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  • Alain K, Olagnon M, Desbruyeres D et al. (2002) Phylogenetic characterization of the bacterial assemblage associated with mucous. Secretions of the hydrothermal vent polychaete Paralvinella palmiformis. FEMS Microbiol Ecol 42: 463476.
  • Arakawa S, Sato T, Sato R et al. (2006) Molecular phylogenetic and chemical analyses of the microbial mats in deep-sea cold seep sediments at the northeastern Japan Sea. Extremophiles 10: 311319.
  • Badger M & Bek E (2008) Multiple Rubisco forms in proteobacteria: their functional significance in relation to CO2 acquisition by the CBB cycle. J Exp Bot 59: 15251541.
  • Baker SH, Jin S, Aldrich HC, Howard GT & Shively JM (1998) Insertion mutation of the form I cbbL gene encoding ribulose bisphosphate carboxylase/oxygenase (RuBisCO) in Thiobacillus neapolitanus results in expression of form II RuBisCO, loss of carboxysomes, and an increased CO2 requirement for growth. J Bacteriol 180: 41334139.
  • Becker PT, Samadi S, Zbinden M, Hoyoux C, Compère P & De Ridder C (2009) First insights into the gut microflora associated with an echinoid from wood falls environments. Cah Biol Mar 50: 343352.
  • Blazejak A, Kuever J, Erseus C, Amann R & Dubilier N (2006) Phylogeny of 16S rRNA, ribulose 1,5-bisphosphate carboxylase/oxygenase, and adenosine 5′-phosphosulfate reductase genes from gamma- and alphaproteobacterial symbionts in gutless marine worms (Oligochaeta) from Bermuda and the Bahamas. Appl Environ Microb 72: 55275536.
  • Bourne DG, McDonald IR & Murrell JC (2001) Comparison of pmoA PCR primer sets as tools for investigating methanotroph diversity in three Danish soils. Appl Environ Microb 67: 38023809.
  • Brazelton WJ, Schrenk MO, Kelley DS & Baross JA (2006) Methane- and sulfur-metabolizing microbial communities dominate the Lost City hydrothermal field ecosystem. Appl Environ Microb 72: 62576270.
  • Brazelton WJ, Sogin ML & Baross JA (2010) Multiple scales of diversification within natural populations of archaea in hydrothermal chimney biofilms. Environ Microbiol Rep 2: 236242.
  • Byrne N, Strous M, Crépeau V et al. (2008) Presence and activity of anaerobic ammonium-oxidizing bacteria at deep-sea hydrothermal vents. ISME J 3: 117123.
  • Campbell BJ & Cary SC (2004) Abundance of reverse tricarboxylic acid cycle genes in free-living microorganisms at deep-sea hydrothermal vents. Appl Environ Microb 70: 62826289.
  • Campbell BJ, Stein JL & Cary SC (2003) Evidence of chemolithoautotrophy in the bacterial community associated with Alvinella pompejana, a hydrothermal vent polychaete. Appl Environ Microb 69: 50705078.
  • Campbell BJ, Engel AS, Porter ML & Takai K (2006) The versatile epsilon-proteobacteria: key players in sulphidic habitats. Nat Rev Microbiol 4: 458468.
  • Chin K, Sharma M, Russell L, O'Neill K & Lovley D (2008) Quantifying expression of a dissimilatory (bi)sulfite reductase gene in petroleum-contaminated marine harbor sediments. Microb Ecol 55: 489499.
  • Corre E, Reysenbach AL & Prieur D (2001) Proteobacterial diversity from a deep-sea hydrothermal vent on the Mid-Atlantic Ridge. FEMS Microbiol Lett 205: 329335.
  • Costello A & Lidstrom M (1999) Molecular characterization of functional and phylogenetic genes from natural populations of methanotrophs in lake sediments. Appl Environ Microb 65: 50665074.
  • Cuvelier D, Sarrazin J, Colaço A et al. (2009) Distribution and spatial variation of hydrothermal faunal assemblages at Lucky Strike (Mid-Atlantic Ridge) revealed by high-resolution video image analysis. Deep-Sea Res Pt I 56: 20262040.
  • Cuvelier D, Sarradin PM, Sarrazin J et al. (2011) Hydrothermal faunal assemblages and habitat characterisation at the Atlantic Eiffel Tower edifice (Lucky Strike vent field). Mar Ecol 33: 113.
  • Dattagupta S, Schaperdoth I, Montanari A, Mariani S, Kita N, Valley JW & Macalady JL (2009) A novel symbiosis between chemoautotrophic bacteria and a freshwater cave amphipod. ISME J 3: 935943.
  • Davis R & Moyer C (2008) Extreme spatial and temporal variability of hydrothermal microbial mat communities along the Mariana Island Arc and southern Mariana back-arc system. J Geophys Res 113: B08S15.
  • De Busserolles F, Sarrazin J, Gauthier O, Gélinas Y, Fabri M, Sarradin P & Desbruyères D (2009) Are spatial variations in the diets of hydrothermal fauna linked to local environmental conditions? Deep-Sea Res Pt II 56: 16491664.
  • Dedysh S, Liesack W, Khmelenina V et al. (2000) Methylocella palustris gen. nov., sp. nov., a new methane-oxidizing acidophilic bacterium from peat bogs, representing a novel subtype of serine-pathway methanotrophs. Int J Syst Evol Micr 50: 955969.
  • Duperron S, Bergin C, Zielinski F et al. (2006) A dual symbiosis shared by two mussel species, Bathymodiolus azoricus and Bathymodiolus puteoserpentis (Bivalvia: Mytilidae), from hydrothermal vents along the northern Mid-Atlantic Ridge. Environ Microbiol 8: 14411447.
  • Duperron S, Fiala-Medioni A, Caprais JC, Olu K & Sibuet M (2007a) Evidence for chemoautotrophic symbiosis in a Mediterranean cold seep clam (Bivalvia: Lucinidae): comparative sequence analysis of bacterial 16S rRNA, APS reductase and RubisCO genes. FEMS Microbiol Ecol 59: 6470.
  • Duperron S, Sibuet M, MacGregor BJ, Kuypers MM, Fisher CR & Dubilier N (2007b) Diversity, relative abundance and metabolic potential of bacterial endosymbionts in three Bathymodiolus mussel species from cold seeps in the Gulf of Mexico. Environ Microbiol 9: 14231438.
  • Duperron S, Halary S, Lorion J, Sibuet M & Gaill F (2008) Unexpected co-occurrence of six bacterial symbionts in the gills of the cold seep mussel Idas sp. (Bivalvia: Mytilidae). Environ Microbiol 10: 433445.
  • Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 119.
  • Elsaied H & Naganuma T (2001) Phylogenetic diversity of ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes from deep-sea microorganisms. Appl Environ Microb 67: 17511765.
  • Elsaied HE, Kimura H & Naganuma T (2007) Composition of archaeal, bacterial, and eukaryal RuBisCO genotypes in three Western Pacific arc hydrothermal vent systems. Extremophiles 11: 191202.
  • Engel AS, Lee N, Porter ML, Stern LA, Bennett PC & Wagner M (2003) Filamentous ‘Epsilonproteobacteria’ dominate microbial mats from sulfidic cave springs. Appl Environ Microb 69: 55035511.
  • Engel AS, Porter ML, Stern LA, Quinlan S & Bennett PC (2004) Bacterial diversity and ecosystem function of filamentous microbial mats from aphotic (cave) sulfidic springs dominated by chemolithoautotrophic ‘Epsilonproteobacteria. FEMS Microbiol Ecol 51: 3153.
  • Fuse H, Ohta M, Takimura O et al. (1998) Oxidation of trichloroethylene and dimethyl sulfide by a marine Methylomicrobium strain containing soluble methane monooxygenase. Biosci Biotech Bioch 62: 19251931.
  • Galtier N, Gouy M & Gautier C (1996) SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12: 543548.
  • Gerasimchuk AL, Shatalov AA, Novikov AL et al. (2010) The search for sulfate-reducing bacteria in mat samples from the lost city hydrothermal field by molecular cloning. Microbiology 79: 96105.
  • Gilhooly WP, Carney RS & Macko SA (2007) Relationships between sulfide-oxidizing bacterial mats and their carbon sources in northern Gulf of Mexico cold seeps. Org Geochem 38: 380393.
  • Goffredi SK, Jones WJ, Erhlich H, Springer A & Vrijenhoek RC (2008) Epibiotic bacteria associated with the recently discovered Yeti crab, Kiwa hirsuta. Environ Microbiol 10: 26232634.
  • Haygood M (1996) The potential role of functional differences between Rubisco forms in governing expression in chemoautotrophic symbioses. Limnol Oceanogr 41: 370371.
  • Heijs SK, Damste JSS & Forney LJ (2005) Characterization of a deep-sea microbial mat from an active cold seep at the Milano mud volcano in the Eastern Mediterranean Sea. FEMS Microbiol Ecol 54: 4756.
  • Heyer J, Berger U, Hardt M & Dunfield PF (2005) Methylohalobius crimeensis gen. nov., sp. nov., a moderately halophilic, methanotrophic bacterium isolated from hypersaline lakes of Crimea. Int J Syst Evol Micr 55: 18171826.
  • Hirayama H, Sunamura M, Takai K et al. (2007) Culture-dependent and -independent characterization of microbial communities associated with a shallow submarine hydrothermal system occurring within a coral reef off Taketomi Island, Japan. Appl Environ Microb 73: 76427656.
  • Holmes AJ, Costello A, Lidstrom ME & Murrell JC (1995) Evidence that particulate methane monooxygenase and ammonia monooxygenase may be evolutionarily related. FEMS Microbiol Lett 132: 203208.
  • Huber J, Butterfield D & Baross J (2003) Bacterial diversity in a subseafloor habitat following a deep-sea volcanic eruption. FEMS Microbiol Ecol 43: 393409.
  • Inagaki F, Takai K, Nealson KH & Horikoshi K (2004a) Sulfurovum lithotrophicum gen. nov., sp. nov., a novel sulfur-oxidizing chemolithoautotroph within the epsilon-Proteobacteria isolated from Okinawa Trough hydrothermal sediments. Int J Syst Evol Micr 54: 14771482.
  • Inagaki F, Tsunogai U, Suzuki M et al. (2004b) Characterization of C-1-metabolizing prokaryotic communities in methane seep habitats at the Kuroshima Knoll, southern Ryukyu arc, by analyzing pmoA, mmoX, mxaF, mcrA, and 16S rRNA genes. Appl Environ Microb 70: 74457455.
  • Jacq E, Prieur D, Nichols P, White D, Porter T & Geesey G (1989) Microscopic examination and fatty acid characterization of filamentous bacteria colonizing substrata around subtidal hydrothermal vents. Arch Microbiol 152: 6471.
  • Jannasch H & Wirsen C (1981) Morphological survey of microbial mats near deep-sea thermal vents. Appl Environ Microb 41: 528538.
  • Johnson K, Childress J, Beehler C & Sakamoto C (1994) Biogeochemistry of hydrothermal vent mussel communities: the deep-sea analogue to the intertidal zone. Deep-Sea Res Pt I 41: 9931011.
  • Kalanetra KM, Huston SL & Nelson DC (2004) Novel, attached, sulfur-oxidizing bacteria at shallow hydrothermal vents possess vacuoles not involved in respiratory nitrate accumulation. Appl Environ Microb 70: 74877496.
  • Kato S, Kobayashi C, Kakegawa T & Yamagishi A (2009) Microbial communities in iron–silica-rich microbial mats at deep-sea hydrothermal fields of the Southern Mariana Trough. Environ Microbiol 11: 20942111.
  • Kirchman D (2002) The ecology of CytophagaFlavobacteria in aquatic environments. FEMS Microbiol Ecol 39: 91100.
  • Kolganova T, Kuznetsov B & Tourova T (2002) Designing and testing oligonucleotide primers for amplification and sequencing of archaeal 16S rRNA genes. Microbiology 71: 243246.
  • Konneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB & Stahl DA (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437: 543546.
  • Lane D (1991) 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics, Vol. 1 (StackebrandtE & GoodfellowM eds), pp. 115176. John Wiley & Sons, Chichester.
  • Lane D, Pace B, Olsen G, Stahl D, Sogin M & Pace N (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. P Natl Acad Sci USA 82: 69556659.
  • Larimer F, Lu T & Bailey D (1995) Sequence and expression of the form II ribulose bisphosphate carboxylase/oxygenase (RUBISCO) gene from Rhodobacter capsulatus. FASEB J 9: A1275.
  • Lloyd KG, Albert DB, Biddle JF, Chanton JP, Pizarro O & Teske A (2010) Spatial structure and activity of sedimentary microbial communities underlying a Beggiatoa spp. mat in a Gulf of Mexico hydrocarbon seep. PLoS One 5: e8738.
  • 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.
  • Lopez-Garcia P, Lopez-Lopez A, Moreira D & Rodriguez-Valera F (2001) Diversity of free-living prokaryotes from a deep-sea site at the Antarctic Polar Front. FEMS Microbiol Ecol 36: 192202.
  • Lopez-Garcia P, Gaill F & Moreira D (2002) Wide bacterial diversity associated with tubes of the vent worm Riftia pachyptila. Environ Microbiol 4: 204215.
  • Lösekann T, Robador A, Niemann H, Knittel K, Boetius A & Dubilier N (2008) Endosymbioses between bacteria and deep-sea siboglinid tubeworms from an Arctic Cold Seep (Haakon Mosby Mud Volcano, Barents Sea). Environ Microbiol 10: 32373254.
  • Martins I, Colaço A, Santos R, Lesongeur F, Godfroy A, Sarradin P & Cosson R (2009) Relationship between the occurrence of filamentous bacteria on Bathymodiolus azoricus shell and the physiological and toxicological status of the vent mussel. J Exp Mar Biol Ecol 376: 16.
  • Meyer B & Kuever J (2007a) Molecular analysis of the distribution and phylogeny of dissimilatory adenosine-5′-phosphosulfate reductase-encoding genes (aprBA) among sulfur-oxidizing prokaryotes. Microbiology 153: 34783498.
  • Meyer B & Kuever J (2007b) Phylogeny of the alpha and beta subunits of the dissimilatory adenosine-5′-phosphosulfate (APS) reductase from sulfate-reducing prokaryotes – origin and evolution of the dissimilatory sulfate-reduction pathway. Microbiology 153: 20262044.
  • Meyer B, Imhoff JF & Kuever J (2007) Molecular analysis of the distribution and phylogeny of the soxB gene among sulfur-oxidizing bacteria – evolution of the Sox sulfur oxidation enzyme system. Environ Microbiol 9: 29572977.
  • Moyer C, Dobbs F & Karl D (1995) Phylogenetic diversity of the bacterial community from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii. Appl Environ Microb 61: 15551562.
  • Mukhopadhyaya P, Deb C, Lahiri C & Roy P (2000) A soxA gene, encoding a diheme cytochrome c, and a sox locus, essential for sulfur oxidation in a new sulfur lithotrophic bacterium. J Bacteriol 182: 42784287.
  • Muller F, Brissac T, Le Bris N, Felbeck H & Gros O (2010) First description of giant Archaea (Thaumarchaeota) associated with putative bacterial ectosymbionts in a sulfidic marine habitat. Environ Microbiol 12: 23712383.
  • Nelson DC, Wirsen CO & Jannasch HW (1989) Characterization of large, autotrophic Beggiatoa sp. abundant at hydrothermal vent of Guayamas basin. Appl Environ Microb 55: 29092917.
  • Nercessian O, Bienvenu N, Moreira D, Prieur D & Jeanthon C (2005) Diversity of functional genes of methanogens, methanotrophs and sulfate reducers in deep-sea hydrothermal environments. Environ Microbiol 7: 118132.
  • Nold SC, Zhou J, Devol AH & Tiedje JM (2000) Pacific northwest marine sediments contain ammonia-oxidizing bacteria in the beta subdivision of the proteobacteria. Appl Environ Microb 66: 45324535.
  • Omoregie EO, Mastalerz V, de Lange G et al. (2008) Biogeochemistry and community composition of iron- and sulfur-precipitating microbial mats at the Chefren mud volcano (Nile Deep Sea fan, Eastern Mediterranean). Appl Environ Microb 74: 31983215.
  • Petri R, Podgorsek L & Imhoff JF (2001) Phylogeny and distribution of the soxB gene among thiosulfate-oxidizing bacteria. FEMS Microbiol Lett 197: 171178.
  • Rabus R, Hansen T & Widdel F (2006) Dissimilatory sulfate- and sulfur-reducing prokaryotes. Prokaryotes 2: 659768.
  • Reysenbach AL, 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 Microb 66: 37983806.
  • Roussel E, Sauvadet A, Allard J, Chaduteau C, Richard P, Bonavita M & Chaumillon E (2009) Archaeal methane cycling communities associated with gassy subsurface sediments of Marennes-Oléron Bay (France). Geomicrobiol J 26: 3143.
  • Salerno JL, Macko SA, Hallam SJ, Bright M, Won YJ, McKiness Z & Van Dover CL (2005) Characterization of symbiont populations in life-history stages of mussels from chemosynthetic environments. Biol Bull 208: 145155.
  • Santelli C, Orcutt B, Banning E et al. (2008) Abundance and diversity of microbial life in ocean crust. Nature 453: 653656.
  • Sarradin P, Waeles M, Bernagout S, Le Gall C, Sarrazin J & Riso R (2009) Speciation of dissolved copper within an active hydrothermal edifice on the Lucky Strike vent field (MAR, 37°N). Sci Total Environ 407: 869878.
  • Sarradin P-M, Caprais J-C, Riso R, Kerouel R & Aminot A (1999) Chemical environment of the hydrothermal mussel communities in the Lucky Strike and Menez Gwen vent fields, Mid Atlantic Ridge. Cah Biol Mar 40: 93104.
  • Schloss PD & Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microb 71: 15011506.
  • Schwedock J, Harmer TL, Scott KM et al. (2004) Characterization and expression of genes from the RubisCO gene cluster of the chemoautotrophic symbiont of Solemya velum: cbbLSQO. Arch Microbiol 182: 1829.
  • Seckbach J & Oren A (2010) Microbial Mats: Modern and Ancient Microorganisms in Stratified Systems, Cellular Origin, Life in Extreme Habitats and Astrobiology. Springer, Berlin.
  • Shigematsu T, Hanada S, Eguchi M, Kamagata Y, Kanagawa T & Kurane R (1999) Soluble methane monooxygenase gene clusters from trichloroethylene-degrading Methylomonas sp. strains and detection of methanotrophs during in situ bioremediation. Appl Environ Microb 65: 51985206.
  • Stevens H, Stubner M, Simon M & Brinkhoff T (2005) Phylogeny of Proteobacteria and Bacteroidetes from oxic habitats of a tidal flat ecosystem. FEMS Microbiol Ecol 54: 351365.
  • Takai K, Campbell BJ, Cary SC et al. (2005) Enzymatic and genetic characterization of carbon and energy metabolisms by deep-sea hydrothermal chemolithoautotrophic isolates of Epsilonproteobacteria. Appl Environ Microb 71: 73107320.
  • Takai K, Suzuki M, Nakagawa S, Miyazaki M, Suzuki Y, Inagaki F & Horikoshi K (2006) Sulfurimonas paralvinellae sp. nov., a novel mesophilic, hydrogen- and sulfur-oxidizing chemolithoautotroph within the Epsilonproteobacteria isolated from a deep-sea hydrothermal vent polychaete nest, reclassification of Thiomicrospira denitrificans as Sulfurimonas denitrificans comb. nov. and emended description of the genus Sulfurimonas. Int J Syst Evol Micr 56: 17251733.
  • Teske A & Nelson DC (2006) The genera Beggiatoa and Thioploca. Prokaryotes 6: 784810.
  • Teske A & Sorensen KB (2008) Uncultured archaea in deep marine subsurface sediments: have we caught them all? ISME J 2: 318.
  • Teske A, Brinkhoff T, Muyzer G, Moser DP, Rethmeier J & Jannasch HW (2000) Diversity of thiosulfate-oxidizing bacteria from marine sediments and hydrothermal vents. Appl Environ Microb 66: 31253133.
  • Van Dover CL, Jenkins CD & Turnipseed M (2001) Corralling of larvae in the deep sea. J Mar Biol Assoc UK 81: 823826.
  • Vrijenhoek RC, Duhaime M & Jones WJ (2007) Subtype variation among bacterial endosymbionts of tubeworms (Annelida: Siboglinidae) from the Gulf of California. Biol Bull 212: 180184.
  • Walker C, De la Torre J, Klotz M et al. (2010) Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. P Natl Acad Sci USA 107: 88188823.
  • Webster G, Newberry CJ, Fry JC & Weightman AJ (2003) Assessment of bacterial community structure in the deep sub-seafloor biosphere by 16S rDNA-based techniques: a cautionary tale. J Microbiol Meth 55: 155164.
  • Wintzingerode F, Göbel U & Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21: 213229.
  • Won Y, Jones W & Vrijenhoek R (2008) Absence of cospeciation between deep-sea mytilids and their thiotrophic endosymbionts. J Shellfish Res 27: 129138.
  • Won Y-J, Hallam SJ, O'Mullan GD, Pan IL, Buck KR & Vrijenhoek RC (2003) Environmental acquisition of thiotrophic endosymbionts by deep-sea mussels of the genus Bathymodiolus. Appl Environ Microb 69: 67856792.
  • Zbinden M, Shillito B, Le Bris N et al. (2008) New insights on the metabolic diversity among the epibiotic microbial community of the hydrothermal shrimp Rimicaris exoculata. J Exp Mar Biol Ecol 359: 131140.