• [1]
    MacDonald, I.R., Guinasso, N.L., Sassen, R., Brooks, J.M., Lee, L., Scott, K.T. (1994) Gas hydrate that breaches the sea-floor on the continental-slope of the Gulf of Mexico. Geology 22, 699702.
  • [2]
    Milkov, A.V., Sassen, R. (2001) Estimate of gas hydrate resource, northwestern Gulf of Mexico continental slope. Mar. Geol. 179, 7183.
  • [3]
    Buffett, B.A. (2000) Clathrate hydrates. Annu. Rev. Earth Planet. Sci. 28, 477507.
  • [4]
    Kvenvolden, K.A. (1993) Gas hydrates – geological perspective and global change. Rev. Geophys. 31, 173187.
  • [5]
    Kvenvolden, K.A. (1988) Methane hydrate – a major reservoir of carbon in the shallow geosphere. Chem. Geol. 71, 4151.
  • [6]
    Carpenter, G. (1981) Coincident sediment slump/clathrate complexes on the U.S. Atlantic continental slope. Geo-Mar. Lett. 1, 2932.
  • [7]
    Paull, C.K., Buelow, W.J., Ussler, W., Borowski, W.S. (1996) Increased continental-margin slumping frequency during sea-level lowstands above gas hydrate-bearing sediments. Geology 24, 143146.
  • [8]
    Rothwell, R.G., Thomson, J., Kahler, G. (1998) Low-sea-level emplacement of a very large Late Pleistocene ‘megaturbidite’ in the western Mediterranean Sea. Nature 392, 377380.
  • [9]
    MacDonald, I.R., Reilly, J.F., Guinasso, N.L., Brooks, J.M., Carney, R.S., Bryant, W.A., Bright, T.J. (1990) Chemosynthetic mussels at a brine-filled pockmark in the northern Gulf of Mexico. Science 248, 10961099.
  • [10]
    Lashof, D.A., Ahuja, D.R. (1990) Relative contributions of greenhouse gas emissions to global warming. Nature 344, 529531.
  • [11]
    Nisbet, E.G. (1992) Sources of atmospheric CH4 in early postglacial time. J. Geophys. Res. Atmos. 97, 1285912867.
  • [12]
    Paull, C.K., Ussler, W., Dillon, W.P. (1991) Is the extent of glaciation limited by marine gas-hydrates. Geophys. Res. Lett. 18, 432434.
  • [13]
    Miller, S.L., Smythe, W.D. (1970) Carbon dioxide clathrate in the Martian ice cap. Science 170, 531533.
  • [14]
    Baker, V.R., Strom, R.G., Gulick, V.C., Kargel, J.S., Komatsu, G., Kale, V.S. (1991) Ancient oceans, ice sheets and the hydrological cycle on Mars. Nature 352, 589594.
  • [15]
    Zahnle, K., Pollack, J.B., Grinspoon, D., Dones, L. (1992) Impact-generated atmospheres over Titan, Ganymede, and Callisto. Icarus 95, 123.
  • [16]
    Joye, S.B., Boetius, A., Orcutt, B.N., Montoya, J.P., Schulz, H.N., Erickson, M.J. and Lugo, S.K. (2003) Sediment signatures of the anaerobic oxidation of methane and sulfate reduction at Gulf of Mexico cold seeps. Chem. Geol. (in press).
  • [17]
    Cragg, B.A., Parkes, R.J., Fry, J.C., Weightman, A.J., Rochelle, P.A., Maxwell, J.R. (1996) Bacterial populations and processes in sediments containing gas hydrates (ODP Leg 146: Cascadia Margin). Earth Planet. Sci. Lett. 139, 497507.
  • [18]
    Kosiur, D.R., Warford, A.L. (1979) Methane production and oxidation in Santa Barbara Basin sediments. Estuar. Coast. Mar. Sci. 8, 379385.
  • [19]
    Iversen, N., Jorgensen, B.B. (1985) Anaerobic methane oxidation rates at the sulfate-methane transition in marine sediments from Kattegat and Skagerrak (Denmark). Oceanography 30, 944955.
  • [20]
    Borowski, W.S., Paull, C.K., Ussler, W. (1997) Carbon cycling within the upper methanogenic zone of continental rise sediments: An example from the methane-rich sediments overlying the Blake Ridge gas hydrate deposits. Mar. Chem. 57, 299311.
  • [21]
    Bidle, K.A., Kastner, M., Bartlett, D.H. (1999) A phylogenetic analysis of microbial communities associated with methane hydrate containing marine fluids and sediments in the Cascadia margin (ODP site 892B). FEMS Microbiol. Lett. 177, 101108.
  • [22]
    Marchesi, J.R., Weightman, A.J., Cragg, B.A., Parkes, R.J., Fry, J.C. (2001) Methanogen and bacterial diversity and distribution in deep gas hydrate sediments from the Cascadia Margin as revealed by 16S rRNA molecular analysis. FEMS Microbiol. Ecol. 34, 221228.
  • [23]
    Hinrichs, K.U., Hayes, J.M., Sylva, S.P., Brewer, P.G., DeLong, E.F. (1999) Methane-consuming archaebacteria in marine sediments. Nature 398, 802805.
  • [24]
    Orphan, V.J., Hinrichs, K.U., Ussler, W., C.K. Paull, IIITaylor, L.T., Sylva, S.P., Hayes, J.M., Delong, E.F. (2001) Comparative analysis of methane-oxidizing archaea and sulfate-reducing bacteria in anoxic marine sediments. Appl. Environ. Microbiol. 67, 19221934.
  • [25]
    Boetius, A., Ravenschlag, K., Schubert, C.J., Rickert, D., Widdel, F., Gieseke, A., Amann, R., Jorgensen, B.B., Witte, U., Pfannkuche, O. (2000) A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407, 623626.
  • [26]
    Orphan, V.J., House, C.H., Hinrichs, K.U., McKeegan, K.D., DeLong, E.F. (2001) Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science 293, 484487.
  • [27]
    Orphan, V.J., House, C.H., Hinrichs, K.U., McKeegan, K.D., DeLong, E.F. (2002) Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments. Proc. Natl. Acad. Sci. USA 99, 76637668.
  • [28]
    Thomsen, T.R., Finster, K., Ramsing, N.B. (2001) Biogeochemical and molecular signatures of anaerobic methane oxidation in a marine sediment. Appl. Environ. Microbiol. 67, 16461656.
  • [29]
    Teske, A., Hinrichs, K.U., Edgcomb, V., de Vera 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.
  • [30]
    Powers, L.G., Mills, H.J., Palumbo, A.V., Zhang, C.L., Delaney, K., Sobecky, P.A. (2002) Introduction of a plasmid-encoded phoA gene for constitutive overproduction of alkaline phosphatase in three subsurface Pseudomonas isolates. FEMS Microbiol. Ecol. 41, 115123.
  • [31]
    Miller, D.N., Bryant, J.E., Madsen, E.L., Ghiorse, W.C. (1999) Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl. Environ. Microbiol. 65, 47154724.
  • [32]
    Tebbe, C.C., Vahjen, W. (1993) Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant-DNA from bacteria and a yeast. Appl. Environ. Microbiol. 59, 26572665.
  • [33]
    Daly, K., Sharp, R.J., McCarthy, A.J. (2000) Development of oligonucleotide probes and PCR primers for detecting phylogenetic subgroups of sulfate-reducing bacteria. Microbiol. 146, 16931705.
  • [34]
    Johnson, J.L. (1994) Similarity analysis of rRNAs. In: Methods for General and Molecular Bacteriology (Gerhardt, P., Murray, R.G.E., Wood, W.A. and Krieg, N.R., Eds.), pp. 683–700. American Society for Microbiology, Washington, DC.
  • [35]
    DeLong, E.F. (1992) Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89, 56855689.
  • [36]
    Tatusova, T.A., Madden, T.L. (1999) BLAST 2 SEQUENCES, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol. Lett. 174, 247250.
  • [37]
    Hall, T.A. (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41, 9598.
  • [38]
    Maidak, B.L., Cole, J.R., C.T. Parker, Jr.Garrity, G.M., Larsen, N., Li, B., Lilburn, T.G., McCaughey, M.J., Olsen, G.J., Overbeek, R., Pramanik, S., Schmidt, T.M., Tiedje, J.M., Woese, C.R. (1999) A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res. 27, 171173.
  • [39]
    Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G. (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 48764882.
  • [40]
    Perriere, G., Gouy, M. (1996) WWW-query: an on-line retrieval system for biological sequence banks. Biochimie 78, 364369.
  • [41]
    Heck, K.L., Belle, G.v., Simberloff, D. (1975) Explict calculation of the rarefaction diversity measurement and the determination of sufficient sample size. Ecology 56, 14591461.
  • [42]
    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.
  • [43]
    Teske, A., Brinkhoff, T., Muyzer, G., Moser, D.P., Rethmeier, J., Jannasch, H.W. (2000) Diversity of thiosulfate-oxidizing bacteria from marine sediments and hydrothermal vents. Appl. Environ. Microbiol. 66, 31253133.
  • [44]
    Zhang, C.L., Li, Y., Wall, J.D., Larsen, L., Sassen, R., Huang, Y., Wang, Y., Peacock, A., White, D.C., Horita, J., Cole, D.R. (2002) Lipid and carbon isotopic evidence of methane-oxidizing and sulfate-reducing bacteria in association with gas hydrates from the Gulf of Mexico. Geology 30, 239242.
  • [45]
    Radjasa, O.K., Urakawa, H., Kita-Tsukamoto, K., Ohwada, K. (2001) Characterization of psychrotrophic bacteria in the surface and deep-sea waters from the northwestern Pacific Ocean based on 16S ribosomal DNA analysis. Mar. Biotechnol. 3, 454462.
  • [46]
    Fujiwara, Y., Kato, C., Masui, N., Fujikura, K., Kojima, S. (2001) Dual symbiosis in the cold-seep thyasirid clam Maorithyas hadalis from the hadal zone in the Japan Trench, western Pacific. Mar. Ecol. Prog. Ser. 214, 151159.
  • [47]
    Wu, J.H., Liu, W.T., Tseng, I.C., Cheng, S.S. (2001) Characterization of a 4-methylbenzoate-degrading methanogenic consortium as determined by small-subunit rDNA sequence analysis. J. Biosci. Bioeng. 91, 449455.
  • [48]
    Derakshani, M., Lukow, T., Liesack, W. (2001) Novel bacterial lineages at the (sub)division level as detected by signature nucleotide-targeted recovery of 16S rRNA genes from bulk soil and rice roots of flooded rice microcosms. Appl. Environ. Microbiol. 67, 623631.
  • [49]
    Devereux, R., Kane, M.D., Winfrey, J., Stahl, D.A. (1992) Genus- and group-specific hybridization probes for determinative and environmental studies of sulfate-reducing bacteria. Syst. Appl. Microbiol. 15, 601609.
  • [50]
    Stackebrandt, E., Sproer, C., Rainey, F.A., Burghardt, J., Pauker, O., Hippe, H. (1997) Phylogenetic analysis of the genus Desulfotomaculum: Evidence for the misclassification of Desulfotomaculum guttoideum and description of Desulfotomaculum orientis as Desulfosporosinus orientis gen. nov., comb. nov. Int. J. Syst. Bacteriol. 47, 11341139.
  • [51]
    Hernandez-Eugenio, G., Fardeau, M.L., Cayol, J.L.A., Patel, B.K.C., Thomas, P., Macarie, H., Garcia, J.L., Ollivier, B. (2002) Clostridium thiosulfatireducens sp nov., a proteolytic, thiosulfate- and sulfur-reducing bacterium isolated from an upflow anaerobic sludge blanket (UASB) reactor. Int. J. Syst. Evol. Microbiol. 52, 14611468.
  • [52]
    Mechichi, T., Fardeau, M.L., Labat, M., Garcia, J.L., Verhe, F., Patel, B.K.C. (2000) Clostridium peptidivorans sp nov., a peptide-fermenting bacterium from an olive mill wastewater treatment digester. Int. J. Syst. Evol. Microbiol. 50, 12591264.
  • [53]
    Reed, D.W., Fujita, Y., Delwiche, M.E., Blackwelder, D.B., Sheridan, P.P., Uchida, T., Colwell, F.S. (2002) Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin. Appl. Environ. Microbiol. 68, 37593770.
  • [54]
    Lanoil, B.D., Sassen, R., La Duc, M.T., Sweet, S.T., Nealson, K.H. (2001) Bacteria and Archaea physically associated with Gulf of Mexico gas hydrates. Appl. Environ. Microbiol. 67, 51435153.
  • [55]
    Eggen, R., Harmsen, H., Geerling, A., Devos, W.M. (1989) Nucleotide sequence of a 16S ribosomal RNA encoding gene from the Archaebacterium Methanothrix soehngenii. Nucl. Acids Res. 17, 94699469.
  • [56]
    Munson, M.A., Nedwell, D.B., Embley, T.M. (1997) Phylogenetic diversity of Archaea in sediment samples from a coastal salt marsh. Appl. Environ. Microbiol. 63, 47294733.
  • [57]
    Moeseneder, M.M., Winter, C., Arrieta, J.M., Herndl, G.J. (2001) Terminal-restriction fragment length polymorphism (T-RFLP) screening of a marine archaeal clone library to determine the different phylotypes. J. Microbiol. Methods 44, 159172.
  • [58]
    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.
  • [59]
    Takai, K., Horikoshi, K. (1999) Genetic diversity of archaea in deep-sea hydrothermal vent environments. Genetics 152, 12851297.
  • [60]
    Boone, D.R., Mathrani, I.M., Liu, Y.T., Menaia, J., Mah, R.A., Boone, J.E. (1993) Isolation and characterization of Methanohalophilus portucalensis sp. nov. and DNA reassociation study of the genus Methanohalophilus. Int. J. Syst. Bacteriol. 43, 430437.