D. Karl, Dinitrogen fixation in the world???s oceans, Biogeochemistry, vol.5758, pp.47-98, 2002.
DOI : 10.1007/978-94-017-3405-9_2

M. Mcfall-ngai, Are biologists in 'future shock'? Symbiosis integrates biology across domains, Nature Reviews Microbiology, vol.151, issue.10, pp.789-792, 2008.
DOI : 10.1073/pnas.0400706101

M. Martinez-garcia, Unveiling in situ interactions between marine protists and bacteria through single cell sequencing, The ISME Journal, vol.6, issue.3, pp.703-707, 2012.
DOI : 10.1038/nature07236

A. W. Thompson, Unicellular Cyanobacterium Symbiotic with a Single-Celled Eukaryotic Alga, Science, vol.337, issue.6101, pp.1546-1550, 2012.
DOI : 10.1126/science.1222700
URL : https://hal.archives-ouvertes.fr/hal-01254002

J. P. Montoya, High rates of N2 fixation by unicellular diazotrophs in the oligotrophic Pacific Ocean, Nature, vol.185, issue.7003, pp.1027-1032, 2004.
DOI : 10.1029/2000GB001291

L. Jardillier, M. V. Zubkov, J. Pearman, and D. J. Scanlan, Significant CO2 fixation by small prymnesiophytes in the subtropical and tropical northeast Atlantic Ocean, The ISME Journal, vol.147, issue.9, pp.1180-1192, 2010.
DOI : 10.1038/nature07236

N. L. Goebel, Abundance and distribution of major groups of diazotrophic cyanobacteria and their potential contribution to N2 fixation in the tropical Atlantic Ocean, Environmental Microbiology, vol.322, issue.12, pp.3272-3289, 2010.
DOI : 10.1111/j.1462-2920.2010.02303.x

J. P. Zehr and R. M. Kudela, Nitrogen Cycle of the Open Ocean: From Genes to Ecosystems, Annual Review of Marine Science, vol.3, issue.1, pp.197-225, 2011.
DOI : 10.1146/annurev-marine-120709-142819

A. M. Cabello, Global distribution and vertical patterns of a prymnesiophyte???cyanobacteria obligate symbiosis, The ISME Journal, vol.322, issue.3, pp.693-706, 2015.
DOI : 10.1038/ismej.2015.147
URL : https://hal.archives-ouvertes.fr/hal-01289124

J. P. Zehr, Globally Distributed Uncultivated Oceanic N2-Fixing Cyanobacteria Lack Oxygenic Photosystem II, Science, vol.322, issue.5904, pp.1110-1112, 2008.
DOI : 10.1126/science.1165340

H. J. Tripp, Metabolic streamlining in an open-ocean nitrogen-fixing cyanobacterium, Nature, vol.36, issue.7285, pp.90-94, 2010.
DOI : 10.1038/nature08786

D. Bombar, Comparative genomics reveals surprising divergence of two closely related strains of uncultivated UCYN-A cyanobacteria, The ISME Journal, vol.64, issue.12, pp.2530-2542, 2014.
DOI : 10.1038/35088063

K. Hagino, R. Onuma, M. Kawachi, and T. Horiguchi, Discovery of an Endosymbiotic Nitrogen-Fixing Cyanobacterium UCYN-A in Braarudosphaera bigelowii (Prymnesiophyceae), PLoS ONE, vol.412, issue.12, p.81749, 2013.
DOI : 10.1371/journal.pone.0081749.t001

A. Thompson, Genetic diversity of the unicellular nitrogen-fixing cyanobacteria UCYN-A and its prymnesiophyte host, Environmental Microbiology, vol.52, issue.Suppl. 2, pp.3238-3249, 2014.
DOI : 10.1111/1462-2920.12490

A. Krupke, In situ identification and N2 and C fixation rates of uncultivated cyanobacteria populations, Systematic and Applied Microbiology, vol.36, issue.4, pp.259-271, 2013.
DOI : 10.1016/j.syapm.2013.02.002

L. Moal, M. Collin, H. Biegala, and I. C. , Intriguing diversity among diazotrophic picoplankton along a Mediterranean transect: a dominance of rhizobia, Biogeosciences, vol.8, issue.3, pp.827-840, 2011.
DOI : 10.5194/bg-8-827-2011
URL : https://hal.archives-ouvertes.fr/hal-00701430

A. Krupke, fixing cyanobacterium UCYN-A in the North Atlantic Ocean, Environmental Microbiology, vol.455, issue.10, pp.3153-3167, 2014.
DOI : 10.1111/1462-2920.12431

A. Krupke, The effect of nutrients on carbon and nitrogen fixation by the UCYN-A???haptophyte symbiosis, The ISME Journal, vol.412, issue.7, pp.1635-1647, 2015.
DOI : 10.1038/ismej.2014.253

J. P. Zehr, Nitrogen fixation by marine cyanobacteria, Trends in Microbiology, vol.19, issue.4, pp.162-173, 2011.
DOI : 10.1016/j.tim.2010.12.004

W. H. Li, Unbiased estimation of the rates of synonymous and nonsynonymous substitution, Journal of Molecular Evolution, vol.3, issue.1, pp.96-99, 1993.
DOI : 10.1007/BF02407308

L. Hurst, The Ka/Ks ratio: diagnosing the form of sequence evolution, Trends in Genetics, vol.18, issue.9, pp.486-487, 2002.
DOI : 10.1016/S0168-9525(02)02722-1

J. H. Mcdonald and M. Kreitman, Adaptive protein evolution at the Adh locus in Drosophila, Nature, vol.351, issue.6328, pp.652-654, 1991.
DOI : 10.1038/351652a0

A. M. Peleo-alampay, G. A. Mead, and W. Wei, Unusual Oligocene Braarudo-sphaera-rich layers of the South Atlantic and their palaeoceanographic implications, J. Nannoplankton Res, vol.21, pp.17-26, 1999.

A. L. Cardenas and P. J. Harries, Effect of nutrient availability on marine origination rates throughout the Phanerozoic eon, Nature Geoscience, vol.359, issue.6, pp.430-434, 2010.
DOI : 10.1038/ngeo869

J. Decelle, An original mode of symbiosis in open ocean plankton, Proc. Natl Acad. Sci. USA, pp.18000-18005, 2012.
DOI : 10.1073/pnas.1212303109
URL : https://hal.archives-ouvertes.fr/hal-01258241

C. Kneip, P. Lockhart, C. Voss, and U. Maier, Nitrogen fixation in eukaryotes ??? New models for symbiosis, BMC Evolutionary Biology, vol.7, issue.1, p.55, 2007.
DOI : 10.1186/1471-2148-7-55

T. Nakayama, Spheroid bodies in rhopalodiacean diatoms were derived from a single endosymbiotic cyanobacterium, Journal of Plant Research, vol.412, issue.1, pp.93-97, 2011.
DOI : 10.1007/s10265-010-0355-0

E. Karsenti, A Holistic Approach to Marine Eco-Systems Biology, PLoS Biology, vol.6, issue.10, p.1001177, 2011.
DOI : 10.1371/journal.pbio.1001177.g002
URL : https://hal.archives-ouvertes.fr/hal-00691580

S. Sunagawa, Structure and function of the global ocean microbiome, Science, vol.348, issue.6237, p.1261359, 2015.
DOI : 10.1126/science.1261359
URL : https://hal.archives-ouvertes.fr/hal-01233742

R. Logares, Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities, Environmental Microbiology, vol.6, issue.Suppl 1, pp.2659-2671, 2013.
DOI : 10.1111/1462-2920.12250
URL : https://hal.archives-ouvertes.fr/hal-01258219

D. Vargas and C. , Eukaryotic plankton diversity in the sunlit ocean, Science, vol.348, issue.6237, p.1261605, 2015.
DOI : 10.1126/science.1261605

S. Pesant, Open science resources for the discovery and analysis of Tara Oceans data, Scientific Data, vol.43, issue.26, p.150023, 2015.
DOI : 10.1146/annurev-marine-120308-080950
URL : https://hal.archives-ouvertes.fr/hal-01253984

L. Guillou, The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy, Nucleic Acids Research, vol.41, issue.D1, pp.597-604, 2013.
DOI : 10.1093/nar/gks1160
URL : https://hal.archives-ouvertes.fr/hal-01253994

K. Katoh, K. Misawa, K. Kuma, and T. Miyata, MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform, Nucleic Acids Research, vol.30, issue.14, pp.3059-3066, 2002.
DOI : 10.1093/nar/gkf436

A. Stamatakis, 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

I. Letunic and P. Bork, Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation, Bioinformatics, vol.23, issue.1, pp.127-128, 2007.
DOI : 10.1093/bioinformatics/btl529

I. Letunic and P. Bork, Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy, Nucleic Acids Research, vol.39, issue.suppl, pp.475-478, 2011.
DOI : 10.1093/nar/gkr201

N. Simon, Oligonucleotide Probes for the Identification of Three Algal Groups by Dot Blot and Fluorescent Whole-Cell Hybridization, The Journal of Eukaryotic Microbiology, vol.51, issue.1, pp.76-84, 2000.
DOI : 10.1017/S096702629700139X

A. Pernthaler, J. Pernthaler, and R. Amann, Sensitive multi-color fluorescence in situ hybridization for the identification of environmental microorganisms, Mol. Microb. Ecol. Man, vol.3, pp.2613-2627, 2004.

A. Alberti, Comparison of library preparation methods reveals their impact on interpretation of metatranscriptomic data, BMC Genomics, vol.15, issue.1, p.912, 2014.
DOI : 10.1186/1471-2164-10-531

A. Caro-quintero and K. T. Konstantinidis, Bacterial species may exist, metagenomics reveal, Environmental Microbiology, vol.37, issue.1, pp.347-355, 2011.
DOI : 10.1111/j.1462-2920.2011.02668.x

C. E. Blank and P. Sánchez-baracaldo, Timing of morphological and ecological innovations in the cyanobacteria ?????? a key to understanding the rise in atmospheric oxygen, Geobiology, vol.16, issue.1, pp.1-23, 2010.
DOI : 10.1111/j.1472-4669.2009.00220.x

Z. Yang, PAML 4: Phylogenetic Analysis by Maximum Likelihood, Molecular Biology and Evolution, vol.24, issue.8, pp.1586-1591, 2007.
DOI : 10.1093/molbev/msm088

N. Lartillot, T. Lepage, and S. Blanquart, PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating, Bioinformatics, vol.25, issue.17, pp.2286-2288, 2009.
DOI : 10.1093/bioinformatics/btp368

A. J. Drummond, S. Y. Ho, M. J. Phillips, and A. Rambaut, Relaxed Phylogenetics and Dating with Confidence, PLoS Biology, vol.20, issue.5, pp.699-710, 2006.
DOI : 10.1371/journal.pbio.0040088.sd001

P. Sánchez-baracaldo, A. Ridgwell, and J. A. Raven, A Neoproterozoic Transition in the Marine Nitrogen Cycle, Current Biology, vol.24, issue.6, pp.652-657, 2014.
DOI : 10.1016/j.cub.2014.01.041

T. Lepage, D. Bryant, H. Philippe, and N. Lartillot, A General Comparison of Relaxed Molecular Clock Models, Molecular Biology and Evolution, vol.24, issue.12, pp.2669-2680, 2007.
DOI : 10.1093/molbev/msm193
URL : https://hal.archives-ouvertes.fr/lirmm-00193697

M. Hasegawa, H. Kishino, and T. Yano, Dating of the human-ape splitting by a molecular clock of mitochondrial DNA, Journal of Molecular Evolution, vol.275, issue.3, pp.160-174, 1985.
DOI : 10.1007/BF02101694

Z. Yang and B. Rannala, Bayesian Estimation of Species Divergence Times Under a Molecular Clock Using Multiple Fossil Calibrations with Soft Bounds, Molecular Biology and Evolution, vol.23, issue.1, pp.212-226, 2006.
DOI : 10.1093/molbev/msj024

J. J. Brocks, R. Buick, R. E. Summons, and G. A. Logan, A reconstruction of Archean biological diversity based on molecular fossils from the 2.78 to 2.45 billion-year-old Mount Bruce Supergroup, Hamersley Basin, Western Australia, Geochimica et Cosmochimica Acta, vol.67, issue.22, pp.4321-4335, 2003.
DOI : 10.1016/S0016-7037(03)00209-6

A. Bekker, Dating the rise of atmospheric oxygen, Nature, vol.427, issue.6970, pp.117-120, 2004.
DOI : 10.1038/nature02260

A. Tomitani, A. H. Knoll, C. M. Cavanaugh, and T. Ohno, The evolutionary diversification of cyanobacteria: Molecular-phylogenetic and paleontological perspectives, Proc. Natl Acad. Sci. USA 103, pp.5442-5447, 2006.
DOI : 10.1073/pnas.0600999103

Y. Zhang and S. Golubic, Endolithic microfossils (cyanophyta) from early Proterozoic stromatolites, Acta Micropaleontol. Sin, vol.4, pp.1-3, 1987.