O. Bergh, K. Børsheim, G. Bratbak, and M. Heldal, High abundance of viruses found in aquatic environments, Nature, vol.340, issue.6233, pp.467-468
DOI : 10.1038/340467a0

C. Suttle, Marine viruses ??? major players in the global ecosystem, Nature Reviews Microbiology, vol.46, issue.10, pp.801-812, 1750.
DOI : 10.1038/nrmicro1750

F. Rodriguez-valera, A. Martin-cuadrado, B. Rodriguez-brito, . Pasic´lpasic´pasic´l, T. Thingstad et al., Explaining microbial population genomics through phage predation, Nature Reviews Microbiology, vol.62, issue.11, pp.828-836, 2009.
DOI : 10.1038/nrmicro2235
URL : http://doi.org/10.1038/npre.2009.3489.1

P. Forterre, The origin of viruses and their possible roles in major evolutionary transitions, Virus Research, vol.117, issue.1, pp.5-16, 2006.
DOI : 10.1016/j.virusres.2006.01.010
URL : https://hal.archives-ouvertes.fr/hal-00068013

G. Dimijian, Pathogens and parasites: strategies and challenges, Proceedings (Baylor University, pp.19-29, 2000.

F. Rohwer, A. Segall, G. Steward, V. Seguritan, M. Breitbart et al., The complete genomic sequence of the marine phage Roseophage SIO1 shares homology with nonmarine phages, Limnology and Oceanography, vol.45, issue.2, pp.408-418, 2000.
DOI : 10.4319/lo.2000.45.2.0408

N. Mann, A. Cook, A. Millard, S. Bailey, and M. Clokie, Marine ecosystems: Bacterial photosynthesis genes in a virus, Nature, vol.424, issue.6950, pp.741-751, 2003.
DOI : 10.1038/424741a

D. Lindell, M. Sullivan, Z. Johnson, A. Tolonen, F. Rohwer et al., Transfer of photosynthesis genes to and from Prochlorococcus viruses, Proc. Natl Acad. Sci. USA 101, pp.13-24, 2004.
DOI : 10.1073/pnas.0401526101

P. López-garcía and D. Moreira, Yet viruses cannot be included in the tree of life, Nature Reviews Microbiology, vol.7, issue.8, pp.615-617, 2009.
DOI : 10.1038/nrmicro2108-c7

E. Ludmir and L. Enquist, Viral genomes are part of the phylogenetic tree of life, Nature Reviews Microbiology, vol.7, issue.8, pp.615-615, 2009.
DOI : 10.1038/nrmicro2108-c4

R. Edwards and F. Rohwer, Opinion: Viral metagenomics, Nature Reviews Microbiology, vol.51, issue.6, pp.504-510, 2005.
DOI : 10.1073/pnas.93.12.5854

T. Ng, Broad Surveys of DNA Viral Diversity Obtained through Viral Metagenomics of Mosquitoes, PLoS ONE, vol.89, issue.6, 2011.
DOI : 10.1371/journal.pone.0020579.s008

S. Roux, F. Enault, R. A. Ravet, V. Personnic, S. Theil et al., Assessing the Diversity and Specificity of Two Freshwater Viral Communities through Metagenomics, PLoS ONE, vol.23, issue.1, p.33641
DOI : 10.1371/journal.pone.0033641.s009
URL : https://hal.archives-ouvertes.fr/hal-00819334

R. Vega-thurber, Metagenomic analysis indicates that stressors induce production of herpeslike viruses in the coral Porites compressa, Proc. Natl Acad. Sci. USA 105, pp.413-431, 2008.

E. Dinsdale, Functional metagenomic profiling of nine biomes, Nature, vol.32, issue.7187, pp.629-632, 2008.
DOI : 10.1038/nature06810

D. Kristensen, A. Mushegian, V. Dolja, and E. Koonin, New dimensions of the virus world discovered through metagenomics, Trends in Microbiology, vol.18, issue.1, pp.11-19
DOI : 10.1016/j.tim.2009.11.003

M. Kanehisa, S. Goto, Y. Sato, M. Furumichi, and M. Tanabe, KEGG for integration and interpretation of large-scale molecular data sets, Nucleic Acids Research, vol.40, issue.D1, pp.109-114
DOI : 10.1093/nar/gkr988

K. Pruitt, T. Tatusova, and D. Maglott, NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins, Nucleic Acids Research, vol.35, issue.Database, pp.61-65
DOI : 10.1093/nar/gkl842

A. López-bueno, J. Tamames, D. Velázquez, A. Moya, A. Quesada et al., High Diversity of the Viral Community from an Antarctic Lake, Science, vol.326, issue.5954, pp.858-861
DOI : 10.1126/science.1179287

S. Minot, R. Sinha, J. Chen, H. Li, S. Keilbaugh et al., The human gut virome: Inter-individual variation and dynamic response to diet, Genome Research, vol.21, issue.10, pp.1616-1625
DOI : 10.1101/gr.122705.111

M. Kim, E. Park, S. Roh, and J. Bae, Diversity and Abundance of Single-Stranded DNA Viruses in Human Feces, Applied and Environmental Microbiology, vol.77, issue.22, pp.8062-8070
DOI : 10.1128/AEM.06331-11

Y. Huang, P. Gilna, and W. Li, Identification of ribosomal RNA genes in metagenomic fragments, Bioinformatics, vol.25, issue.10, pp.1338-1340, 2009.
DOI : 10.1093/bioinformatics/btp161

C. Quast, E. Pruesse, P. Yilmaz, J. Gerken, T. Schweer et al., The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic Acids Research, vol.41, issue.D1, pp.590-596
DOI : 10.1093/nar/gks1219

S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman, 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

S. Akhter, R. Aziz, and R. Edwards, 2012 PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity-and composition-based strategies, Nucleic Acids Res, vol.40, pp.1-13

G. Lima-mendez, J. Van-helden, A. Toussaint, and R. Leplae, Prophinder: a computational tool for prophage prediction in prokaryotic genomes, Bioinformatics, vol.24, issue.6, pp.863-865, 2008.
DOI : 10.1093/bioinformatics/btn043

F. Angly, D. Willner, F. Rohwer, P. Hugenholtz, and G. Tyson, Grinder: a versatile amplicon and shotgun sequence simulator, Nucleic Acids Research, vol.40, issue.12, pp.94-104
DOI : 10.1093/nar/gks251

A. Lang, O. Zhaxybayeva, and J. Beatty, 2012 Gene transfer agents: phage-like elements of genetic exchange, Nat. Rev. Microbiol, vol.10, pp.472-482

E. Matson, M. Thompson, S. Humphrey, R. Zuerner, and T. Stanton, Identification of Genes of VSH-1, a Prophage-Like Gene Transfer Agent of Brachyspira hyodysenteriae, Journal of Bacteriology, vol.187, issue.17, pp.5885-5892, 2005.
DOI : 10.1128/JB.187.17.5885-5892.2005

A. Lang and J. Beatty, Importance of widespread gene transfer agent genes in ??-proteobacteria, Trends in Microbiology, vol.15, issue.2, pp.54-62, 2007.
DOI : 10.1016/j.tim.2006.12.001

E. Biers, K. Wang, C. Pennington, R. Belas, F. Chen et al., Occurrence and Expression of Gene Transfer Agent Genes in Marine Bacterioplankton, Applied and Environmental Microbiology, vol.74, issue.10, 2008.
DOI : 10.1128/AEM.02129-07

M. Krupovic, P. Forterre, and D. Bamford, Comparative Analysis of the Mosaic Genomes of Tailed Archaeal Viruses and Proviruses Suggests Common Themes for Virion Architecture and Assembly with Tailed Viruses of Bacteria, Journal of Molecular Biology, vol.397, issue.1, 2010.
DOI : 10.1016/j.jmb.2010.01.037
URL : https://hal.archives-ouvertes.fr/hal-00506375

F. Eiserling, A. Pushkin, M. Gingery, and G. Bertani, Bacteriophage-like particles associated with the gene transfer agent of Methanococcus voltae PS, Journal of General Virology, vol.80, issue.12, 1999.
DOI : 10.1099/0022-1317-80-12-3305

F. Meyer, The metagenomics RAST server ??? a public resource for the automatic phylogenetic and functional analysis of metagenomes, BMC Bioinformatics, vol.9, issue.1, pp.386-396, 2008.
DOI : 10.1186/1471-2105-9-386

K. Aoki-kinoshita and M. Kanehisa, Gene Annotation and Pathway Mapping in KEGG, Methods Mol. Biol, vol.396, pp.71-91, 2007.
DOI : 10.1007/978-1-59745-515-2_6

S. Casjens, Prophages and bacterial genomics: what have we learned so far?, Molecular Microbiology, vol.141, issue.Suppl. 1, pp.277-300, 2003.
DOI : 10.1046/j.1365-2958.2003.03580.x

F. Angly, The Marine Viromes of Four Oceanic Regions, PLoS Biology, vol.8, issue.11, 2006.
DOI : 10.1371/journal.pbio.0040368.sd001

R. Vega-thurber, M. Haynes, M. Breitbart, L. Wegley, and F. Rohwer, Laboratory procedures to generate viral metagenomes, Nature Protocols, vol.7, issue.4, pp.470-483, 2009.
DOI : 10.1593/neo.05754

P. Forterre, N. Soler, M. Krupovic, E. Marguet, and H. Ackermann, Fake virus particles generated by fluorescence microscopy, Trends in Microbiology, vol.21, issue.1, pp.1-5
DOI : 10.1016/j.tim.2012.10.005
URL : https://hal.archives-ouvertes.fr/hal-00779641

H. Yen, N. Hu, and B. Marrs, Characterization of the gene transfer agent made by an overproducer mutant of Rhodopseudomonas capsulata, Journal of Molecular Biology, vol.131, issue.2, pp.157-168
DOI : 10.1016/0022-2836(79)90071-8

M. Solioz, H. Yen, and M. B. , Release and uptake of gene transfer agent by Rhodopseudomonas capsulata, J. Bacteriol, vol.123, pp.651-657, 1975.

L. Mcdaniel, E. Young, J. Delaney, F. Ruhnau, K. Ritchie et al., High Frequency of Horizontal Gene Transfer in the Oceans, Science, vol.330, issue.6000, pp.50-60
DOI : 10.1126/science.1192243

I. Sharon, Photosystem I gene cassettes are present in marine virus genomes, Nature, vol.18, issue.7261, pp.258-262
DOI : 10.1038/nature08284
URL : https://hal.archives-ouvertes.fr/hal-01218513

A. Philosof, N. Battchikova, E. Aro, and O. Béjà, 2011 Marine cyanophages: tinkering with the electron transport chain, ISME J, vol.5

R. Poole and G. Cook, Redundancy of aerobic respiratory chains in bacteria? Routes, reasons and regulation, Adv. Microbial Physiol, vol.43, issue.00, pp.165-224, 2000.
DOI : 10.1016/S0065-2911(00)43005-5

L. Thompson, Q. Zeng, L. Kelly, K. Huang, A. Singer et al., Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism, Proc. Natl Acad. Sci. USA, pp.757-764, 2011.
DOI : 10.1073/pnas.1102164108

M. Sullivan, M. Coleman, P. Weigele, F. Rohwer, and S. Chisholm, Three Prochlorococcus Cyanophage Genomes: Signature Features and Ecological Interpretations, PLoS Biology, vol.183, issue.5, p.144, 2005.
DOI : 10.1371/journal.pbio.0030144.sg006
URL : http://doi.org/10.1371/journal.pbio.0030144

M. Sullivan, Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments, Environmental Microbiology, vol.4, issue.11, pp.3035-3056, 2010.
DOI : 10.1111/j.1462-2920.2010.02280.x

D. Arslan, M. Legendre, V. Seltzer, C. Abergel, and J. Claverie, 2011 Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae, Proc. Natl Acad. Sci. USA, pp.486-503

M. Fischer, M. Allen, W. Wilson, and C. Suttle, 2010 Giant virus with a remarkable complement of genes infects marine zooplankton, Proc. Natl Acad. Sci. USA, pp.1-6

R. Hendrix, Jumbo Bacteriophages, Curr. Top. Microbiol. Immunol, vol.328, pp.229-240, 2009.
DOI : 10.1007/978-3-540-68618-7_7

J. Klappenbach, P. Saxman, J. Cole, and T. Schmidt, rrndb: the Ribosomal RNA Operon Copy Number Database, Nucleic Acids Research, vol.29, issue.1, pp.181-184, 2001.
DOI : 10.1093/nar/29.1.181

C. Brochier, P. Hervé, and D. Moreira, The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome, Trends in Genetics, vol.16, issue.12, pp.529-533, 2000.
DOI : 10.1016/S0168-9525(00)02142-9

S. Garcia-vallvé, F. Simó, M. Montero, L. Arola, and A. Romeu, Simultaneous Horizontal Gene Transfer of a Gene Coding for Ribosomal Protein L27 and Operational Genes in Arthrobacter Sp., Journal of Molecular Evolution, vol.55, issue.6, pp.632-637
DOI : 10.1007/s00239-002-2358-5

T. Coenye and P. Vandamme, ribosomal protein gene clusters in prokaryotic genomes, FEMS Microbiology Letters, vol.242, issue.1, pp.117-126, 2005.
DOI : 10.1016/j.femsle.2004.10.050

M. Krupovic, D. Prangishvili, R. Hendrix, and D. Bamford, Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere, Microbiology and Molecular Biology Reviews, vol.75, issue.4, pp.610-635
DOI : 10.1128/MMBR.00011-11

R. Hazan and H. Engelberg-kulka, Escherichia coli mazEF-mediated cell death as a defense mechanism that inhibits the spread of phage P1, Molecular Genetics and Genomics, vol.272, issue.2, pp.227-234, 2004.
DOI : 10.1007/s00438-004-1048-y

M. Liu, Y. Zhang, M. Inouye, and N. Woychik, Bacterial addiction module toxin Doc inhibits translation elongation through its association with the 30S ribosomal subunit, Proc. Natl Acad. Sci. USA 105, pp.5885-5890, 2008.
DOI : 10.1073/pnas.0711949105

L. Aseev and I. Boni, Extraribosomal functions of bacterial ribosomal proteins, Molecular Biology, vol.45, issue.5, pp.739-750
DOI : 10.1134/S0026893311050025

S. Copley, Moonlighting is mainstream: Paradigm adjustment required, BioEssays, vol.144, issue.7, pp.578-588, 201100191.
DOI : 10.1002/bies.201100191

A. Wahba, M. Miller, A. N. Landers, T. Carmichael, G. Weber et al., 1974 Subunit I of Qb replicase and 30S ribosomal protein S1 of Escherichia coli, J. Biol. Chem, vol.249, pp.3314-3316

D. Raoult and P. Forterre, Redefining viruses: lessons from Mimivirus, Nature Reviews Microbiology, vol.79, issue.4, pp.315-319, 1858.
DOI : 10.1038/nrmicro1858
URL : https://hal.archives-ouvertes.fr/hal-00297223

J. Brum, A. Culley, and G. Steward, 2013 Assembly of a marine viral metagenome after physical fractionation, PloS ONE Open Biol, vol.8, issue.3, p.130160