A. Pernthaler and J. , Contribution of Archaea to total prokaryotic production in the deep Atlantic Ocean, 2005.

I. Hewson and J. Fuhrman, Covariation of viral parameters with bacterial assemblage richness and diversity in the water column and sediments, Deep Sea Research Part I: Oceanographic Research Papers, vol.54, issue.5, pp.811-830, 2007.
DOI : 10.1016/j.dsr.2007.02.003

I. Hewson, J. Steele, D. Capone, and J. Fuhrman, Remarkable heterogeneity in meso- and bathypelagic bacterioplankton assemblage composition, Limnology and Oceanography, vol.51, issue.3, pp.1274-1283, 2006.
DOI : 10.4319/lo.2006.51.3.1274

H. Hoppe and S. Ullrich, Profiles of ectoenzymes in the Indian Ocean: phenomena of phosphatase activity in the mesopelagic zone, Aquatic Microbial Ecology, vol.19, pp.139-148, 1999.
DOI : 10.3354/ame019139

H. Hoppe, C. Arnosti, and G. Herndl, Ecological Significance of Bacterial Enzymes in the Marine Environment, Enzymes in the environment: activity, ecology, and applications. Marcel Dekker, pp.73-108, 2002.
DOI : 10.1201/9780203904039.ch3

A. Ingalls, S. Shah, R. Hansman, L. Aluwihare, G. Santos et al., Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon, Proceedings of the National Academy of Sciences, vol.103, issue.17, pp.6442-6447, 2006.
DOI : 10.1073/pnas.0510157103

K. Kaiser and R. Benner, Major bacterial contribution to the ocean reservoir of detrital organic carbon and nitrogen, Limnology and Oceanography, vol.53, issue.1, pp.99-112, 2008.
DOI : 10.4319/lo.2008.53.1.0099

E. Kaiser and G. Herndl, Rapid recovery of marine bacterioplankton activity after inhibition by UV radiation in coastal waters, Appl Environ Microbiol, vol.63, pp.4026-4031, 1997.

D. Karentz, J. Cleaver, and D. Mitchell, CELL SURVIVAL CHARACTERISTICS AND MOLECULAR RESPONSES OF ANTARCTIC PHYTOPLANKTON TO ULTRAVIOLET-B RADIATION1, Journal of Phycology, vol.27, issue.3, pp.326-341, 1991.
DOI : 10.1111/j.0022-3646.1991.00326.x

D. Karl, Microbial oceanography: paradigms, processes and promise, Nature Reviews Microbiology, vol.112, issue.10, pp.759-769, 2007.
DOI : 10.1038/nrmicro1749

M. Karner, E. Delong, and D. Karl, Archaeal dominance in the mesopelagic zone of the Pacific Ocean, Nature, vol.409, issue.6819, pp.507-510, 2001.
DOI : 10.1038/35054051

D. Kirchman, The uptake of inorganic nutrients by heterotrophic bacteria, Microbial Ecology, vol.21, issue.2, pp.255-271, 1994.
DOI : 10.1007/BF00166816

D. Kirchman, H. Elifantz, A. Dittel, R. Malmstrom, and M. Cottrell, Standing stocks and activity of Archaea and Bacteria in the western Arctic Ocean, Limnology and Oceanography, vol.52, issue.2, pp.495-507, 2007.
DOI : 10.4319/lo.2007.52.2.0495

M. Könneke, A. Bernhard, J. De-la-torre, C. Walker, J. Waterbury et al., Isolation of an autotrophic ammonia-oxidizing marine archaeon, Nature, vol.16, issue.7058, pp.543-546, 2005.
DOI : 10.1093/nar/gkh293

B. Kuipers, G. Van-noort, J. Vosjan, and G. Herndl, Diel periodicity of bacterioplankton in the euphotic zone of the subtropical Atlantic Ocean, Marine Ecology Progress Series, vol.201, pp.13-25, 2000.
DOI : 10.3354/meps201013

F. Lauro and D. Bartlett, Prokaryotic lifestyles in deep sea habitats, Extremophiles, vol.6, issue.1, pp.15-25, 2007.
DOI : 10.1007/s00792-006-0059-5

F. Lauro, R. Chastain, L. Blankenship, A. Yayanos, and D. Bartlett, The Unique 16S rRNA Genes of Piezophiles Reflect both Phylogeny and Adaptation, Applied and Environmental Microbiology, vol.73, issue.3, pp.838-845, 2006.
DOI : 10.1128/AEM.01726-06

J. Lenz, A. Morales, and J. Gunkel, Mesozooplankton standing stock during the North Atlantic spring bloom study in 1989 and its potential grazing pressure on phytoplankton: a comparison between low, medium and high latitudes, Deep Sea Research Part II: Topical Studies in Oceanography, vol.40, issue.1-2, pp.559-572, 1993.
DOI : 10.1016/0967-0645(93)90032-I

R. Lignell, Excretion of organic carbon by phytoplankton:its relation to algal biomass, primary productivity and bacterial secondary productivity in the Baltic Sea, Marine Ecology Progress Series, vol.68, pp.85-99, 1990.
DOI : 10.3354/meps068085

A. Lopez-lopez, S. Bartual, L. Stal, O. Onyshenko, and F. Rodriguez-valera, Genetic analysis of housekeeping genes reveals a deep-sea ecotype of Alteromonas macleodii in the Mediterranean Sea, Environmental Microbiology, vol.63, issue.5, pp.649-659, 2005.
DOI : 10.1093/nar/29.1.344

E. Marañon, Phytoplankton growth rates in the Atlantic subtropical gyres, Limnology and Oceanography, vol.50, issue.1, pp.299-310, 2005.
DOI : 10.4319/lo.2005.50.1.0299

A. Martin-cuadrado, R. Lopez-garcia, J. Alba, D. Moreira, M. Others-moeseneder et al., Metagenomics of the deep Mediterranean , a warm bathypelagic habitat Terminal restriction fragment length polymorphism (T- RFLP) screening of a marine archaeal library to determine the different phylotypes, PLoS One J Microbiol Methods, vol.2, issue.44, pp.914159-172, 2001.

M. Moeseneder, C. Winter, and G. Herndl, Horizontal and vertical complexity of attached and free-living bacteria of the eastern Mediterranean Sea, determined by 16S rDNA and 16S rRNA fingerprints, Limnology and Oceanography, vol.46, issue.1, pp.95-107, 2001.
DOI : 10.4319/lo.2001.46.1.0095

R. Morris, M. Rappé, E. Urbach, S. Connon, and S. Giovannoni, Prevalence of the Chloroflexi-Related SAR202 Bacterioplankton Cluster throughout the Mesopelagic Zone and Deep Ocean, Applied and Environmental Microbiology, vol.70, issue.5, pp.2836-2842, 2004.
DOI : 10.1128/AEM.70.5.2836-2842.2004

B. Mouriño-carballido, D. Mcgillicuddy, and . Jr, Mesoscale variability in the metabolic balance of the Sargasso Sea, Limnology and Oceanography, vol.51, issue.6, pp.2675-2689, 2006.
DOI : 10.4319/lo.2006.51.6.2675

T. Nagata, Production mechanisms of dissolved organic matter Microbial ecology of the oceans, pp.121-152, 2000.

K. Nealson and J. Venter, Metagenomics and the global ocean survey: what's in it for us, and why should we care?, The ISME Journal, vol.5, issue.3, pp.185-187, 2007.
DOI : 10.1038/ismej.2007.43

I. Obernosterer and G. Herndl, Phytoplankton extracellular release and bacterial growth: dependence on the inorganic N: P ratio, Marine Ecology Progress Series, vol.116, pp.247-257, 1995.
DOI : 10.3354/meps116247

I. Obernosterer and G. Herndl, Differences in the optical and biological reactivity of the humic and nonhumic dissolved organic carbon component in two contrasting coastal marine environments, Limnology and Oceanography, vol.45, issue.5, pp.1120-1129, 2000.
DOI : 10.4319/lo.2000.45.5.1120

I. Obernosterer, G. Kraay, E. De-ranitz, and G. Herndl, Concentrations of low molecular weight carboxylic acids and carbonyl compounds in the Aegean Sea (Eastern Mediterranean) and the turnover of pyruvate, Aquatic Microbial Ecology, vol.20, pp.147-156, 1999.
DOI : 10.3354/ame020147

I. Obernosterer, B. Reitner, and G. Herndl, Contrasting effects of solar radiation on dissolved organic matter and its bioavailability to marine bacterioplankton, Limnology and Oceanography, vol.44, issue.7, pp.1645-1654, 1999.
DOI : 10.4319/lo.1999.44.7.1645

I. Obernosterer, P. Ruardij, and G. Herndl, and the photochemical oxygen demand of surface water DOM across the subtropical Atlantic Ocean, Limnology and Oceanography, vol.46, issue.3, pp.632-643, 2001.
DOI : 10.4319/lo.2001.46.3.0632

I. Obernosterer, R. Sempéré, and G. Herndl, Ultraviolet radiation induces reversal of the bioavailability of DOM to marine bacterioplankton, Aquatic Microbial Ecology, vol.24, pp.61-68, 2001.
DOI : 10.3354/ame024061

E. Pakhomov and R. Perissinotto, Mesozooplankton community structure and grazing impact in the region of the Subtropical Convergence south of Africa, Journal of Plankton Research, vol.19, issue.6, pp.675-691, 1997.
DOI : 10.1093/plankt/19.6.675

V. Parada, E. Sintes, H. Van-aken, M. Weinbauer, and G. Herndl, Viral Abundance, Decay, and Diversity in the Meso- and Bathypelagic Waters of the North Atlantic, Applied and Environmental Microbiology, vol.73, issue.14, pp.4429-4438, 2007.
DOI : 10.1128/AEM.00029-07

C. Pausz and G. Herndl, Role of ultraviolet radiation on phytoplankton extracellular release and its subsequent utilization by marine bacterioplankton, Aquatic Microbial Ecology, vol.18, pp.85-93, 1999.
DOI : 10.3354/ame018085

C. Pausz and G. Herndl, Role of nitrogen versus phosphorus availability on the effect of UV radiation on bacterioplankton and their recovery from previous UV stress, Aquatic Microbial Ecology, vol.29, 2002.
DOI : 10.3354/ame029089

M. Pérez, C. Pausz, and G. Herndl, Major shift in bacterioplankton utilization of enantiomeric amino acids between surface waters and the ocean's interior, Limnology and Oceanography, vol.48, issue.2, pp.755-763, 2003.
DOI : 10.4319/lo.2003.48.2.0755

L. Pomeroy, The Ocean's Food Web, A Changing Paradigm, BioScience, vol.24, issue.9, pp.499-504, 1974.
DOI : 10.2307/1296885

T. Reinthaler and G. Herndl, Seasonal dynamics of bacterial growth efficiencies in relation to phytoplankton in the southern North Sea, Aquatic Microbial Ecology, vol.39, pp.7-16, 2005.
DOI : 10.3354/ame039007

T. Reinthaler, H. Van-aken, C. Veth, W. Pjleb, and . Others, Prokaryotic respiration and production in the meso- and bathypelagic realm of the eastern and western North Atlantic basin, Limnology and Oceanography, vol.51, issue.3, pp.1262-1273, 2006.
DOI : 10.4319/lo.2006.51.3.1262

G. Sabehi, A. Loy, K. Jung, and P. R. Others, New Insights into Metabolic Properties of Marine Bacteria Encoding Proteorhodopsins, PLoS Biology, vol.187, issue.8, p.273, 2005.
DOI : 10.1371/journal.pbio.0030273.st006

E. Sano, S. Carlson, L. Wegley, and F. Rohwer, Movement of Viruses between Biomes, Applied and Environmental Microbiology, vol.70, issue.10, pp.5842-5846, 2004.
DOI : 10.1128/AEM.70.10.5842-5846.2004

M. Schwalbach, M. Brown, and J. Fuhrman, Impact of light on marine bacterioplankton community structure, Aquatic Microbial Ecology, vol.39, pp.235-245, 2005.
DOI : 10.3354/ame039235

B. Sherr, E. Sherr, T. Andrew, R. Fallon, and S. Newell, Trophic interactions between heterotrophic Protozoa and bacterioplankton in estuarine water analyzed with selective metabolic inhibitors, Marine Ecology Progress Series, vol.32, pp.169-179, 1986.
DOI : 10.3354/meps032169

E. Sherr and B. Sherr, Bacterivory and herbivory: Key roles of phagotrophic protists in pelagic food webs, Microbial Ecology, vol.5, issue.2, pp.223-235, 1994.
DOI : 10.1007/BF00166812

M. Sogin, H. Morrison, J. Huber, W. Dm, and . Others, Microbial diversity in the deep sea and the underexplored "rare biosphere", Proceedings of the National Academy of Sciences, vol.103, issue.32, pp.12115-12120, 2006.
DOI : 10.1073/pnas.0605127103

K. Stoderegger and G. Herndl, Production and release of bacterial capsular material and its subsequent utilization by marine bacterioplankton, Limnology and Oceanography, vol.43, issue.5, pp.877-884, 1998.
DOI : 10.4319/lo.1998.43.5.0877

K. Stoderegger and G. Herndl, Production of exopolymer particles by marine bacterioplankton under contrasting turbulence conditions, Marine Ecology Progress Series, vol.189, pp.9-16, 1999.
DOI : 10.3354/meps189009

T. Tanaka and F. Rassoulzadegan, Vertical and seasonal variations of bacterial abundance and production in the mesopelagic layer of the NW Mediterranean Sea: bottom-up and top-down controls, Deep Sea Research Part I: Oceanographic Research Papers, vol.51, issue.4, pp.531-544, 2004.
DOI : 10.1016/j.dsr.2003.12.001

E. Teira, P. Lebaron, H. Van-aken, and G. Herndl, Distribution and activity of Bacteria and Archaea in the deep water masses of the North Atlantic, Limnology and Oceanography, vol.51, issue.5, pp.2131-2144, 2006.
DOI : 10.4319/lo.2006.51.5.2131

URL : https://hal.archives-ouvertes.fr/hal-00204798

T. Thingstad, Utilization of N, P, and organic C by heterotrophic bacteria. I. Outline of a chemostat theory with a consistent concept of 'maintenance' metabolism, Marine Ecology Progress Series, vol.35, pp.99-109, 1987.
DOI : 10.3354/meps035099

T. Thingstad, Control of bacterial growth in idealized food webs Microbial ecology of the oceans, pp.229-260, 2000.

P. Tortell, M. Maldonado, and N. Price, The role of heterotrophic bacteria in iron-limited ocean ecosystems, Nature, vol.383, issue.6598, pp.330-332, 1996.
DOI : 10.1038/383330a0

M. Varela, H. Van-aken, and G. Herndl, Abundance and activity of Chloroflexi-type SAR202 bacterioplankton in the meso- and bathypelagic waters of the (sub)tropical Atlantic, Environmental Microbiology, vol.63, issue.7, pp.1903-1911, 2008.
DOI : 10.1016/j.pocean.2005.11.001

A. Vezzi, S. Campanaro, D. Angelo, M. Simonato, and F. Others, Life at Depth: Photobacterium profundum Genome Sequence and Expression Analysis, Science, vol.307, issue.5714, pp.1459-1461, 2005.
DOI : 10.1126/science.1103341

M. Weinbauer, Ecology of prokaryotic viruses, FEMS Microbiology Reviews, vol.28, issue.2, pp.127-181, 2004.
DOI : 10.1016/j.femsre.2003.08.001

M. Weinbauer, I. Brettar, and M. Höfle, Lysogeny and virus-induced mortality of bacterioplankton in surface, deep, and anoxic marine waters, Limnology and Oceanography, vol.48, issue.4, pp.1457-1465, 2003.
DOI : 10.4319/lo.2003.48.4.1457

W. Whitman, D. Coleman, and W. Wiebe, Prokaryotes: The unseen majority, Proceedings of the National Academy of Sciences, vol.95, issue.12, pp.6578-6583, 1998.
DOI : 10.1073/pnas.95.12.6578

C. Winter, M. Moeseneder, and G. Herndl, Impact of UV Radiation on Bacterioplankton Community Composition, Applied and Environmental Microbiology, vol.67, issue.2, pp.665-672, 2001.
DOI : 10.1128/AEM.67.2.665-672.2001

C. Winter, G. Herndl, and M. Weinbauer, Diel cycles in viral infection of bacterioplankton in the North Sea, Aquatic Microbial Ecology, vol.35, pp.207-216, 2004.
DOI : 10.3354/ame035207

C. Winter, A. Smit, G. Herndl, and M. Weinbauer, Impact of Virioplankton on Archaeal and Bacterial Community Richness as Assessed in Seawater Batch Cultures, Applied and Environmental Microbiology, vol.70, issue.2, pp.804-813, 2004.
DOI : 10.1128/AEM.70.2.804-813.2004

A. Worden, S. Chisholm, and B. Binder, In Situ Hybridization of Prochlorococcus and Synechococcus (Marine Cyanobacteria) spp. with rRNA-Targeted Peptide Nucleic Acid Probes, Applied and Environmental Microbiology, vol.66, issue.1, pp.284-289, 2000.
DOI : 10.1128/AEM.66.1.284-289.2000

C. Wuchter, L. Herfort, and M. Coolen, Archaeal nitrification in the ocean, Proceedings of the National Academy of Sciences, vol.103, issue.33, pp.12317-12322, 2006.
DOI : 10.1073/pnas.0600756103

M. Zubkov and G. Tarran, Amino acid uptake of Prochlorococcus spp. in surface waters across the South Atlantic Subtropical Front, Aquatic Microbial Ecology, vol.40, pp.241-249, 2005.
DOI : 10.3354/ame040241