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References

  • Bachmann BJ (1955) Studies on Cytophaga fermentans n. sp. a facultatively anaerobic lower myxobacterium. J Gen Microbiol 13: 541551.
  • Balkwill DL, Leach FR, Wilson JT, McNabb JF & White DC (1988) Equivalence of microbial biomass measures based on membrane lipid and cell wall components, adenosine triphosphate, and direct counts in subsurface sediments. Microb Ecol 16: 7384.
  • Bidle KA, Kastner M & Bartlett DH (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.
  • Blumenberg M, Seifert R, Reitern J, Pape T & Michaelis W (2004) Membrane lipid patterns typify distinct anaerobic methanotrophic consortia. Proc Natl Acad Sci USA 101: 1111111116.
  • Campbell BJ, Stein J & Cary SC (2003) Evidence of chemolithoautotrophy in the symbiont community associated with Alvinella pompejana, a deep sea polychaete. Appl Environ Microbiol 69: 50705078.
  • Cary SC, Cottrell MT, Stein JL, Camacho F & Desbruyeres D (1997) Molecular identification and localization of a filamentous symbiotic bacteria associated with the hydrothermal vent annelid Alvinella pompejana. Appl Environ Microbiol 63: 11241130.
  • Cavanaugh CM (1994) Microbial symbiosis: patterns of diversity in the marine environment. Am Zool 34: 7989.
  • Cifuentes A, Anton J, Benlloch S, Donnelly A, Herbert RA & Rodriguez-Valera F (2000) Prokaryotic diversity in Zostera noltii-colonized marine sediments. Appl Environ Microbiol 66: 17151719.
  • Damaste JSS, De Lint S, Van Der Maarel MJEC, Gottschal JC & and the Shipboard Scientific Party (2000) Biomarker evidence for widespread anaerobic methane oxidation in Mediterranean sediments by a consortium of methanogenic archaea and bacteria. Appl Environ Microbiol 66: 11261132.
  • DeLong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci USA 89: 56855689.
  • Dhillon A & Sogin ML (2003) Genomic markers of ancient anaerobic microbial pathways: sulfate reduction, methanogenesis, and methane oxidation. Biol Bull 204: 186191.
  • D'Hondt S, Rutherford S & Spivack AJ (2002) Metabolic activity of subsurface life in deep-sea sediments. Science 295: 20672070.
  • Distel DL, Lane DJ, Olsen GJ, Giovannoni SJ, Pace B, Pace NR, Stahl DA & Felbeck H (1988) Sulfur-oxidizing bacterial endosymbionts: analysis of phylogeny and specificity by 16S rRNA sequences. J Bacteriol 170: 25062510.
  • Dryden SC & Kaplan S (1990) Localization and structural analysis of the ribosomal RNA operons of Rhodobacter sphaeroides. Nucl Acids Res 18: 72677277.
  • Dunkleblum ES, Tan E & Silk PJ (1985) Double-bond location in monounsaturated fatty acids by dimethyl disulfide derivatization and mass spectrometry: application to analysis of fatty acids in pheromone glands of four lepidoptera. J Chem Ecol 11: 265277.
  • Embley RW, Eitttrim SL, McHugh CH, et al. (1990) Geological setting of chemosynthetic communities in the Monterey Fan Valley system. Deep-Sea Res 37: 16511667.
  • Fang J & Findlay RH (1996) The use of a classic lipid extraction method for simultaneous recovery of organic pollutants and microbial lipids from sediments. J Microbiol Methods 27: 6371.
  • 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.
  • Guezennec J & Fiala-Medioni A (1996) Bacterial abundance and diversity in the Barbados Trench determined by phospholipid analysis. FEMS Microbiol Ecol 19: 8393.
  • Hashimoto J, Ohta S, Fujikura K, Fujiwara Y & Sukizaki S (1995) Life habit of vesicomyid clam, Calyptogenasoyoae, and hydrogen sulfide concentration in interstitial waters in Sagami Bay, Japan. J Oceanogr 51: 341350.
  • Hinrichs KU, Hayes JM, Sylva SP, Brewer PG & DeLong EF (1999) Methane-consuming archaebacteria in marine sediments. Nature 398: 802805.
  • Hinrichs KU, Edcomb V, De Vera Gomez A, Kysela D, Sylva S, Sogin ML & Jannasch HW (2002) Microbial diversity of hydrothermal sediments in Guaymas Basin: evidence for anaerobic methanotrophic communities. Appl Environ Microbiol 68: 19942007.
  • House CH, Hinrichs K-U, McKeegan KD & DeLong EF (2001) Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science 293: 484487.
  • Huber J, Butterfield DA & Baross JA (2003) Bacterial diversity in a subseafloor habitat following a deep-sea volcanic eruption. FEMS Microbiol Ecol 43: 393409.
  • Inagaki F, Sakihama Y, Inoue A, Kato C & Horikoshi K (2002) Molecular phylogenetic analyses of reverse-transcribed bacterial rRNA obtained from deep-sea cold seep sediments. Environ Microbiol 4: 277294.
  • Inagaki F, Okada H, Tsapin AI & Nealson KH (2005) The paleome: a sedimentary genetic record of past microbial communities. Astrobiology 5: 141153.
  • Jannasch HW (1985) The chemosynthetic support of life and microbial diversity at deep-sea hydrothermal vents. Proc Roy Soc London 225: 277297.
  • Kato C, Li L, Tamaoka J & Horikoshi K (1997) Molecular analyses of the sediment of the 11 000-m deep Mariana Trench. Extremophiles 1: 117123.
  • Kellogg CA (2004) Tropical Archaea: diversity associated with the surface microlayer of corals. Mar Ecol Prog Ser 273: 8188.
  • Kennicutt II MC, Brooks JM, Bidigare RR, Fay RR, Wade TL & McDonald TJ (1985) Vent-type taxa in a hydrocarbon seep region on the Louisianan slope. Nature 317: 351353.
  • Kobayashi K (2002) Tectonic significance of the cold seepage zones in the eastern Nankai accretionary wedge–an outcome of the 15 years' KAIKO projects. Mar Geol 187: 330.
  • Kulm LD, Suess E, Moore JC, et al. (1986) Oregon subduction zone: venting, fauna, and carbonates. Science 231: 561566.
  • Larkin JM (1980) Isolation of Thiothrix in pure culture and observations of a filamentous epiphyte on Thiothrix. Curr Microbiol 4: 155158.
  • Lee EY, Lee HK, Lee YK, Sim CJ & Lee J-H (2003) Diversity of symbiotic archaeal communities in marine sponges from Korea. Biomol Eng 20: 299304.
  • Li L, Guenzennec J, Nichols P, Henry P, Yanagibayashi M & Kato C (1999a) Microbial diversity in Nankai Trough sediments at a depth of 3843 m. J Oceanogr 55: 635642.
  • Li L, Kato C & Horikoshi K (1999b) Microbial diversity in sediments collected from the deepest cold-seep area, the Japan Trench. Mar Biotechnol 1: 391400.
  • Loesekann T, Nadalig T, Boetius A & Amann R (2003) Anaerobic oxidation of methane (AOM)–microbial diversity and community structure at the Haakon Mosby mud volcano (1250 meter water depth, Barents Sea). 2003 Aquatic Science Meeting, Salt Lake City, Utah, February 8–14, 2003.
  • Londry KL & Des Marais DJ (2004) Stable carbon isotope fractionation by sulfate-reducing bacteria. Appl Environ Microbiol 69: 29422949.
  • Masuzawa T, Handa N, Kitagawa H & Kusakabe M (1992) Sulfate reduction using methane in sediments beneath a bathyal ‘cold seep’ giant clam community off Hatsushima Island, Sagami Bay, Japan. Earth Planet Sci Lett 110: 3950.
  • Mayer LA, Shor AN, Hughes J & Piper DJW (1988) Dense biological communities at 3850 m on the Laurentian Fan and their relationship to the deposits of the 1929 Grand Banks earthquake. Deep-Sea Res 35: 12351246.
  • McCaffrey MA, Farrington JW & Repeta DJ (1989) Geochemical implications of the lipid composition of Thioploca spp. from the Peru upwelling region −15°S. Org Geochem 14: 6168.
  • Mills HJ, Hodges C, Wilson K, MacDonald IR & Sobecky PA (2003) Microbial diversity in sediments associated with surface-breaching gas hydrate mounds in the Gulf of Mexico. FEMS Microbiol Ecol 46: 3952.
  • Miroshnickenko ML, Kostrikina NA, L'Haridon S, Jeanthon C, Hippe H, Stackebrandt E & Bonch-Osmolovskaya E (2002) Nautila lithotrophica gen nov., sp. nov., a thermophilic sulfur-reducing ɛ-proteobacterium isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 52: 12991304.
  • Momma H, Iwase R, Mitsuzawa K, Kaiho Y & Fujiwara Y (1998) Preliminary results of a three-year continuous observation by a deep seafloor in Sagami Bay, central Japan. Phys Earth Planet Interiors 108: 263274.
  • Nepple BB, Kessi J & Bachofen R (2000) Chromate reduction by Rhodobacter sphaeroides. J Ind Microbiol Biotechnol 25: 198203.
  • Newberry CJ, Webster G, Cragg BA, Parkes RJ, Weightman AJ & Fry JC (2004) Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190. Environ Microbiol 6: 274287.
  • Ohta S, Sakai H, Taira A, et al. (1987) Multidisciplinary investigation of the Calyptogena communities at the Hatsushima site, Sagami Bay, central Japan. JAMSTEC Deep-Sea Rep 3: 5160.
  • Olu K, Lance S, Sibuet M, Henry P, Fiala-Médioni A & Dinet A (1997) Cold seep communities as indicators of fluid expulsion patterns through mud volcanoes seaward of the Barbados accretionary prism. Deep-Sea Res 44: 811841.
  • Pancost RD, Hopmans EC, Sinninghe Damsté JC & and the MEDINAUT Shipboard Scientific Party (2001) Archaeal lipids in Mediterranean cold seeps: molecular proxies for anaerobic methane oxidation. Geochim Cosmochim Acta 65: 16111627.
  • Paull CK, Hecker B, Commeau R, Freeman-Lynde RP, Neumann C, Corso WP, Golubic S, Hook JE & Curray J (1984) Biological communities at the Florida escarpment resemble hydrothermal vent taxa. Science 226: 965967.
  • Pearson A, Huang Z, Ingalls AE, Romanek CS, Wiegel J, Freeman KH, Smittenberg RH & Zhang CL (2004) Nonmarine crenarchaeol in Nevada hot springs. Appl Environ Microbiol 70: 52295337.
  • Ratledge C & Wilkinson SG (1988) Microbial Lipids. Academic Press, London.
  • Ravenschla K, Sahm K, Pernthaler J & Amann R (1999) High bacterial diversity in permanently cold marine sediments. Appl Environ Microbiol 65: 39763981.
  • Ravenschlag K, Schubert CJ, Rickert D, Widdel F, Gieseke A, Amann R, Jorgensen BB, Witte U & Pfannkuche O (2000) A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407: 623626.
  • 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. Appl Environ Microbiol 68: 37593770.
  • Robb FT, Place AR, Sowers KR, Schreier HJ, Das-Sarma S & Fleischmann EM (1995) Archaea: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
  • Ryu JS, Lee J-H, Kim S-J & Kato C (2004) Diversity of archaeon community in the deep-sea sediments from Japan Trench and East Sea. Abstract, 10th International Symposium on Microbial Ecology, Cancun, Mexico, August 22, 2004.
  • Saitou N & Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406425.
  • Sassen R, La Duc MT, Sweet ST & Nealson KH (2001) Bacteria and Archaea physically associated with Gulf of Mexico gas hydrates. Appl Environ Microbiol 67: 51435153.
  • Sawayama S, Yagishita T & Tsukahara K (2000) http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=14549203 (last checked, Dec. 29, 2005).
  • Schouten S, Hopmans EC, Pancost RD & Sinninghe Damsté JS (2000) Widespread occurrence of structurally diverse tetraether membrane lipids: evidence for the ubiquitous presence of low-temperature relatives of hyperthermophiles. Proc Natl Acad Sci USA 97: 1442114426.
  • Sibuet M, Juniper SK & Pautot G (1988) Cold-seep benthic communities in the Japan subduction zones: geological control of community development. J Mar Res 46: 333348.
  • Sinninghe Damsté JS, Hopmans EC, Schouten S, Van Duin ACT & Geenevasen JAJ (2002) Crenarchaeol, the characteristic core glycerol dibiphytanyl glycerol tetraether membrane lipid of cosmopolitan pelagic crenarchaeota. J Lipid Res 43: 16411651.
  • Timmer-Ten Hoor A (1975) A new type of thiosulphate oxidizing, nitrate reducing microorganism: Thiomicrospira denitrificans sp. nov. Netherland J Sea Res 9: 344350.
  • Urakawa H, Kita-Tsukamoto K & Ohwada K (1999) Microbial diversity in marine sediments from Sagami Bay and Tokyo Bay, Japan, as determined by 16S rRNA gene analysis. Microbiology 145: 33053315.
  • Urakawa H, Yoshida T, Nishimura M & Ohwada K (2000) Characterization of depth-related population variation in microbial communities of a coastal marine sediment using 16S rDNA-based approaches and quinone profiling. Environ Microbiol 2: 542554.
  • Watanabe K, Watanabe K, Kodama Y, Syutsubo K & Harayama S (2000) Molecular characterization of bacterial populations in petroleum-contaminated groundwater discharged from underground crude oil storage cavities. Appl Environ Microbiol 66: 48034809.
  • Wakeham SG, Hopmans EC, Schouten S & Sinninghe Damsté JS (2003) Archaeal lipids and anaerobic oxidation of methane in euxinic water columns: a comparative study of the Black Sea and Cariaco Basin. Chem Geol 205: 427442.
  • White DC, Star JO & Ringelberg DB (1996) Quantitative comparisons of in situ microbial biodiversity by signature biomarker analysis. J Ind Microbiol Biotechnol 17: 185196.
  • Zhang CL, Huang Z, Cantu J, Pancost RD, Brigmon RL, Lyons TW & Sassen R (2005) Lipid biomarkers and carbon isotope signatures of a microbial (Baggiatoa) mat associated with gas hydrates in the Gulf of Mexico. Appl Environ Microbiol 71: 21062112.