Feast and famine ??? microbial life in the deep-sea bed, Nature Reviews Microbiology, vol.52, issue.10, pp.770-781, 2007. ,
DOI : 10.1038/nrmicro1745
Spatial Structure and Activity of Sedimentary Microbial Communities Underlying a Beggiatoa spp. Mat in a Gulf of Mexico Hydrocarbon Seep, PLoS ONE, vol.5, issue.1, 2010. ,
DOI : 10.1371/journal.pone.0008738.s009
Seafloor oxygen consumption fuelled by methane from cold seeps, Nature Geoscience, vol.9, issue.9, pp.725-734, 2013. ,
DOI : 10.1038/ngeo1926
The anaerobic oxidation of methane: new insights in microbial ecology and biogeochemistry Ocean margin systems, pp.457-477, 2002. ,
Cultivation of Methanogens under Low-Hydrogen Conditions by Using the Coculture Method, Applied and Environmental Microbiology, vol.75, issue.14, pp.4892-4896, 2009. ,
DOI : 10.1128/AEM.02835-08
"Methanoplasmatales," Thermoplasmatales-Related Archaea in Termite Guts and Other Environments, Are the Seventh Order of Methanogens, Applied and Environmental Microbiology, vol.78, issue.23, pp.8245-8253, 2012. ,
DOI : 10.1128/AEM.02193-12
Candidatus Methanogranum caenicola: a Novel Methanogen from the Anaerobic Digested Sludge, and Proposal of Methanomassiliicoccaceae fam. nov. and Methanomassiliicoccales ord. nov., for a Methanogenic Lineage of the Class Thermoplasmata, Microbes and Environments, vol.28, issue.2, pp.244-250, 2013. ,
DOI : 10.1264/jsme2.ME12189
Diversity of Methane-Cycling Archaea in Hydrothermal Sediment Investigated by General and Group-Specific PCR Primers, Applied and Environmental Microbiology, vol.81, issue.4, pp.1426-144103588, 2015. ,
DOI : 10.1128/AEM.03588-14
abundance in a mesophilic biogas plant based on 16S rRNA gene sequence analysis, Canadian Journal of Microbiology, vol.56, issue.5, pp.440-444, 2010. ,
DOI : 10.1139/W10-021
Methanogenium marinum sp. nov., a H 2 -using methanogen from Skan Bay, Alaska, and kinetics of H 2 utilization, Antonie van Leeuwenhoek, vol.81, issue.1, pp.263-2701020535222281, 2002. ,
DOI : 10.1023/A:1020535222281
Enumeration of H 2 -utilizing methanogenic Archaea, acetogenic and Methanogens in the Sonora Margin Sediments, 1995. ,
Detection of methanogenic Archaea in peat: comparison of PCR primers targeting the mcrA gene, Research in Microbiology, vol.157, issue.10, pp.914-921, 2006. ,
DOI : 10.1016/j.resmic.2006.08.006
Cultivation of methanogens from shallow marine sediments at Hydrate Ridge, Oregon, Archaea, vol.50, issue.1, pp.31-38, 2006. ,
DOI : 10.1029/2005JG000025
Methanogenic diversity and activity in hypersaline sediments of the centre of the Napoli mud volcano, Eastern Mediterranean Sea, Environmental Microbiology, vol.62, issue.8, pp.2078-2091, 2011. ,
DOI : 10.1111/j.1462-2920.2011.02425.x
URL : https://hal.archives-ouvertes.fr/hal-00618011
Growth of sulfate-reducing bacteria and methanogenic archaea with methylated sulfur compounds: a commentary on the thermodynamic aspects, Archives of Microbiology, vol.24, issue.2, pp.135-144, 2003. ,
DOI : 10.1016/0168-6496(94)90095-7
Diversity and identification of methanogenic archaea and sulphate-reducing bacteria in sediments from a pristine tropical mangrove, Antonie van Leeuwenhoek, vol.44, issue.4, pp.401-411, 2010. ,
DOI : 10.1007/s10482-010-9422-8
Methanogenesis and sulfate reduction? competitive and noncompetitive substrates in estuarine sediments, Appl Environ Microbiol, vol.44, pp.1270-1276, 1982. ,
Methanosarcina semesiae sp. nov., a dimethylsulfide-utilizing methanogen from mangrove sediment, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.50, issue.1, pp.171-178, 2000. ,
DOI : 10.1099/00207713-50-1-171
Glycine Betaine as a Direct Substrate for Methanogens (Methanococcoides spp.), Applied and Environmental Microbiology, vol.80, issue.1, pp.289-293, 2014. ,
DOI : 10.1128/AEM.03076-13
URL : https://hal.archives-ouvertes.fr/hal-01144924
A survey of culturable methanogens in contrasting marine sediments, their substrates and physiological characteristics, 2012. ,
Phylogenomic Data Support a Seventh Order of Methylotrophic Methanogens and Provide Insights into the Evolution of Methanogenesis, Genome Biology and Evolution, vol.5, issue.10, 2013. ,
DOI : 10.1093/gbe/evt128
Deep-water hydrocarbon seeps in Guaymas Basin, Gulf of California, Applied Geochemistry, vol.5, issue.1-2, pp.41-490883, 1990. ,
DOI : 10.1016/0883-2927(90)90034-3
Archaeal and anaerobic methane oxidizer communities in the Sonora Margin cold seeps, Guaymas Basin (Gulf of California), The ISME Journal, vol.62, issue.8, pp.1595-1608, 2013. ,
DOI : 10.1002/bit.20347
URL : https://hal.archives-ouvertes.fr/hal-00808539
Influence of DNA Extraction Method, 16S rRNA Targeted Hypervariable Regions, and Sample Origin on Microbial Diversity Detected by 454 Pyrosequencing in Marine Chemosynthetic Ecosystems, Applied and Environmental Microbiology, vol.80, issue.15, pp.4626-463900592, 2014. ,
DOI : 10.1128/AEM.00592-14
URL : https://hal.archives-ouvertes.fr/hal-01111489
Methanopyrus kandleri, gen. and sp. nov. represents a novel group of hyperthermophilic methanogens, growing at 110???C, Archives of Microbiology, vol.4, issue.4, pp.239-247, 1991. ,
DOI : 10.1007/BF00262992
Characterization of Methanococcus maripaludis sp. nov., a new methanogen isolated from salt marsh sediment, Archives of Microbiology, vol.21, issue.2, pp.91-97, 1983. ,
DOI : 10.1007/BF00408015
Methanococcus vulcanius sp. nov., a novel hyperthermophilic methanogen isolated from East Pacific Rise, and identification of Methanococcus sp. DSM 4213Tas Methanococcus fervens sp. nov., International Journal of Systematic Bacteriology, vol.49, issue.2, pp.583-58900207713, 1999. ,
DOI : 10.1099/00207713-49-2-583
Biogeochemistry and biodiversity of methane cycling in subsurface marine sediments (Skagerrak, Denmark), Environmental Microbiology, vol.50, issue.5, pp.1146-1161, 2007. ,
DOI : 10.1016/S0146-6380(03)00003-2
Microbial Diversity of Hydrothermal Sediments in the Guaymas Basin: Evidence for Anaerobic Methanotrophic Communities, Applied and Environmental Microbiology, vol.68, issue.4, pp.1994-2007, 1994. ,
DOI : 10.1128/AEM.68.4.1994-2007.2002
Changes in archaeal, bacterial and eukaryal assemblages along a salinity gradient by comparison of genetic fingerprinting methods in a multipond solar saltern, Environmental Microbiology, vol.11, issue.6, pp.338-348, 2002. ,
DOI : 10.1016/S0168-6445(97)00057-0
Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA, Appl Environ Microbiol, vol.63, pp.3367-3373, 1997. ,
PyElph - a software tool for gel images analysis and phylogenetics, BMC Bioinformatics, vol.13, issue.1, 2012. ,
DOI : 10.1093/bioinformatics/17.11.1084
Designing and testing oligonucleotide primers for amplification and sequencing of archaeal 16S rRNA genes, Microbiology, vol.71, issue.2, pp.243-246, 2002. ,
DOI : 10.1023/A:1015122926687
Uncultured archaea in deep marine subsurface sediments: have we caught them all?, The ISME Journal, vol.62, issue.1, pp.3-18, 2008. ,
DOI : 10.1038/nbt1214
Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990. ,
DOI : 10.1016/S0022-2836(05)80360-2
MAFFT version 5: improvement in accuracy of multiple sequence alignment, Nucleic Acids Research, vol.33, issue.2, pp.511-518, 2005. ,
DOI : 10.1093/nar/gki198
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0, Molecular Biology and Evolution, vol.24, issue.8, pp.1596-1599, 2007. ,
DOI : 10.1093/molbev/msm092
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, vol.22, issue.21, pp.2688-2690, 2006. ,
DOI : 10.1093/bioinformatics/btl446
Distribution of coenzyme F420 and properties of its hydrolytic fragments, J Bacteriol, vol.140, pp.20-27, 1979. ,
Role for urea in nitrification by polar marine Archaea, Proceedings of the National Academy of Sciences, vol.109, issue.44, pp.17989-17994, 2012. ,
DOI : 10.1073/pnas.1201914109
Fate of vent-derived methane in seawater above the H??kon Mosby mud volcano (Norwegian Sea), Marine Chemistry, vol.82, issue.1-2, pp.1-11, 2003. ,
DOI : 10.1016/S0304-4203(03)00031-8
Methanogenic activity and diversity in the centre of the Amsterdam Mud Volcano, Eastern Mediterranean Sea, FEMS Microbiology Ecology, vol.81, issue.1, pp.243-254, 2012. ,
DOI : 10.1111/j.1574-6941.2012.01375.x
URL : https://hal.archives-ouvertes.fr/hal-00778830
Comparative Analysis of Methane-Oxidizing Archaea and Sulfate-Reducing Bacteria in Anoxic Marine Sediments, Applied and Environmental Microbiology, vol.67, issue.4, pp.1922-1934, 1922. ,
DOI : 10.1128/AEM.67.4.1922-1934.2001
Diversity and Spatial Distribution of Prokaryotic Communities Along A Sediment Vertical Profile of A Deep-Sea Mud Volcano, Microbial Ecology, vol.143, issue.3???4, pp.655-668, 2011. ,
DOI : 10.1007/s00248-011-9855-2
Archaeal diversity in ODP legacy borehole 892b and associated seawater and sediments of the Cascadia Margin, FEMS Microbiology Ecology, vol.54, issue.2, pp.167-177, 2005. ,
DOI : 10.1016/j.femsec.2005.03.015
Phylogenetic and Functional Diversity of Microbial Communities Associated with Subsurface Sediments of the Sonora Margin, Guaymas Basin, PLoS ONE, vol.108, issue.8, 2014. ,
DOI : 10.1371/journal.pone.0104427.s008
URL : https://hal.archives-ouvertes.fr/insu-01077391
Archaeal Methane Cycling Communities Associated with Gassy Subsurface Sediments of Marennes-Ol??ron Bay (France), Geomicrobiology Journal, vol.152, issue.1, pp.31-43, 2009. ,
DOI : 10.1099/00207713-49-1-247
Characterization and spatial distribution of methanogens and methanogenic biosignatures in hypersaline microbial mats of Baja California, Geobiology, vol.34, issue.4, pp.376-393, 2008. ,
DOI : 10.1111/j.1472-4669.2008.00166.x
Methanogen Diversity Evidenced by Molecular Characterization of Methyl Coenzyme M Reductase A (mcrA) Genes in Hydrothermal Sediments of the Guaymas Basin, Applied and Environmental Microbiology, vol.71, issue.8, pp.4592-4601, 2005. ,
DOI : 10.1128/AEM.71.8.4592-4601.2005
Microbial methane oxidation and sulfate reduction at cold seeps of the deep Eastern Mediterranean Sea, Marine Geology, vol.261, issue.1-4, pp.114-127, 2009. ,
DOI : 10.1016/j.margeo.2009.02.001
URL : https://hal.archives-ouvertes.fr/hal-00407983
Effect of Storage Conditions on Archaeal and Bacterial Communities in Subsurface Marine Sediments, Geomicrobiology Journal, vol.5, issue.3, pp.261-272, 2010. ,
DOI : 10.1080/01490450903410423
Anaerobic oxidation of methane in a cold-water coral carbonate mound from the Gulf of Cadiz, International Journal of Earth Sciences, vol.161, issue.6, pp.1413-1422, 2011. ,
DOI : 10.1007/s00531-010-0528-z
Use of 16S rRNA-targeted oligonucleotide probes to investigate function and phylogeny of sulphate-reducing bacteria and methanogenic archaea in a UK estuary, FEMS Microbiology Ecology, vol.44, issue.3, pp.361-371, 2003. ,
DOI : 10.1016/S0168-6496(03)00078-3
Changes in methanogenic substrate utilization and communities with depth in a salt-marsh, creek sediment in southern England, Estuarine, Coastal and Shelf Science, vol.96, pp.170-178, 2012. ,
DOI : 10.1016/j.ecss.2011.10.025
URL : https://hal.archives-ouvertes.fr/hal-01145275
Infuence of benthic fauna on trimethylamine concentrations in coastal marine sediments, Marine Ecology Progress Series, vol.39, pp.15-21, 1987. ,
DOI : 10.3354/meps039015
Sources and distribution of aliphatic amines in salt marsh sediment, Organic Geochemistry, vol.22, issue.6, pp.1005-10210146, 1994. ,
DOI : 10.1016/0146-6380(94)90034-5
Methanogenesis from choline by a coculture of Desulfovibrio sp. and Methanosarcina barkeri, Appl Environ Microbiol, vol.45, pp.161-168, 1983. ,
Anaerobic degradation of choline. I. Fermentation of choline by an anaerobic, cytochrome-producing bacterium , Vibrio cholinicus n. sp, J Bacteriol, vol.78, pp.557-561, 1959. ,
Betaine fermentation and oxidation by marine Desulfuromonas strains, Appl Environ Microbiol, vol.55, pp.965-969, 1989. ,
Bacterial communities and syntrophic associations involved in anaerobic oxidation of methane process of the Sonora Margin cold seeps, Guaymas Basin, Environmental Microbiology, vol.37, issue.9, pp.2777-2790, 2014. ,
DOI : 10.1111/1462-2920.12324
URL : https://hal.archives-ouvertes.fr/hal-01111546
Methanococcoides vulcani sp. nov., a marine methylotrophic methanogen that uses betaine, choline and N,N-dimethylethanolamine for methanogenesis, isolated from a mud volcano, and emended description of the genus Methanococcoides, Int J Syst Evol Microbiol, vol.64, 1978. ,
URL : https://hal.archives-ouvertes.fr/hal-01019503
Archaeal diversity in tidal flat sediment as revealed by 16S rDNA analysis, J Microbiol, vol.43, pp.144-151, 2005. ,
Temporal evolution of methane cycling and phylogenetic diversity of archaea in sediments from a deep-sea whale-fall in Monterey Canyon, California, The ISME Journal, vol.31, issue.2, pp.204-220, 2008. ,
DOI : 10.1046/j.1462-2920.2003.00418.x
strain, FEMS Microbiology Letters, vol.291, issue.2, pp.247-253, 2009. ,
DOI : 10.1111/j.1574-6968.2008.01464.x
Methanogenesis and sulfate reduction in marine sediments: A new model, Earth and Planetary Science Letters, vol.295, issue.3-4, pp.358-366, 2010. ,
DOI : 10.1016/j.epsl.2010.04.009
Anaerobic oxidation of methane in hypersaline cold seep sediments, FEMS Microbiology Ecology, vol.83, issue.1, pp.214-231, 2013. ,
DOI : 10.1111/j.1574-6941.2012.01466.x
Diversity of Archaea in Marine Sediments from Skan Bay, Alaska, Including Cultivated Methanogens, and Description of Methanogenium boonei sp. nov., Applied and Environmental Microbiology, vol.73, issue.2, pp.407-41401154, 2007. ,
DOI : 10.1128/AEM.01154-06
C-labelling approaches, Environmental Microbiology, vol.28, issue.8, pp.2384-2393, 2013. ,
DOI : 10.1111/1462-2920.12112
On the relationship between methane production and oxidation by anaerobic methanotrophic communities from cold seeps of the Gulf of Mexico, Environmental Microbiology, vol.47, issue.5, pp.1108-1117, 2008. ,
DOI : 10.1016/S0958-1669(00)00209-3
Environmental evidence for net methane production and oxidation in putative ANaerobic MEthanotrophic (ANME) archaea, Methanogens in the Sonora Margin Sediments, pp.2548-2564, 2011. ,
DOI : 10.1111/j.1462-2920.2011.02526.x