D. Divins, Total Sediment Tchickness of the World's Oceans & Marginal Seas, NOAA National Geophysical Data Center, 2003.

E. Roussel, M. Bonavita, J. Querellou, B. Cragg, and G. Webster, Extending the Sub-Sea-Floor Biosphere, Science, vol.320, issue.5879, p.1046, 2008.
DOI : 10.1126/science.1154545

URL : https://hal.archives-ouvertes.fr/hal-00617515

J. Kallmeyer, R. Pockalny, R. Adhikari, D. Smith, D. Hondt et al., Global distribution of microbial abundance and biomass in subseafloor sediment, Proceedings of the National Academy of Sciences, 2012.
DOI : 10.1073/pnas.1203849109

R. Parkes, B. Cragg, and P. Wellsbury, Recent studies on bacterial populations and processes in subseafloor sediments: A review, Hydrogeology Journal, vol.8, issue.1, pp.11-28, 2000.
DOI : 10.1007/PL00010971

Y. Morono, T. Terada, M. Nishizawa, M. Ito, and F. Hillion, Carbon and nitrogen assimilation in deep subseafloor microbial cells, Proceedings of the National Academy of Sciences, vol.108, issue.45, pp.18295-18300, 2011.
DOI : 10.1073/pnas.1107763108

J. Biddle, J. Lipp, M. Lever, K. Lloyd, and K. Sorensen, Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru, Proceedings of the National Academy of Sciences, vol.103, issue.10, pp.3846-3851, 2006.
DOI : 10.1073/pnas.0600035103

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1533785

J. Lipp, Y. Morono, F. Inagaki, and K. Hinrichs, Significant contribution of Archaea to extant biomass in marine subsurface sediments, Nature, vol.409, issue.7207, pp.991-994, 2008.
DOI : 10.1038/nature07174

B. Jørgensen, Deep subseafloor microbial cells on physiological standby, Proceedings of the National Academy of Sciences, vol.108, issue.45, pp.18193-18194, 2011.
DOI : 10.1073/pnas.1115421108

F. Inagaki, M. Suzuki, K. Takai, H. Oida, and T. Sakamoto, Microbial Communities Associated with Geological Horizons in Coastal Subseafloor Sediments from the Sea of Okhotsk, Applied and Environmental Microbiology, vol.69, issue.12, pp.7224-7235, 2003.
DOI : 10.1128/AEM.69.12.7224-7235.2003

F. Inagaki, T. Nunoura, S. Nakagawa, A. Teske, and M. Lever, Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin, Proceedings of the National Academy of Sciences, vol.103, issue.8, pp.2815-2820, 2006.
DOI : 10.1073/pnas.0511033103

D. Hondt, S. Jørgensen, B. Miller, D. Batzke, A. Blake et al., Distributions of Microbial Activities in Deep Subseafloor Sediments, Science, vol.306, issue.5705, pp.2216-2221, 2004.
DOI : 10.1126/science.1101155

G. Webster, R. Parkes, J. Fry, and A. Weightman, Widespread Occurrence of a Novel Division of Bacteria Identified by 16S rRNA Gene Sequences Originally Found in Deep Marine Sediments, Applied and Environmental Microbiology, vol.70, issue.9, pp.5708-5713, 2004.
DOI : 10.1128/AEM.70.9.5708-5713.2004

C. Newberry, G. Webster, B. Cragg, R. Parkes, and A. Weightman, Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190, Environmental Microbiology, vol.180, issue.3, pp.274-287, 2004.
DOI : 10.1038/45777

B. Orcutt, J. Sylvan, N. Knab, and K. Edwards, Microbial Ecology of the Dark Ocean above, at, and below the Seafloor, Microbiology and Molecular Biology Reviews, vol.75, issue.2, pp.361-422, 2011.
DOI : 10.1128/MMBR.00039-10

A. Teske and K. Sorensen, 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

W. Orsi, V. Edgcomb, G. Christman, and J. Biddle, Gene expression in the deep biosphere, Nature, vol.6, issue.7457, pp.205-208, 2013.
DOI : 10.1038/nature12230

J. Biddle, S. Fitz-gibbon, S. Schuster, J. Brenchley, and C. House, Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment, Proceedings of the National Academy of Sciences, vol.105, issue.30, pp.10583-10588, 2008.
DOI : 10.1073/pnas.0709942105

K. Lloyd, L. Schreiber, D. Petersen, K. Kjeldsen, and M. Lever, Predominant archaea in marine sediments degrade detrital proteins, Nature, vol.250, issue.7444, 2013.
DOI : 10.1038/nature12033

A. Vigneron, P. Cruaud, P. Pignet, J. Caprais, and N. Gayet, 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, 2014.
DOI : 10.1111/1462-2920.12324

URL : https://hal.archives-ouvertes.fr/hal-01111546

A. Vigneron, P. Cruaud, P. Pignet, J. Caprais, and M. Cambon-bonavita, Archaeal and anaerobic methane oxidizer communities in the Sonora Margin cold seeps, Guaymas Basin (Gulf of California), The ISME Journal, vol.62, issue.8, 2013.
DOI : 10.1002/bit.20347

URL : https://hal.archives-ouvertes.fr/hal-00808539

C. Lazar, L. Haridon, S. Pignet, P. Toffin, and L. , Archaeal Populations in Hypersaline Sediments Underlying Orange Microbial Mats in the Napoli Mud Volcano, Applied and Environmental Microbiology, vol.77, issue.9, pp.3120-3131, 2011.
DOI : 10.1128/AEM.01296-10

URL : https://hal.archives-ouvertes.fr/hal-00618019

S. Fonselius, D. Dyrssen, and B. Yhlen, Determination of hydrogen sulphide. Methods of Seawater Analysis, pp.91-100, 2007.

P. Sarradin and J. Caprais, Analysis of dissolved gases by headspace sampling gas chromatography with column and detector switching. Preliminary results, Analytical Communications, vol.33, issue.10, 1996.
DOI : 10.1039/ac9963300371

M. Ciobanu, M. Rabineau, L. Droz, S. Révillon, and J. Ghiglione, Paleoenvironmental imprint on subseafloor microbial communities in Western Mediterranean Sea Quaternary sediments, Biogeosciences Discussions, vol.9, issue.1, pp.253-310, 2012.
DOI : 10.5194/bgd-9-253-2012-supplement

N. Callac, C. Rommevaux-jestin, O. Rouxel, F. Lesongeur, and C. Liorzou, Microbial colonization of basaltic glasses in hydrothermal organic-rich sediments at Guaymas Basin, Frontiers in Microbiology, vol.4, 2013.
DOI : 10.3389/fmicb.2013.00250

URL : https://hal.archives-ouvertes.fr/insu-00933493

J. Zhou, M. Bruns, and J. Tiedje, DNA recovery from soils of diverse composition, Appl Environ Microbiol, vol.62, pp.316-322, 1996.

C. Lazar, J. Dinasquet, P. Pignet, D. Prieur, and L. Toffin, Active Archaeal Communities at Cold Seep Sediments Populated by Siboglinidae Tubeworms from the Storegga Slide, Microbial Ecology, vol.62, issue.536, pp.516-527, 2010.
DOI : 10.1007/s00248-010-9654-1

URL : https://hal.archives-ouvertes.fr/hal-00616965

Ø. Hammer, D. Th, and P. R. , PAST: Paleontological Statistics Software Package for Education and Data Analysis, Palaeontologia Electronica, vol.4, 2001.

Z. Lu, Z. He, V. Parisi, S. Kang, and Y. Deng, GeoChip-Based Analysis of Microbial Functional Gene Diversity in a Landfill Leachate-Contaminated Aquifer, Environmental Science & Technology, vol.46, issue.11, pp.5824-5833, 2012.
DOI : 10.1021/es300478j

J. Zhou, GeoChip: A high throughput genomics technology for characterizing microbial functional community structure, Phytopathology, vol.99, pp.164-164, 2009.

Y. Chan, J. Van-nostrand, J. Zhou, S. Pointing, and R. Farrell, Functional ecology of an Antarctic Dry Valley, Proceedings of the National Academy of Sciences, vol.110, issue.22, pp.8990-8995, 2013.
DOI : 10.1073/pnas.1300643110

Z. He, Y. Deng, J. Van-nostrand, Q. Tu, and M. Xu, GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity, The ISME Journal, vol.62, issue.9, pp.1167-1179, 2010.
DOI : 10.1073/pnas.0709016105

H. Cheshire, J. Thurow, and A. Nederbragt, Late Quaternary climate change record from two long sediment cores from Guaymas Basin, Gulf of California, Journal of Quaternary Science, vol.23, issue.5, pp.457-469, 2005.
DOI : 10.1002/jqs.944

P. Kemp, S. Lee, and J. Laroche, Estimating the Growth Rate of Slowly Growing Marine Bacteria from RNA Content, Applied and Environmental Microbiology, vol.59, pp.2594-2601, 1993.

L. Kerkhof and B. Ward, Comparison of Nucleic Acid Hybridization and Fluorometry for Measurement of the Relationship between RNA/DNA Ratio and Growth Rate in a Marine Bacterium, Applied and Environmental Microbiology, vol.59, pp.1303-1309, 1993.

R. Danovaro, A. Pusceddu, A. Fabiano, and M. , Nucleic acid concentrations (DNA, RNA) in the continental and deep-sea sediments of the eastern Mediterranean: relationships with seasonally varying organic inputs and bacterial dynamics. Deep Sea Research Part I: Oceanographic Research Papers, pp.1077-1094, 1999.

K. Kubo, K. Lloyd, J. Fb, R. Amann, and A. Teske, Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments, The ISME Journal, vol.65, issue.10, 2012.
DOI : 10.1016/j.syapm.2010.08.001

A. Blazejak and A. Schippers, in deeply buried marine sediments revealed by quantitative, real-time PCR, FEMS Microbiology Ecology, vol.72, issue.2, pp.198-207, 2010.
DOI : 10.1111/j.1574-6941.2010.00838.x

L. Guy and T. Ettema, The archaeal ???TACK??? superphylum and the origin of eukaryotes, Trends in Microbiology, vol.19, issue.12, pp.580-587, 2011.
DOI : 10.1016/j.tim.2011.09.002

M. Carmona, M. Zamarro, B. Blázquez, G. Durante-rodríguez, and J. Juárez, Anaerobic Catabolism of Aromatic Compounds: a Genetic and Genomic View, Microbiology and Molecular Biology Reviews, vol.73, issue.1, pp.71-133, 2009.
DOI : 10.1128/MMBR.00021-08

J. Arensdorf and D. Focht, A meta cleavage pathway for 4-chlorobenzoate, an intermediate in the metabolism of 4-chlorobiphenyl by Pseudomonas cepacia P166, Appl Environ Microbiol, vol.61, pp.443-447, 1995.

K. Knittel and A. Boetius, Anaerobic Oxidation of Methane: Progress with an Unknown Process, Annual Review of Microbiology, vol.63, issue.1, pp.311-334, 2009.
DOI : 10.1146/annurev.micro.61.080706.093130

C. Vetriani, H. Tran, and L. Kerkhof, Fingerprinting Microbial Assemblages from the Oxic/Anoxic Chemocline of the Black Sea, Applied and Environmental Microbiology, vol.69, issue.11, pp.6481-6488, 2003.
DOI : 10.1128/AEM.69.11.6481-6488.2003

K. Lloyd, D. Albert, J. Biddle, J. Chanton, and O. Pizarro, 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, p.8738, 2010.
DOI : 10.1371/journal.pone.0008738.s009

A. Durbin and A. Teske, Microbial diversity and stratification of South Pacific abyssal marine sediments, Environmental Microbiology, vol.62, issue.12, pp.3219-3234, 2011.
DOI : 10.1111/j.1462-2920.2011.02544.x

B. Simoneit, P. Lonsdale, J. Edmond, and W. Shanks, Deep-water hydrocarbon seeps in Guaymas Basin, Gulf of California, Applied Geochemistry, vol.5, issue.1-2, pp.41-49, 1990.
DOI : 10.1016/0883-2927(90)90034-3

S. Jorgensen, B. Hannisdal, A. Lanzen, T. Baumberger, and K. Flesland, Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge, Proceedings of the National Academy of Sciences, vol.109, issue.42, pp.2846-2855, 2012.
DOI : 10.1073/pnas.1207574109

A. Govin, U. Holzwarth, D. Heslop, F. Keeling, L. Zabel et al., Distribution of major elements in Atlantic surface sediments (36uN?49uS): Imprint of terrigenous input and continental weathering, p.1013, 2012.

B. Nath, V. Rao, and K. Becker, Geochemical evidence of terrigenous influence in deep-sea sediments up to 8??S in the Central Indian Basin, Marine Geology, vol.87, issue.2-4, pp.301-313, 1989.
DOI : 10.1016/0025-3227(89)90067-4

B. Lomstein, A. Langerhuus, D. Hondt, S. Jorgensen, B. Spivack et al., Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment, Nature, vol.201, issue.7392, pp.101-104, 2012.
DOI : 10.1038/nature10905

B. Simoneit, M. Mazurek, S. Brenner, P. Crisp, and I. Kaplan, Organic geochemistry of recent sediments from Guaymas Basin, Gulf of California, Deep Sea Research Part A. Oceanographic Research Papers, vol.26, issue.8, pp.879-891, 1979.
DOI : 10.1016/0198-0149(79)90102-X

T. Futagami, Y. Morono, T. Terada, A. Kaksonen, and F. Inagaki, Dehalogenation Activities and Distribution of Reductive Dehalogenase Homologous Genes in Marine Subsurface Sediments, Applied and Environmental Microbiology, vol.75, issue.21, pp.6905-6909, 2009.
DOI : 10.1128/AEM.01124-09

R. Roy, Short-term variability in halocarbons in relation to phytoplankton pigments in coastal waters of the central eastern Arabian Sea, Estuarine, Coastal and Shelf Science, vol.88, issue.3, pp.311-321, 2010.
DOI : 10.1016/j.ecss.2010.04.011

F. Löffler, J. Yan, K. Ritalahti, A. L. Edwards, and E. , Dehalococcoides mccartyi gen. nov., sp. nov., obligate organohalide-respiring anaerobic bacteria, relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidetes classis nov., within the phylum Chloroflexi, International Journal of Systematic and Evolutionary Microbiology, 2012.

J. Meng, J. Xu, D. Qin, Y. He, and X. Xiao, Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analyses, The ISME Journal, vol.62, issue.3, 2013.
DOI : 10.1093/bioinformatics/17.9.847

K. Sowers and J. Ferry, Isolation and Characterization of a Methylotrophic Marine Methanogen, Methanococcoides methylutens gen. nov., sp. nov, Appl Environ Microbiol, vol.45, pp.684-690, 1983.

R. Parkes, B. Cragg, N. Banning, F. Brock, and G. Webster, 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

R. Parkes, G. Webster, B. Cragg, A. Weightman, and C. Newberry, Deep sub-seafloor prokaryotes stimulated at interfaces over geological time, Nature, vol.436, issue.7049, pp.390-394, 2005.
DOI : 10.1038/nature03796

J. Leigh, Nitrogen fixation in methanogens: the archaeal perspective, Curr Issues Mol Biol, vol.2, pp.125-131, 2000.

J. Raymond, J. Siefert, C. Staples, and R. Blankenship, The Natural History of Nitrogen Fixation, Molecular Biology and Evolution, vol.21, issue.3, pp.541-554, 2004.
DOI : 10.1093/molbev/msh047

A. Dekas, R. Poretsky, and V. Orphan, Deep-Sea Archaea Fix and Share Nitrogen in Methane-Consuming Microbial Consortia, Science, vol.326, issue.5951, pp.422-426, 2009.
DOI : 10.1126/science.1178223

A. Meyerdierks, M. Kube, I. Kostadinov, H. Teeling, and F. Glockner, Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group, Environmental Microbiology, vol.62, issue.2, pp.422-439, 2010.
DOI : 10.1111/j.1462-2920.2009.02083.x

E. Roussel, A. Sauvadet, C. Chaduteau, Y. Fouquet, and J. Charlou, Archaeal communities associated with shallow to deep subseafloor sediments of the New Caledonia Basin, Environmental Microbiology, vol.21, issue.9, pp.2446-2462, 2009.
DOI : 10.1111/j.1462-2920.2009.01976.x

URL : https://hal.archives-ouvertes.fr/hal-00617523

M. Mussmann, I. Brito, A. Pitcher, S. Damste, J. Hatzenpichler et al., Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers, Proceedings of the National Academy of Sciences, vol.108, issue.40, pp.16771-16776, 2011.
DOI : 10.1073/pnas.1106427108

L. Russ, B. Kartal, . Op-den, H. Camp, M. Sollai et al., Presence and diversity of anammox bacteria in cold hydrocarbon-rich seeps and hydrothermal vent sediments of the Guaymas Basin, Frontiers in Microbiology, vol.4, 2013.
DOI : 10.3389/fmicb.2013.00219

URL : https://hal.archives-ouvertes.fr/hal-01025534