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References

  • [1]
    D.M. Karl Ecology of free-living, hydrothermal vent microbial communities D.M. Karl The Microbiology of Deep-sea Hydrothermal Vents 1995 CRC Press Inc. Boca Raton, FL 35 124.
  • [2]
    Delaney, J.R., Kelly, D.S., Lilley, M.D., Butterfield, D.A., Baross, J.A., Wilcock, W.S.D., Embley, R.W., Summit, M. (1998) The quantum event of oceanic crustal accretion: impacts of diking at mid-ocean ridges. Science 281, 222230.
  • [3]
    Summit, M., Baross, J.A. (2001) A novel microbial habitat in the mid-ocean ridge subseafloor. Proc. Natl. Acad. Sci. USA 98, 21582163.
  • [4]
    Takai, K., Gamo, T., Tsunogai, U., Nakayama, N., Hirayama, H., Nealson, K.H., Horikoshi, H. (2004) Geochemical and microbiological evidence for a hydrogen-based, hyperthermophilic subsurface Lithoautotrophic microbial ecosystem (HyperSLiME) beneath an active deep-sea hydrothermal field. Extremophiles 8, 269282.
  • [5]
    Prieur, D., Erauso, G., Jeanthon, C. (1995) Hyperthermophilic life at deep-sea hydrothermal vents. Planet Space Sci. 43, 115122.
  • [6]
    Takai, K., Horikoshi, K. (1999) Genetic diversity of archaea in deep-sea hydrothermal vent environments. Genetics 152, 12851297.
  • [7]
    Reysenbach, A.-L., Longnecker, K., 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, 37983806.
  • [8]
    Teske, A., Hinrichs, K.-U., Edgcomb, V., de Versa Gomez, A., Kysela, D., Sylva, S.P., Sogin, M.L., Jannasch, H.W. (2002) Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities. Appl. Environ. Microbiol. 68, 19942007.
  • [9]
    Huber, J.A., Butterfield, D.A., Baross, J.A. (2003) Bacterial diversity in a subseafloor habitat following a deep-sea volcanic eruption. FEMS Microbiol. Ecol. 43, 393409.
  • [10]
    Harmsen, H.J.M., Prier, D., Jeanthon, C. (1997) Distribution of microorganisms in deep-sea hydrothermal vent chimneys investigated by whole-cell hybridization and enrichment culture of themophilic subpopulations. Appl. Environ. Microbiol. 63, 28762883.
  • [11]
    Takai, K., Komatsu, T., Inagaki, F., Horikoshi, K. (2001) Distribution of archaea in a black smoker chimney structure. Appl. Environ. Microbiol. 67, 36183629.
  • [12]
    van Dover, C.L, Humphris, S.E., Fornari, D., Cavanaugh, C.M., Collier, R., Goffredi, S.K., Hashimoto, J., Lilley, M.D., Reysenbach, A.-L., Shank, T.M., von Damm, K.L., Banta, A., Gallant, R.M., Götz, D., Green, D., Hall, J., Harmer, T.L., Hurtado, L.A., Johnson, P., McKiness, Z.P., Meredith, C., Olson, E., Pan, I.L., Turnipseed, M., Won, Y. C.R. Young IIIVrijenhoek, R.C. (2001) Biogeography and ecological setting of Indian Ocean hydrothermal vents. Science 294, 818823.
  • [13]
    von Damm, K.L. (1990) Seafloor hydrothermal activity: black smoker chemistry and chimneys. Annu. Rev. Earth Planet. Sci. 18, 173204.
  • [14]
    Massoth, G.J., Butterfield, D.A., Lupton, J.E., McDuff, R.E., Lilley, M.D., Jonasson, I.R. (1989) Submarine venting of phase-separated hydrothermal fluids at Axial Volcano, Juan de Fuca Ridge. Nature 340, 702705.
  • [15]
    Polz, M.F., Cavanaugh, C.M. (1995) Dominance of one bacterial phylotype at a Mid-Atlantic Ridge hydrothermal vent site. Proc. Natl. Acad. Sci. USA 92, 72327236.
  • [16]
    Longnecker, K., Reysenbach, A.-L. (2001) Expansion of the geographic distribution of a novel lineage of epsilon-Proteobacteria to a hydrothermal vent site on the Southern East Pacific Rise. FEMS Microbiol. Ecol. 35, 287293.
  • [17]
    Alain, K., Olagnon, M., Desbruyères, D., Pagé, A., Barbier, G., Juniper, S.K., Quérellow, J., Cambon-Bonavita, M.-A. (2002) Phylogenetic characterization of the bacterial assemblage associated with mucous secretions of the hydrothermal vent polychaete Paralvinella palmiformis. FEMS Microbiol. Ecol. 42, 463476.
  • [18]
    Huber, J.A., Butterfield, D.A., Baross, J.A. (2002) Temporal changes in archaeal diversity and chemistry in a mid-ocean ridge subseafloor habitat. Appl. Environ. Microbiol. 68, 15851594.
  • [19]
    Schrenk, M.O., Kelley, D.S., Delaney, J.R., Baross, J.A. (2003) Incidence and diversity of microorganisms within the walls of an active deep-sea sulfide chimney. Appl. Environ. Microbiol. 69, 35803592.
  • [20]
    Reysenbach, A.-L., Banta, A.B., Boone, D.R., Cary, S.C., Luther, G.W., Microbial essentials at hydrothermal vents. Nature. 404, 2000, 835.
  • [21]
    Campbell, B.J., Jeanthon, C., Kostka, J.E., Luther, G.W., Cary, S.C. (2001) Growth and phylogenetic properties of novel bacteria belonging to the epsilon subdivision of the Proteobacteria enriched from Alvinella pompejana and deep-sea hydrothermal vents. Appl. Environ. Microbiol. 67, 45664572.
  • [22]
    Alain, K., Querellou, J., Lesongeur, F., Pignet, P., Crassous, P., Raguenes, G., Cueff, V., Cambon-Bonavita, M.A. (2002) Caminibacter hydrogeniphilus gen. nov., sp. nov., a novel thermophilic, hydrogen-oxidizing bacterium isolated from an East Pacific Rise hydrothermal vent. Int. J. Syst. Evol. Microbiol. 52, 13171323.
  • [23]
    Miroshnichenko, M.L., Kostrikina, N.A., L’ Haridon, S., Jeanthon, C., Hippe, H., Stackebrandt, E., Bonch-Osmolovskaya, E.A. (2002) Nautilia lithotrophica gen. nov., sp. nov., a thermophilic sulfur-reducing epsilon-proteobacterium isolated from a deep-sea hydrothermal vent. Int. J. Syst. Evol. Microbiol. 52, 12991304.
  • [24]
    Inagaki, F., Takai, K., Kobayashi, H., Nealson, K.H., Horikoshi, H. (2003) Sulfurimonas autotrophica gen. nov., sp.nov., a novel sulfur-oxidizing epsilon-proteobacterium isolated from hydrothermal sediments in the mid-Okinawa Trough. Int. J. Syst. Evol. Microbiol. 53, 18011805.
  • [25]
    Nakagawa, S., Takai, K., Horikoshi, K., Sako, Y. (2003) Persephonella hydrogeniphila sp. nov., a novel thermophilic, hydrogen-oxidizing bacterium from a deep-sea hydrothermal vent chimney. Int. J. Syst. Evol. Microbiol. 53, 863869.
  • [26]
    Takai, K., Inagaki, F., Nakagawa, S., Hirayama, H., Nunoura, T., Sako, Y., Nealson, K.H., Horikoshi, K. (2003) Isolation and phylogenetic diversity of members of previously uncultivated epsilon-Proteobacteria in deep-sea hydrothermal fields. FEMS Microbiol. Lett. 218, 167174.
  • [27]
    Miroshnichenko, M.L., L’ Haridon, S., Schumann, P., Spring, S., Bonch-Osmolovskaya, E.A., Jeanthon, C., Stackebrandt, E. (2004) Caminibacter profundus sp. nov., a novel thermophile of Nautiliales ord. nov. within the class ‘Epsilonproteobacteria’, isolated from a deep-sea hydrothermal vent. Int. J. Syst. Evol. Microbiol. 54, 4145.
  • [28]
    Nakagawa, S., Inagaki, F., Takai, K., Horikoshi, K., Sako, Y. (2005) Thioreductor micantisoli gen. nov., sp. nov., a novel mesophilic, sulfur-reducing chemolithoautotroph within the ɛ-Proteobacteria isolated from the hydrothermal sediments in the Mid-Okinawa Trough. Int. J. Syst. Evol. Microbiol. 55, 599605.
  • [29]
    Nakagawa, S., Takai, K., Inagaki, F., Horikoshi, K., Sako, Y. (2005) Nitratiruptor tergarcus gen. nov., sp. nov., Nitratifractor salsuginis gen. nov., sp. nov., nitrate-reducing chemolithoautotrophs of the ɛ-Proteobacteria isolated from a deep-sea hydrothermal system in the Mid-Okinawa Trough. Int. J. Syst. Evol. Microbiol. 55, 925933.
  • [30]
    Takai, K., Oida, H., Suzuki, Y., Hirayama, H., Nakagawa, S., Nunoura, T., Inagaki, F., Nealson, K.H., Horikoshi, K. (2004) Spatial distribution of Marine Crenarchaeota Group I (MGI) in the vicinity of deep-sea hydrothermal systems. Appl. Environ. Microbiol. 70, 24042413.
  • [31]
    Glasby, G.P., Notsu, K. (2003) Submarine hydrothermal mineralization in the Okinawa Trough, SW of Japan: an overview. Ore Geol. Rev. 23, 299339.
  • [32]
    Ishibashi, J., Sano, Y., Wakita, H., Gamo, T., Tsutsumi, M., Sakai, H. (1995) Helium and carbon geochemistry of hydrothermal fluids from the Mid-Okinawa Trough back arc basin, southwest of Japan. Chem. Geol. 123, 115.
  • [33]
    Sako, Y, Takai, K., Ishida, Y., Uchida, A., Katayama, Y. (1996) Rhodothermus obamensis sp. nov., a modern lineage of extremely thermophilic marine bacteria. Int. J. Syst. Bacteriol. 46, 10991104.
  • [34]
    Porter, K.G., Feig, Y.S. (1980) The use of DAPI for identifying and counting aquatic microflora. Limnol. Oceanogr. 25, 943948.
  • [35]
    Weinbauer, M.G, Beckmann, C., Hofle, M.G. (1998) Utility of green fluorescent nucleic acid dyes and aluminum oxide membrane filters for rapid epifluorescence enumeration of soil and sediment bacteria. Appl. Environ. Microbiol. 64, 50005003.
  • [36]
    Sakai, H., Gamo, T., Kim, E.-S., Shitashima, K., Yanagisawa, F., Tsutsumi, M., Ishibashi, J., Sano, Y., Wakita, H., Tanaka, T., Matsumoto, T., Naganuma, T., Mitsuzawa, K. (1990) Unique chemistry of the hydrothermal solution in the mid-Okinawa Trough backarc basin. Geophys. Res. Lett. 17, 21332136.
  • [37]
    Tsunogai, U., Toki, T., Nakayama, N., Gamo, T., Kato, H., Kaneko, S., WHATS: a new multi-bottle gas-tight sampler for sea-floor vent fluids. Chikyukagaku (Geochemistry). 37, 2003, 101–109 (In Japanese with English abstract).
  • [38]
    Gamo, T., Chiba, H., Yamanaka, T., Okudaira, T., Hashimoto, J., Tsuchida, S., Ishibashi, J., Kataoka, S., Tsunogai, U., Okamura, K., Sano, Y., Shinjo, R. (2001) Chemical characteristics of newly discovered black smoker fluids and associated hydrothermal plumes at the Rodriguez Triple Junction, Central Indian Ridge. Earth Planet. Sci. Lett. 193, 371379.
  • [39]
    von Damm, K.L., Edmond, J.M., Grant, B., Measures, C.I., Malden, B., Weiss, R.F. (1985) Chemistry of submarine hydrothermal solutions at 21°N, East Pacific Rise. Geochim. Cosmochim. Acta 49, 21972220.
  • [40]
    Sako, Y., Nakagawa, S., Takai, K., Horikoshi, K. (2003) Marinithermus hydrothermalis gen. nov., sp. nov., a strictly aerobic, thermophilic bacterium from a deep-sea hydrothermal vent chimney. Int. J. Syst. Evol. Microbiol. 53, 5965.
  • [41]
    Balch, W.E., Fox, G.E., Magrum, L.J., Woese, C.R., Wolfe, R.S. (1979) Methanogens: reevaluation of a unique biological group. Microbiol. Rev. 43, 260296.
  • [42]
    Takai, K., Inoue, A., Horikoshi, K. (2002) Methanothermococcus okinawensis sp. nov., a thermophilic, methane-producing archaeon isolated from a Western Pacific deep-sea hydrothermal system. Int. J. Syst. Evol. Microbiol. 52, 10891095.
  • [43]
    Lane, D.J., 16S/23S sequencing, Stackbrandt, E., Goodfellow, M., Eds. 1985, Wiley, New York, NY, 115–176.
  • [44]
    DeLong, E.F. (1992) Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89, 56855689.
  • [45]
    Lipman, D.J., Pearson, W.R (1985) Rapid and sensitive protein similarity searches. Science 227, 14351441.
  • [46]
    Maidak, B.L., Cole, J.R., Lilburn, T.G. Parker Jr., C.T., Saxman, P.R., Farris, R.J., Garrity, G.M., Olsen, G.J., Schmidt, T.M., Tiedje, J.M. (2001) The RDP-II (Ribosomal Database Project). Nucleic Acids Res. 29, 173174.
  • [47]
    Ludwig, W., Bauer, S.H., Bauer, M., Held, I., Kirchhof, G., Schulze, R., Huber, I., Spring, S., Hartmann, A., Schleifer, K.H (1997) Detection and in situ identification of representatives of a widely distributed new bacterial phylum. FEMS Microbiol. Lett. 153, 181190.
  • [48]
    Good, I.J. (1953) The population frequencies of species and the estimation of population parameters. Biometrica 40, 237264.
  • [49]
    Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, B.A., Lai, T., Steppi, S., Jobb, G., Förster, W., Brettske, I., Gerber, S., Ginhart, A.W., Gross, O., Grumann, S., Hermann, S., Jost, R., König, A., Liss, T., Lüßmann, R., May, M., Nonhoff, B., Reichel, B., Strehlow, R., Stamatakis, A., Stuckmann, N., Vilbig, A., Lenke, M., Ludwig, T., Bode, A., Schleifer, K.H. (2004) ARB: a software environment for sequence data. Nucleic Acids Res. 32, 13631371.
  • [50]
    D.L. Swofford PAUP*. Phylogenetic analysis using parsimony (and other methods), version 4 2000 Sinauer Associates Sunderland, MA.
  • [51]
    Takai, K., Horikoshi, K. (2000) Rapid detection and quantification of members of the archaeal community by quantitative PCR using fluorogenic probes. Appl. Environ. Microbiol. 66, 50665072.
  • [52]
    Chao, A. (1987) Estimating the population size for capture-recapture data with unequal catchability. Biometrics 43, 783791.
  • [53]
    Magurran, A.E., Ecological Diversity and its Measurement 1988, Princeton University Press, Princeton, NJ pp. 7–47.
  • [54]
    C.J. Krebs Similarity coefficients and cluster analysis C.J. Krebs Ecological Methodology 1998 Benjamin Cummings Menlo Park, Calif 375 409.
  • [55]
    Singleton, D.R., Furlong, M.A., Rathbun, S.L., Whitman, W.B. (2001) Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl. Environ. Microbiol. 67, 43744376.
  • [56]
    A.N. Pettitt Cramer-von Mises statistic N.L. Johnson S. Kotz Encyclopedia of Statistical Sciences 1982 Wiley-Interscience New York, NY 220 221.
  • [57]
    J. Felsenstein PHYLIP (phylogenetic inference package) version 3.6b 1993 University of Washington Seattle.
  • [58]
    Butterfield, D.A., McDuff, R.E., Mottl, M.J., Lilley, M.D., Lupton, J.E., Massoth, G.J. (1994) Gradients in the composition of hydrothermal fluids from the Endeavour Ridge vent field: phase separation and brine loss. J. Geophys. Res. 99, 95619583.
  • [59]
    López-Garcia, P., Duperron, S., Philippot, P., Foriel, J., Susini, J., Moreira, D. (2003) Bacterial diversity in hydrothermal sediment and epsilonproteobacterial dominance in experimental microcolonizers at Mid-Atlantic Ridge. Environ. Microbiol. 5, 961976.
  • [60]
    Corre, E., Reysenbach, A.-L., Prieur, D. (2001) Epsilon-proteobacterial diversity from a deep-sea hydrothermal vent on the Mid-Atlantic Ridge. FEMS Microbiol. Lett. 205, 329335.
  • [61]
    Zhou, J.Z., Xia, B.C., Treves, D.S., Wu, L.Y., Marsh, T.L., O’ Neill, R.V., Palumbo, A.V., Tiedje, J.M. (2002) Spatial and resource factors influencing high microbial diversity in soil. Appl. Environ. Microbiol. 68, 326334.
  • [62]
    Jeanthon, C. (2000) Molecular ecology of hydrothermal vent microbial communities. Anton. Leeuw. 77, 117133.
  • [63]
    Nakagawa, T., Nakagawa, S., Inagaki, F., Takai, K., Horikoshi, K. (2004) Phylogenetic diversity of sulfate-reducing prokaryotes in active deep-sea hydrothermal vent chimney structures. FEMS Microbiol. Lett. 232, 145152.
  • [64]
    Tivey, M.K. (2004) Environmental conditions within active seafloor vent structures: sensitivity to vent fluid composition and fluid flow. In: The subseafloor biosphere at mid-Ocean Ridges, Geophysical Monograph 144 (Wilcock, W.S.D., DeLong, E.F., Kelley, D.S., Baross, J.A., Cary, S.C., Eds.), pp. 137–152. American Geophysical Union, Washington DC