P. Hugenholtz, Exploring prokaryotic diversity in the genomic era, Genome Biol, vol.3, p.3, 2002.

B. Finlay, Global Dispersal of Free-Living Microbial Eukaryote Species, Science, vol.296, issue.5570, pp.1061-1063, 2002.
DOI : 10.1126/science.1070710

R. Morris, M. Rappe, S. Connon, K. Vergin, and W. Siebold, SAR11 clade dominates ocean surface bacterioplankton communities, Nature, vol.345, issue.6917, pp.806-810, 1240.
DOI : 10.1073/pnas.95.12.6578

E. Delong, Archaea in coastal marine environments., Proceedings of the National Academy of Sciences, vol.89, issue.12, pp.5685-5689, 1992.
DOI : 10.1073/pnas.89.12.5685

P. López-garcía, F. Rodríguez-valera, C. Pedrós-alió, and D. Moreira, Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton, Nature, vol.409, issue.6820, pp.603-607, 2001.
DOI : 10.1038/35054537

C. Lepère, I. Domaizon, and D. Debroas, Unexpected Importance of Potential Parasites in the Composition of the Freshwater Small-Eukaryote Community, Applied and Environmental Microbiology, vol.74, issue.10, 2008.
DOI : 10.1128/AEM.01156-07

J. Mangot, D. Debroas, and I. Domaizon, Perkinsozoa, a well-known marine protozoan flagellate parasite group, newly identified in lacustrine systems: a review, Hydrobiologia, vol.28, issue.1, pp.37-48, 2011.
DOI : 10.1007/s10750-010-0268-x

P. Galand, E. Casamayor, D. Kirchman, and C. Lovejoy, Ecology of the rare microbial biosphere of the Arctic Ocean, Proceedings of the National Academy of Sciences, vol.106, issue.52, pp.22427-22432, 2009.
DOI : 10.1073/pnas.0908284106

B. Campbell, L. Yu, J. Heidelberg, and D. Kirchman, Activity of abundant and rare bacteria in a coastal ocean, Proceedings of the National Academy of Sciences, vol.108, issue.31, pp.12776-12781, 2011.
DOI : 10.1073/pnas.1101405108

L. Roesch, R. Fulthorpe, A. Riva, G. Casella, and A. Hadwin, Pyrosequencing enumerates and contrasts soil microbial diversity, The ISME Journal, vol.7, 2007.
DOI : 10.1038/ismej.2007.53
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970868

M. Brown, G. Philip, J. Bunge, M. Smith, and A. Bissett, Microbial community structure in the North Pacific ocean, The ISME Journal, vol.1, issue.12, pp.1374-1386, 2009.
DOI : 10.1111/j.1574-6941.2006.00171.x

A. Andersson, M. Lindberg, H. Jakobsson, F. Bä-ckhed, and P. Nyrén, Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing, PLoS ONE, vol.11, issue.7, 2008.
DOI : 10.1371/journal.pone.0002836.s003

S. Monchy, G. Sanciu, M. Jobard, S. Rasconi, and M. Gerphagnon, Exploring and quantifying fungal diversity in freshwater lake ecosystems using rDNA cloning/sequencing and SSU tag pyrosequencing, Environmental Microbiology, vol.7, issue.6, pp.1433-1453, 2011.
DOI : 10.1111/j.1462-2920.2011.02444.x
URL : https://hal.archives-ouvertes.fr/hal-00759180

V. Nolte, R. Pandey, S. Jost, R. Medinger, and B. Ottenwä-lder, Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity, Molecular Ecology, vol.312, issue.s1, pp.2908-2915, 2010.
DOI : 10.1111/j.1365-294X.2010.04669.x

J. Cole, Q. Wang, E. Cardenas, J. Fish, and B. Chai, The Ribosomal Database Project: improved alignments and new tools for rRNA analysis, Nucleic Acids Research, vol.37, issue.Database, pp.141-145, 2009.
DOI : 10.1093/nar/gkn879

A. Giongo, D. Crabb, A. Davis-richardson, D. Chauliac, and J. Mobberley, PANGEA: pipeline for analysis of next generation amplicons, The ISME Journal, vol.1, issue.7, pp.852-861, 2010.
DOI : 10.1089/10665270050081478

R. Pandey, V. Nolte, and C. Schlötterer, CANGS: a user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies, BMC Research Notes, vol.3, issue.1, 2010.
DOI : 10.1186/1756-0500-3-3

H. Mori, F. Maruyama, and K. Kurokawa, VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences, BMC Bioinformatics, vol.11, issue.1, pp.332-342, 2010.
DOI : 10.1186/1471-2105-11-332

P. Schloss, S. Westcott, T. Ryabin, J. Hall, and M. Hartmann, Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities, Applied and Environmental Microbiology, vol.75, issue.23, pp.7537-7541, 2009.
DOI : 10.1128/AEM.01541-09

J. Caporaso, J. Kuczynski, J. Stombaugh, K. Bittinger, and F. Bushman, QIIME allows analysis of high-throughput community sequencing data, Nature Methods, vol.8, issue.5, pp.335-336, 2010.
DOI : 10.1038/nmeth.f.303

T. Stoeck, A. Behnke, R. Christen, L. Amaral-zettler, and M. Rodriguez-mora, Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities, BMC Biology, vol.7, issue.1, pp.72-82, 2009.
DOI : 10.1186/1741-7007-7-72
URL : https://hal.archives-ouvertes.fr/hal-00484166

T. Stoeck, D. Bass, M. Nebel, C. R. Jones, and M. , Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water, Molecular Ecology, vol.52, issue.2, 2010.
DOI : 10.1111/j.1365-294X.2009.04480.x
URL : https://hal.archives-ouvertes.fr/hal-00497208

M. Cheung, C. Au, K. Chu, H. Kwan, and C. Wong, Composition and genetic diversity of picoeukaryotes in subtropical coastal waters as revealed by 454 pyrosequencing, The ISME Journal, vol.1, issue.8, pp.1053-1059, 2010.
DOI : 10.1111/j.1574-6941.2006.00171.x

J. Pawlowski, R. Christen, B. Lecroq, D. Bachar, and H. Shahbazkia, Eukaryotic Richness in the Abyss: Insights from Pyrotag Sequencing, PLoS ONE, vol.35, issue.Suppl.1, 2011.
DOI : 10.1371/journal.pone.0018169.s004
URL : https://hal.archives-ouvertes.fr/hal-00604768

V. Edgcomb, W. Orsi, J. Bunge, S. Jeon, and R. Christen, Protistan microbial observatory in the Cariaco Basin, Caribbean. I. Pyrosequencing vs Sanger insights into species richness, The ISME Journal, vol.58, issue.8, pp.1344-1356, 2011.
DOI : 10.1093/nar/22.22.4673
URL : https://hal.archives-ouvertes.fr/hal-00604769

H. Bik, W. Sung, D. Ley, P. Baldwin, J. Sharma et al., Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments, Molecular Ecology, vol.7, issue.Suppl. 1, 2012.
DOI : 10.1111/j.1365-294X.2011.05297.x

C. Von-mering, P. Hugenholtz, J. Raes, S. Tringe, and T. Doerks, Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments, Science, vol.315, issue.5815, pp.1126-1130, 2007.
DOI : 10.1126/science.1133420

H. Bik, D. Porazinska, S. Creer, J. Caporaso, and R. Knight, Sequencing our way towards understanding global eukaryotic biodiversity, Trends in Ecology & Evolution, vol.27, issue.4, pp.233-243, 2012.
DOI : 10.1016/j.tree.2011.11.010
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3311718

P. Jeraldo, N. Chia, and N. Goldenfeld, On the suitability of short reads of 16S rRNA for phylogeny-based analyses in environmental surveys, Environmental Microbiology, vol.75, issue.11, pp.3000-3009, 2011.
DOI : 10.1111/j.1462-2920.2011.02577.x

C. Lozupone and R. Knight, Species divergence and the measurement of microbial diversity, FEMS Microbiology Reviews, vol.32, issue.4, pp.557-578, 2008.
DOI : 10.1111/j.1574-6976.2008.00111.x

Z. Liu, C. Lozupone, M. Hamady, F. Bushman, and R. Knight, Short pyrosequencing reads suffice for accurate microbial community analysis, Nucleic Acids Research, vol.35, issue.18, 2007.
DOI : 10.1093/nar/gkm541
URL : http://doi.org/10.1093/nar/gkm541

Z. Liu, T. Desantis, G. Andersen, and R. Knight, Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers, Nucleic Acids Research, vol.36, issue.18, 2008.
DOI : 10.1093/nar/gkn491

M. Kim, M. Morrison, and Z. Yu, Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes, Journal of Microbiological Methods, vol.84, issue.1, pp.81-87, 2011.
DOI : 10.1016/j.mimet.2010.10.020

R. Medinger, V. Nolte, R. Pandey, S. Jost, and B. Ottenwälder, Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms, Molecular Ecology, vol.52, 2010.
DOI : 10.1111/j.1365-294X.2009.04478.x

J. Thompson, D. Higgins, and T. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Research, vol.22, issue.22, pp.4673-4680, 1994.
DOI : 10.1093/nar/22.22.4673

S. Guindon and O. Gascuel, A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood, Systematic Biology, vol.52, issue.5, pp.696-704, 2003.
DOI : 10.1080/10635150390235520

M. Lefranc, A. Thénot, C. Lepère, and D. Debroas, Genetic Diversity of Small Eukaryotes in Lakes Differing by Their Trophic Status, Applied and Environmental Microbiology, vol.71, issue.10, pp.5935-5942, 2005.
DOI : 10.1128/AEM.71.10.5935-5942.2005

T. Schoener, The Newest Synthesis: Understanding the Interplay of Evolutionary and Ecological Dynamics, Science, vol.331, issue.6016, pp.426-429, 2011.
DOI : 10.1126/science.1193954

A. Behnke, M. Engel, C. R. Nebel, M. Klein, and R. , Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions, Environmental Microbiology, vol.28, issue.2, pp.340-349, 2010.
DOI : 10.1111/j.1462-2920.2010.02332.x
URL : https://hal.archives-ouvertes.fr/hal-00604771

S. Dawson and K. Hagen, Mapping the protistan 'rare biosphere', Journal of Biology, vol.8, issue.12, 2009.
DOI : 10.1186/jbiol201

A. Hartman, S. Riddle, T. Mcphillips, B. Ludascher, J. Eisen et al., Introducing W.A.T.E.R.S.: a Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences, Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences, pp.317-327, 2010.
DOI : 10.1186/1471-2105-11-317

Q. Wang, G. Garrity, J. Tiedje, and J. Cole, Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy, Applied and Environmental Microbiology, vol.73, issue.16, pp.5261-5267, 2007.
DOI : 10.1128/AEM.00062-07

J. Werner, O. Koren, P. Hugenholtz, T. Desantis, and W. Walters, Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys, The ISME Journal, vol.5, issue.1, pp.94-103, 2012.
DOI : 10.1073/pnas.1015676108

P. Schloss, The Effects of Alignment Quality, Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies, PLoS Computational Biology, vol.6, issue.7, 2010.
DOI : 10.1371/journal.pcbi.1000844.t004

M. Price, P. Dehal, and A. Arkin, FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix, Molecular Biology and Evolution, vol.26, issue.7, pp.1641-1650, 2009.
DOI : 10.1093/molbev/msp077

F. Matsen, R. Kodner, and E. Armbrust, pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree, BMC Bioinformatics, vol.11, issue.1, pp.538-548, 2010.
DOI : 10.1186/1471-2105-11-538

S. Huse, L. Dethlefsen, J. Huber, M. Welch, D. Welch et al., Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing, PLoS Genetics, vol.16, issue.11, 2008.
DOI : 10.1371/journal.pgen.1000255.t003
URL : http://doi.org/10.1371/journal.pgen.1000255

K. Bowen-de-león, R. B. Fields, and M. , Quality-Score Refinement of SSU rRNA Gene Pyrosequencing Differs Across Gene Region for Environmental Samples. Microbial Ecology: 1?10, 2012.

N. Youssef, C. Sheik, L. Krumholz, F. Najar, B. Roe et al., Comparison of Species Richness Estimates Obtained Using Nearly Complete Fragments and Simulated Pyrosequencing-Generated Fragments in 16S rRNA Gene-Based Environmental Surveys, Applied and Environmental Microbiology, vol.75, issue.16, pp.5227-5236, 2009.
DOI : 10.1128/AEM.00592-09

T. Richards, A. Vepritskiy, D. Gouliamova, and S. Nierzwicki-bauer, The molecular diversity of freshwater picoeukaryotes from an oligotrophic lake reveals diverse, distinctive and globally dispersed lineages, Environmental Microbiology, vol.51, issue.9, pp.1413-1425, 2005.
DOI : 10.1093/nar/25.24.4876

D. Wu, A. Hartman, N. Ward, and J. Eisen, An Automated Phylogenetic Tree- Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP), PLoS ONE, vol.3, 2008.
DOI : 10.1371/journal.pone.0002566
URL : http://doi.org/10.1371/journal.pone.0002566

D. Ward, F. Cohan, D. Bhaya, J. Heidelberg, and M. Kühl, Genomics, environmental genomics and the issue of microbial species, Heredity, vol.62, issue.2, pp.207-219, 2007.
DOI : 10.1128/AEM.72.1.723-732.2006

M. Achtman and M. Wagner, Microbial diversity and the genetic nature of microbial species, Nature Reviews Microbiology, vol.71, pp.431-440, 2008.
DOI : 10.1038/nrmicro1872

D. Caron, P. Countway, P. Savai, R. Gast, and A. Schnetzer, Defining DNA-Based Operational Taxonomic Units for Microbial-Eukaryote Ecology, Applied and Environmental Microbiology, vol.75, issue.18, 2009.
DOI : 10.1128/AEM.00298-09

A. Alverson and L. Kolnick, INTRAGENOMIC NUCLEOTIDE POLYMORPHISM AMONG SMALL SUBUNIT (18S) RDNA PARALOGS IN THE DIATOM GENUS SKELETONEMA (BACILLARIOPHYTA)1, Journal of Phycology, vol.41, issue.6, pp.1248-1257, 2005.
DOI : 10.1111/j.1529-8817.2005.00136.x

J. Mangot, I. Domaizon, N. Taib, N. Marouni, and E. Duffaud, Shortterm dynamics of diversity patterns: evidence of continual reassembly within lacustrine small eukaryotes. Environmental Microbiology, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00821927

M. Jones, I. Forn, C. Gadelha, M. Egan, and D. Bass, Discovery of novel intermediate forms redefines the fungal tree of life, Nature, vol.86, issue.7350, pp.200-203, 2011.
DOI : 10.1038/nature09984

S. Rasconi, M. Jobard, and T. Simengando, Parasitic fungi of phytoplankton: ecological roles and implications for microbial food webs, Aquatic Microbial Ecology, vol.62, issue.2, pp.123-137, 1448.
DOI : 10.3354/ame01448
URL : https://hal.archives-ouvertes.fr/hal-00527379

C. Lepère, D. Boucher, L. Jardillier, I. Domaizon, and D. Debroas, Succession and regulation factors of small eukaryote community composition in a lacustrine ecosystem (Lake Pavin) Applied and environmental microbiology 72, p.2971, 2006.

A. Tarbe, S. Stenuite, V. Balagu, D. Sinyinza, and J. Descy, Molecular characterisation of the small-eukaryote community in a tropical Great Lake (Lake Tanganyika, East Africa), Aquatic Microbial Ecology, vol.62, issue.2, pp.177-190, 1465.
DOI : 10.3354/ame01465

C. Lepère, S. Masquelier, J. Mangot, D. Debroas, and I. Domaizon, Vertical structure of small eukaryotes in three lakes that differ by their trophic status: a quantitative approach, The ISME Journal, vol.65, issue.12, pp.1509-1519, 2010.
DOI : 10.1038/nature07236

F. Not, J. Del-campo, V. Balagué, C. De-vargas, and R. Massana, New Insights into the Diversity of Marine Picoeukaryotes, PLoS ONE, vol.67, issue.9, 2009.
DOI : 10.1371/journal.pone.0007143.s006
URL : https://hal.archives-ouvertes.fr/hal-01258270

C. Lepère, I. Domaizon, and D. Debroas, Community composition of lacustrine small eukaryotes in hyper-eutrophic conditions in relation to top-down and bottom-up factors, FEMS Microbiology Ecology, vol.61, issue.3, pp.483-495, 2007.
DOI : 10.1111/j.1574-6941.2007.00359.x

B. Marin and M. Melkonian, Molecular Phylogeny and Classification of the Mamiellophyceae class. nov. (Chlorophyta) based on Sequence Comparisons of the Nuclear- and Plastid-encoded rRNA Operons, Protist, vol.161, issue.2, pp.304-336, 2010.
DOI : 10.1016/j.protis.2009.10.002

D. Vaulot, W. Eikrem, M. Viprey, and H. Moreau, The diversity of small eukaryotic phytoplankton (???3 ??m) in marine ecosystems, FEMS Microbiology Reviews, vol.32, issue.5, pp.795-820, 2008.
DOI : 10.1111/j.1574-6976.2008.00121.x

F. Not, M. Latasa, D. Marie, T. Cariou, and D. Vaulot, A Single Species, Micromonas pusilla (Prasinophyceae), Dominates the Eukaryotic Picoplankton in the Western English Channel, Applied and Environmental Microbiology, vol.70, issue.7, pp.4064-4072, 2004.
DOI : 10.1128/AEM.70.7.4064-4072.2004

M. Holzmann, A. Habura, H. Giles, S. Bowser, and J. Pawlowski, Freshwater Foraminiferans Revealed by Analysis of Environmental DNA Samples, The Journal of Eukaryotic Microbiology, vol.62, issue.2, pp.135-139, 2003.
DOI : 10.1093/bioinformatics/14.9.817

F. Zhu, R. Massana, F. Not, M. D. Vaulot, and D. , Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene, FEMS Microbiology Ecology, vol.52, issue.1, pp.79-92, 2005.
DOI : 10.1016/j.femsec.2004.10.006

M. Sogin, H. Morrison, J. Huber, D. Welch, and S. Huse, 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

P. Rice, I. Longden, and A. Bleasby, EMBOSS: The European Molecular Biology Open Software Suite, Trends in Genetics, vol.16, issue.6, pp.276-277, 2000.
DOI : 10.1016/S0168-9525(00)02024-2

R. Edgar, Search and clustering orders of magnitude faster than BLAST, Bioinformatics, vol.26, issue.19, pp.2460-2461, 2010.
DOI : 10.1093/bioinformatics/btq461

E. Pruesse, C. Quast, K. Knittel, B. Fuchs, and W. Ludwig, SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB, Nucleic Acids Research, vol.35, issue.21, pp.7188-7196, 2007.
DOI : 10.1093/nar/gkm864

S. Eddy, Profile hidden Markov models, Bioinformatics, vol.14, issue.9, pp.755-763, 1998.
DOI : 10.1093/bioinformatics/14.9.755

M. Price, P. Dehal, and A. Arkin, FastTree 2 ??? Approximately Maximum-Likelihood Trees for Large Alignments, PLoS ONE, vol.5, issue.3, 2010.
DOI : 10.1371/journal.pone.0009490.s003

G. Zwart, B. Crump, M. Agterveld, F. Hagen, and S. Han, Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers, Aquatic Microbial Ecology, vol.28, pp.141-155, 2002.
DOI : 10.3354/ame028141

A. Groisillier, R. Massana, K. Valentin, D. Vaulot, and L. Guillou, Genetic diversity and habitats of two enigmatic marine alveolate lineages, Aquatic Microbial Ecology, vol.42, pp.277-291, 2006.
DOI : 10.3354/ame042277

T. Hill, K. Walsh, J. Harris, and B. Moffett, Using ecological diversity measures with bacterial communities, FEMS Microbiology Ecology, vol.43, issue.1, pp.1-11, 2003.
DOI : 10.1111/j.1574-6941.2003.tb01040.x

T. Gihring, S. Green, and C. Schadt, Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes, Environmental Microbiology, vol.75, issue.2, pp.285-290, 2012.
DOI : 10.1111/j.1462-2920.2011.02550.x

Y. Van-de-peer, E. Robbrecht, S. De-hoog, A. Caers, D. Rijk et al., Database on the structure of small subunit ribosomal RNA R Core Team (2012) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Nucleic Acids Res, vol.2780, pp.179-183, 1999.