Microbial diversity in hydrothermal systems and their influence on geological environments

Resource Geology

Volumn 52, Issue 2, 2002, Pages 135-146

  Ishii, Kousuke ^a   Marumo, Katsumi ^a  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

Habitat; Heat resistance; Heavy metal resistance; Hydrothermal system; Hyperthermophile; Metabolism

Indexed keywords

AMINO ACID; BIOENERGETICS; BIOLOGICAL PUMP; CARBON DIOXIDE; EXTREMOPHILE; HABITAT STRUCTURE; HYDROTHERMAL SYSTEM; METABOLISM; METHANE; MICROBIAL COMMUNITY; SEAFLOOR; THERMOPHILIC BACTERIUM;

EID: 0041883542     PISSN: 13441698     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1751-3928.2002.tb00126.x     Document Type: Review

References (91)

1. Adams, M. W. W. (1990) The structure and mechanism of iron-hydrogenase. Biochim. Biophys. Acta, 1020, 115-145.
2. Adams, M. W. W. (1993) Enzymes and proteins from organisms that grow near and above 100°C. Ann. Rev. Microbiol., 47, 627-658.
3. Ahmann, D., Roberts, A. L., Krumholz, L. R. and Morel, F. M. M. (1994) Microbe grows by reducing arsenic. Nature, 371, 750.
4. Aiking, H., Kok, K., van Heerikhuizen, H. and van't Riet, J. (1982) Adaptation to cadmium by Klebsiella aerogenes growing in continuous culture proceeds mainly via formation of cadmium sulfide. Appl. Environ. Microbiol., 44, 938-944.
5. Amend, J. P. and Shock, E. L. (2001) Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and Bacteria. FEMS Microbiol. Rev., 25, 175-243.
6. Babich, H. and Stotzky, G. (1977) Sensitivity of various bacteria, including actinomycetes, and fungi to cadmium and the influence of pH on sensitivity. Appl. Environ. Microbiol., 33, 681-695.
7. Barns, S. M., Fundyga, R. E., Jeffries, M. W. and Pace, N. R. (1994) Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc. Natl. Acad. Sci. USA, 91, 1609-1613.
8. Barns, S. M., Fundyga, R. E., Jeffries, M. W. and Pace, N. R. (1996) Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc. Natl. Acad. Sci. USA, 93, 9188-9193.
9. Bazylinski, D. A., Wirsen, C. O. and Jannasch, H. W. (1989) Microbial utilisation of naturally-occurring hydrocarbons at the Guaymas Basin Hydrothermal vent site. Appl. Environ. Microbiol., 55, 2832-2836.
10. Belkin, S. and Jannasch, H. W. (1985) A new extremely thermophilic, sulfur-reducing heterotrophic marine bacterium. Arch. Microbiol., 141, 181-186.
11. Belkin, S., Wirsen, C. O. and Jannasch, H. W. (1985) Biological and abiological sulfur reduction at high temperatures. Appl. Environ. Microbiol., 49, 1057-1061.
12. Blake, P. R., Day, M. W., Hsu, B. T., Joshua-Tor, L., Park, J.-B., Hare, D. R., Adams, M. W. W., Rees, D. C. and Summers, M. F. (1992a) Comparison of the X-ray structure of native rubredoxin from Pyrococcus furiosus with the NMR structure of the zinc substituted protein. Protein Sci., 1, 1522-1525.
13. Blake, P. R., Park, J.-B., Zhou, Z. H., Hare, D. R., Adams, M. W. W. and Summers, M. F. (1992b) Solution-state structure by NMR of zinc-substituted rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus friosus. Protein Sci., 1, 1508-1521.
14. Bonch-Osmolovskaja, E. A., Slesarev, A. I., Miroschnichenko, M. L., Svetlichnaya, T. P. and Alekseev, V. A. (1988) Characteristics of Desulfurococcus amylolyticus - a new extremely thermophilic archaebacterium isolated from thermal springs of Kamchatka and Kunashir island. Mikrobiologiya, 57, 78-85.
15. Bonch-Osmolovskaja, E. A., Miroschnichenko, M. L., Kostrikina, N. A., Chernych, N. A. and Zavarzin, G. A. (1990) Thermoproteus uzoniensis sp. nov., a new extremely thermophilic archaebacterium from Kamchatka continental hot spring. Arch. Microbiol., 154, 556-559.
16. Bonch-Osmolovskaja, E. A. and Stetter, K. O. (1991) Interspecies hydrogen transfer in cocultures of thermophilic Archaea. System. Appl. Microbiol., 14, 205-208.
17. Burggraf, S., Fricke, H., Neuner, A., Kristjansson, J. K. and Rouvier, P. (1990a) Methanococcus igneus sp. nov., a novel hyperthermophilic methanogen from a shallow submarine hydrothermal system. System. Appl. Microbiol., 13, 263-269.
18. Burggraf, S., Jannasch, H. W., Nicolaus, B. and Stetter, K. O. (1990b) Archaeoglobus profundus sp. nov., represent a new species within the sulfate-reducing archaebacteria. System. Appl. Microbiol., 13, 24-28.
19. Burggraf, S., Huber, H. and Stetter, K. O. (1997) Reclassification of the crenarchaeal orders and families in accordance with 16S rRNA sequence data. Intn. Jour. System. Bacteriol., 47, 657-660.
20. Chapelle, F. H., O'Neill, K., Bradley, P. M., Methe, B. A., Ciufo, S. A., Knobel, L. L. and Lovley, D. R. (2002) A hydrogen-based subsurface microbial community dominated by methanogens. Nature, 415, 312-315.
21. Corliss, J. B., Dymond, J., Gordon, L. I., Edmond, J. M., Herzen, R. P. v., Ballard, R. D., Green, K., Williams, D., Bainbridge, A., Crane, K. and van Andel, T. H. (1979) Submarine thermal springs on the Galapagos Rift. Science, 203, 1073-1083.
22. Cowen, J. P., Massoth, G. J. and Feely, R. A. (1990) Scavenging rates of dissolved manganese in a hydrothermal vent plume. Deep-Sea Research, 37, 1619-1637.
23. Cunningham, D. P. and Lundie Jr., L. L. (1993) Precipitation of cadmium by Clostridium thermoaceticum. Appl. Environ. Microbiol., 59, 7-14.
24. De Angeris, M. A., Lilley, M. D., Olson, E. J. and Baross, J. A. (1993) Methane oxidation in deep-sea hydrothermal plumes of the Endevour segment of the Juan de Fuca Ridge. Deep-Sea Research, Part I, 40, 1169-1186.
25. Fiala, G. and Stetter, K. O. (1986) Pyrococcus furiosus sp. nov. represents a novel genus of marine heterotrophic archaebacteria growing optimally at 100°C. Arch. Microbiol., 145, 56-61.
26. Fiala, G., Stetter, K. O., Jannasch, H. W., Langworthy, T. A. and Madson, J. (1986) Staphylothermus marinus sp. nov. represents a novel genus of extremely thermophilic submarine heterotrophic archaebacteria growing up to 98°C. System. Appl. Microbiol., 8, 106-113.
27. Fredrickson, J. K., Kostandarithes, H. M., Li, S. W., Plymale, A. E. and Daly, M. J. (2000) Reduction of Fe(III), Cr(VI), U(VI), and Tc(VII) by Deinococcus radiodurans R1. Appl. Environ. Microbiol., 66, 2006-2011.
28. Grayling, R. A., Sandman, K. and Reeve, J. N. (1996) Histones and chromatin structure in hyperthermophilic Archaea. FEMS Microbiol. Rev., 18, 203-213.
29. Hannington, M. D. and Jonasson, I. R. (1995) Physical and chemical processes of seafloor mineralization at mid-ocean ridge. in Humphris, S. E., Zierenberg, R. A., Mullineaux, L. S. and Thomson, R. E. (eds.) Seafloor Hydrothermal Systems: Physical, Chemical, Biological, and Geological Interactions. 115-157, American Geophysical Union, Washington.
30. Hattori, S., Kamagata, Y., Hanada, S. and Shoun, H. (2000) Thermacetogenium phaeum gen. nov., sp. nov., a strictly anaerobic, thermophilic, syntrophic acetate-oxidizing bacterium. Intn. Jour. System. Evol. Microbiol., 50, 1601-1609.
31. Hoaki, T., Wirsen, C. O., Hanzawa, S., Maruyama, T. and Jannasch, H. W. (1993) Amino acid requirements of two hyperthermophilic archaeal isolates from deep-sea vents, Desulfurococcus strain SY and Pyrococcus strain GB-D. Appl. Environ. Microbiol., 59, 610-613.
32. Hoaki, T., Nishijima, M., Kato, M., Adachi, K., Shigeyuki, M., Hazawa, N. and Maruyama, T. (1994) Growth requirements of hyperthermophilic sulfur-dependent heterotrophic archaea isolated from a shallow submarine geothermal system with reference to their essential amino acid. Appl. Environ. Microbiol., 60, 2898-2904.
33. Hoaki, T., Nishijima, M., Miyashita, H. and Maruyama, T. (1995) Dense community of hyperthermophilic sulfur-dependent heterotrophs in a geothermally heated shallow submarine biotope near Kodakara-Jima Island, Kagoshima, Japan. Appl. Environ. Microbiol., 61, 1931-1937.
34. Howarth, R. W. (1979) Pyrite: its rapid formation in a salt marsh and its importance in ecosystem metabolism. Science, 4375, 49.
35. Huber, R., Langworthy, T. A., König, H., Thomm, M., Woese, C. R. and Sleytr, U. B. (1986) Thermotoga maritima sp. nov. represents a new genus of unique extremely thermophilic eubacteria growing up to 90°C. Arch. Microbiol., 144, 324-333.
36. Huber, R., Kristjansson, J. K. and Stetter, K. O. (1989) Pyrobaculum gen. nov., a new genus of neutrophic, rod-shaped archaebacteria from continental solfataras growing optimally at 100°C. Arch. Microbiol., 149, 95-101.
37. Huber, R., Wilharm, T., Huber, D., Trincone, A., Burggraf, S., König, H., Rachel, R., Rockinger, I., Fricke, H. and Stetter, K. O. (1992) Aquifex pyrophilus gen. nov., sp. nov., represents a novel group of marine hyperthermophilic hydrogen oxidizing bacteria. Arch. Microbiol., 15, 340-351.
38. Huber, R., Eder, W., Heldwein, S., Wanner, G., Huber, H., Rachel, R. and Stetter, K. O. (1998a) Thermocrinis ruber gen. nov., sp. nov., a pink-filament-forming hyperthermophilic bacterium isolated from Yellowstone National Park. Appl. Environ. Microbiol., 64, 3576-3583.
39. Huber, R., Dyba, D., Huber, H., Burggraf, S. and Rachel, R. (1998b) Sulfur-inhibited Thermosphaera aggregans sp. nov., a new genus of hyperthermophilic archaea isolated after its prediction from environmentally derived 16S rRNA sequences. Intn. Jour. System. Bacteriol., 48, 31-38.
40. Huber, H., Burggraf, S., Mayer, T., Wyschkony, I., Rachel, R. and Stetter, K. O. (2000) Ignicoccus gen. nov., a novel genus of hyperthermophilic, chemolithoautotrophic Archaea, represented by two new species, Ignicoccus islandicus sp. nov. and Ignicoccus pacificus sp. nov. Intn. Jour. System. Evol. Microbiol., 50, 2093-2100.
41. Hugenholtz, P., Pitulle, C., Hershberger, K. L. and Pace, N. R. (1998) Novel division level bacterial diversity in a Yellowstone Hot Spring. Jour. Bacteriol., 180, 366-376.
42. Itoh, T., Suzuki, K., Sanchez, P. C. and Nakase, T. (1999) Caldivirga maquilingensis gen. nov., sp. nov., a new genus of rod-shaped crenarchaeote isolated from a hot spring in the Philippines. Intn. Jour. System. Bacteriol., 49, 1157-1163.
43. Jannasch, H. W. (1995) Microbial interaction with hydrothermal fluids. in Humphris, S. E., Zierenberg, R. A., Mullineaux, L. S. and Thomson, R. E. (eds.) Seafloor Hydrothermal Systems: Physical, Chemical, Biological, and Geological Interactions. 273-296, American Geophysical Union, Washington.
44. Jannasch, H. W. and Wirsen, C. O. (1981) Morphological survey of microbial mats near deep-sea thermal vents. Appl. Environ. Microbiol., 41, 528-538.
45. Jannasch, H. W. and Motti, M. J. (1985) Geomicrobiology of deep-sea hydrothermal vent. Science, 229, 717-725.
46. Jeanthon, C. and Prieur, D. (1990) Susceptibility to heavy metals and characterization of heterotrophic bacteria isolated from two hydrothermal vent polychaete annelids, Alvinella pompejana and Alvinella caudata. Appl. Environ. Microbiol., 56, 3308-3314.
47. Jeanthon, C., L'Haridon, S., Reysenbach, A.-L., Corre, E., Vernet, M., Messner, P., Sleytr, U. B. and Prieur, D. (1998) Methanococcus infernus sp. nov., a novel hyperthermophilic lithotrophic methanogen isolated from a deep-sea hydrothermal vent. Intn. Jour. System. Bacteriol., 48, 913-919.
48. Jeanthon, C., L'Haridon, S., Reysenbach, A.-L., Corre, E., Vernet, M., Messner, P., Sleytr, U. B. and Prieur, D. (1999) Methanococcus vulcanius sp. nov., a novel hyperthermophilic methanogen isolated from East Pacific Rise, and identification of Methanococcus sp. DSM 4213 T as Methanococcus fervens sp. nov. Intn. Jour. System. Bacteriol., 49, 583-589.
49. Juniper, S. K. and Fouquet, Y. (1988) Filamentous iron-silica deposits from modern and ancient hydrothermal sites. Canad. Mineral., 26, 859-869.
50. Juniper, S. K. and Sarrazin, J. (1995) Interaction of vent biota and hydrothermal deposits: present evidence and future experimentation. in Humphris, S. E., Zierenberg, R. A., Mullineaux, L. S. and Thomson, R. E. (eds.) Seafloor Hydrothermal Systems: Physical, Chemical, Biological, and Geological Interactions. 178-193, American Geophysical Union, Washington.
51. Jørgensen, B. B., Zawacki, L. X. and Jannasch, H. W. (1990) Thermophilic bacterial sulfate reduction in deep-sea sediments at the Guaymas Basin hydrothermal vent site. Deep-Sea Research, 37, 695-710.
52. Jørgensen, B. B., Isaksen, M. F. and Jannasch, H. W. (1992) Bacterial sulfate reduction above 100°C in deep-sea hydrothermal vent sediment. Science, 258, 1756-1757.
53. Kashefi, K. and Lovley, D. R. (2000) Reduction of Fe(III), Mn(IV), and toxic metals at 100°C by Pyrobaculum islandicum. Appl. Environ. Microbiol., 66, 1050-1056.
54. Kashefi, K., Tor, J. M., Nevin, K. P. and Lovley, D. R. (2001) Reductive precipitation of gold by dissimilatory Fe(III)-reducing bacteria and archaea. Appl. Environ. Microbiol., 67, 3275-3279.
55. Kelly, R. M. and Adams, M. W. W. (1994) Metabolism in hyperthermophilic microorganisms. Antonie Van Leewenhoek, 66, 247-270.
56. Kurosawa, N., Itoh, Y. H., Iwai, T., Sugai, A., Uda, I., Kimura, N., Horiuchi, T. and Itoh, T. (1998) Sulfurisphaera ohwakuensis gen. nov., sp. nov., a novel extremely thermophilic acidophile of the order Sulfolobales. Intn. Jour. System. Bacteriol., 48, 451-456.
57. Kurr, M., Huber, R., König, H., Jannasch, H. W., Fricke, H., Trincone, A., Kristjansson, J. K. and Stetter, K. O. (1991) Methanopyrus kanderli, gen. and sp. nov. represents a novel group of hyperthermophilic methanogens, growing at 110°C. Arch. Microbiol., 156, 239-247.
58. Laverman, A. M., Blum, J. S., Schaefer, J. K., Phillips, E. J. P., Lovley, D. R. and Oremland, R. S. (1995) Growth of strain SES-3 with arsenate and other diverse electron acceptors. Appl. Environ. Microbiol., 61, 3556-3561.
59. Les, A. and Walker, R. W. (1984) Toxicity and binding of copper, zinc, and cadmium by the blue-green alga, Chroococcus paris. Water, Air, and Soil Pollut., 23, 129-139.
60. 0 reduction by Pelobacter carbinolicus. Appl. Environ. Microbiol., 61, 2132-2138.
61. Madigan, M. T., Martinko, J. M. and Parker, J. (2000) Brock Biology of Microorganisms, edn. 9, Prentice Hall, Upper Saddle River, NJ.
62. Maher, K. A. and Stevenson, D. J. (1988) Impact frustration of the origin of life. Nature, 331, 612-614.
63. McCollom, T. M. and Shock, E. L. (1997) Geochemical constraints on chemolithoautotrophic metabolism by microorganisms in sea floor hydrothermal systems. Geochim. Cosmochim. Acta, 61, 4375-4391.
64. Mukund, S. and Adams, M. W. W. (1991) The novel tungsten-iron-sulfur protein of the hyperthermophilic archaebacterium, Pyrococcus furiosus, is an aldehyde ferredoxin oxidoreductase: evidence for its participation in a unique glycolytic pathway. Jour. Biol. Chem., 266, 14208-14216.
65. Mullen, M. D., Wolf, D. C., Ferris, F. G., Beveridge, T. J., Flemming, C. A. and Bailey, G. W. (1989) Bacterial sorption of heavy metals. Appl. Environ. Microbiol., 55, 3143-3149.
66. Nisbet, E. (2000) The realms of Archaean life. Nature, 405, 625-626.
67. Prokofeva, M. I., Miroshnichenko, M. L., Kostrikina, N. A., Chernyh, N. A., Kuznetsov, B. B., Tourova, T. P. and Bonch-Osmolovskaya, E. A. (2000) Acidilobus aceticus gen. nov., sp. nov., a novel anaerobic thermoacidophilic archaeon from continental hot vents in Kamchatka. Intn. Jour. System. Evol. Microbiol., 50, 2001-2008.
68. Rasmussen, B. (2000) Filamentous microfossils in a 3,235-million-year-old volcanogenic massive sulphide deposit. Nature, 405, 676-679.
69. Reysenbach, A.-L., Longnecker, K. and Kirshtein, J. (2000) Novel bacterial and archaeal lineages from an in situ growth chamber deployed at a Mid-Atlantic Ridge hydrothermal vent. Appl. Environ. Microbiol., 66, 3798-3816.
70. Roth, S. E. and Dymond, J. (1989) Transport and settling of organic material in a deep-sea hydrothermal plume: evidence from particle flux measurements. Deep-Sea Research, 36, 1237-1254.
71. Sandaa, R.-A., Enger, Ø. and Torsvik, V. (1999) Abundance and diversity of Archaea in heavy-metal-contaminated soils. Appl. Environ. Microbiol., 65, 3293-3297.
72. Scandurra, R., Consalvi, V., Chiaraluce, R., Politi, L. and Engel, P. C. (1998) Protein thermostability in extremophiles. Biochimie, 80, 933-941.
73. Segerer, A., Neuner, A., Kristjansson, J. K. and Stetter, K. O. (1986) Acidianus infernus gen. nov., sp. nov., and Acidianus brierleyi comb, nov.: facultatively aerobic, extremely acidophilic thermophilic sulfur-metabolizing archaebacteria. Intn. Jour. System. Bacteriol., 36, 559-564.
74. Silver, S. (1996) Bacterial resistances to toxic metal ions - a review. Gene, 179, 9-19.
75. Stetter, K. O. (1986) Diversity of extremely thermophilic archaebacteria. in Brock, T. D. (ed.) The Thermophiles, General, Molecular and Applied Microbiology. 39-74, Wiley, New York.
76. Stetter, K. O. (1988) Archaeoglobus fulgidis gen. nov., sp. nov.: a new taxon of extremely thermophilic archaebacteria. System. Appl. Microbiol., 10, 172-173.
77. Stetter, K. O. (1996) Hyperthermophilic procaryotes. FEMS Microbiol. Rev., 18, 149-158.
78. Stetter, K. O. and Gaag, G. (1983) Reduction of molecular sulphur by methanogenic bacteria. Nature, 305, 309-311.
79. Stetter, K. O., Thomm, M., Winter, J., Wildegruber, G., Huber, H., Zillig, W., Janekovic, D., König, H., Palm, P. and Wunderl, S. (1981) Methanothermus fervidus, sp. nov., a novel extremely thermophilic methanogen isolated from an Icelandic hot spring. Zentrabl. Bakteriol. Parasitenkd. Infektionskr, Hyg. Abt. 1: Orig. Reihe C, 2, 166-178.
80. Stetter, K. O., König, H. and Stackebrandt, E. (1983) Pyrodictim gen. nov., a new genus of submarine disc-shaped sulfur reducing archaebacteria growing optimally at 105°C. System. Appl. Microbiol., 4, 535-551.
81. Takai, K. and Horikoshi, K. (1999) Genetic diversity of archaea in deep-sea hydrothermal vent environments. Genetics, 152, 1285-1297.
82. Takai, K. and Sako, Y. (1999) A molecular view of archaeal diversity in marine and terrestrial hot water environments. FEMS Microbiol. Ecol., 28, 177-188.
83. Trent, J. D. (1996) A review of acquired thermotolerance, heat-shock proteins, and molecular chaperones in archaea. FEMS Microbiol. Rev., 18, 249-258.
84. Vargas, M., Kashefi, K., Blunt-Harris, E. L. and Lovley, D. R. (1998) Microbiological evidence for Fe(III) reduction on early earth. Nature, 395, 65-67.
85. Völkl, P., Huber, R., Drobner, E., Rachel, R., Burggraf, S., Trincone, A. and Stetter, K. O. (1993) Pyrobaculum aerophilum sp. nov., a novel nitrate-reducing hyperthermophilic archaeum. Appl. Environ. Microbiol., 59, 2918-2926.
86. Wang, C. L., Michels, P. C., Dawson, S. C., Kitisakkul, S., Baross, J. A., Keasling, J. D. and Clark, D. S. (1997) Cadmium removal by a new strain of Pseudomonas aeruginosa in aerobic culture. Appl. Environ. Microbiol., 63, 4075-4078.
87. Wirsen, C. O., Jannasch, H. W. and Molyneaux, S. J. (1993) Chemosynthetic microbial activity at Mid-Atlantic Ridge hydrothermal vent sites. Jour. Geophys. Research, 98, 9693-9703.
88. Woese, C. R., Kandler, O. and Wheelis, M. L. (1990) Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA, 87, 4576-4579.
89. Zillig, W., Gierl, A., Schäfer, W., Wunderl, S., Janekovic, D., Stetter, K. O. and Klenk, H. P. (1983a) The archaebacterium Thermofilum pendens represents a novel genus of thermophilic, anaerobic sulfur respiring Thermoproteales. System. Appl. Microbiol., 4, 79-87.
90. Zillig, W., Holtz, I., Janekovic, D., Klenk, H.-P., Imsel, E., Trent, J., Wunderl, S., Forjaz, V. H., Coutinho, R. and Ferreira, T. (1983b) Hyperthermus butylicus, a hyperthermophilic sulfur-reducing archaebacterium that ferments peptides. Jour. Bacteriol., 172, 3959-3965.
91. Zillig, W., Holtz, I., Janekovic, D., Schafer, W. and Reiter, W. D. (1983c) The archaebacterium Thermococcus celer represents a novel genus within the thermophilic branch of the archaebacteria. System. Appl. Microbiol., 4, 88-94.