombard D Amend JP ( 2005a) Geochemical sources of energy for microbial metabolism in hydrothermal ecosystems: Obsidian Pool, Yellowstone National Park, USA. Geothermal Biology and Geochemistry in Yellowstone National Park (eds Inskeep WP McDermott TR). Thermal Biology Institute, Montana State University, pp. 95 112.
67. Shock EL Holland ME Meyer-Dombard DR Amend JP Osburn GR Fisher T ( 2005b) Quantifying Inorganic Sources of Energy in Hydrothermal Systems, Yellowstone National Park, USA. In Preparation.
68. Spear JR Walker JJ McCollom TM Pace NR ( 2005) Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem. Proceedings of the National Academy of Sciences, USA 102, 2555 2560.
69. Takai K Horikoshi K ( 1999) Genetic diversity of Archaea in deep-sea hydrothermal vent environments. Genetics 152, 1285 1297.
70. Takai K Komatsu T Inagaki F Horikoshi K ( 2001) Distribution of archaea in a black smoker chimney structure. Applied and Environmental Microbiology 67, 3618 3629.
71. Takai K Sako Y ( 1999) A molecular view of archaeal diversity in marine and terrestrial hot water environments. FEMS Microbiology Ecology 28, 177 188.
72. White DE Muffler LJP Truesdell AH ( 1971) Vapor-dominated hydrothermal systems compared with hot-water systems. Economic Geology 66, 75 97.
73. Whittlesey L ( 1988) Wonderland Nomenclature: A History of the Place Names of Yellowstone National Park. Montana Historical Society Press.
74. Wiegel J Ljungdahl LG ( 1981) Thermoanaerobacter ethanolicus gen. nov., sp. nov., a new, extreme thermophilic, anaerobic bacterium. Archives of Microbiology 128, 343 348.
75. Zeikus GJ Dawson MA Thompson TE Ingvorsen K Hatchikian EC ( 1983) Microbial ecology of volcanic sulphidogenesis: isolation and characterization of Thermodesulfobacterium commune gen. nov. and sp. nov. Journal of General Microbiology 129, 1159 1169.
76. Zeikus GJ Hegge PW Anderson MA ( 1979) Thermoanaerobium brockii gen. nov. and sp. nov., a new chemoorganotrophic, caldoactive, anaerobic bacterium. Archives of Microbiology 122, 41 48.
77. Zhang CL Fauke BW Bonheyo GT Peacock AD White DC Huang Y Romanek CS ( 2004) Lipid biomarkers and carbon-isotopes of modern travertine deposits (Yellowstone National Park, USA): implications for biogeochemical dynamics in hot-spring systems. Geochimica et Cosmochimica Acta 68, 3157 3169.
78. Zohdy AAR Anderson LA Muffler LJP ( 1973) Resistivity, self-potential, induced-polarization and surveys of a vapor-dominated geothermal system. Geophysics 38, 1130 1144.