F. Azam, T. Fenchel, J. Field, J. Gray, and L. Meyer-reil, The Ecological Role of Water-Column Microbes in the Sea, Marine Ecology Progress Series, vol.10, pp.257-263, 1983.
DOI : 10.3354/meps010257

J. Laybourn-parry and J. Parry, Flagellates and the microbial loop In The flagellates: Unity, diversity and evolution, pp.216-239, 2000.

J. Gasol and D. Vaqué, Lack of coupling between heterotrophic nanoflagellates and bacteria: A general phenomenon across aquatic systems?, Limnology and Oceanography, vol.38, issue.3, pp.657-665, 1993.
DOI : 10.4319/lo.1993.38.3.0657

J. Gonzalez and C. Suttle, Grazing by marine nanofiagellates on viruses and virus-sized particles: ingestion and digestion, Marine Ecology Progress Series, vol.94, pp.1-10, 1993.
DOI : 10.3354/meps094001

Y. Bettarel, T. Sime-ngando, M. Bouvy, R. Arfi, and C. Amblard, Low consumption of virus-sized particles by heterotrophic nanoflagellates in two lakes of the French Massif Central, Aquatic Microbial Ecology, vol.39, pp.205-209, 2005.
DOI : 10.3354/ame039205
URL : https://hal.archives-ouvertes.fr/hal-00527473

E. Sherr, Direct use of high molecular weight polysaccharide by heterotrophic flagellates, Nature, vol.335, issue.6188, pp.348-351, 1988.
DOI : 10.1038/335348a0

L. Tranvik, E. Sherr, and B. Sherr, Uptake and utilization of 'colloidal DOM' by heterotrophic flagellates in seawater, Marine Ecology Progress Series, vol.92, pp.301-309, 1992.
DOI : 10.3354/meps092301

D. Patterson, The Current Status of the Free-Living Heterotrophic Flagellates, The Journal of Eukaryotic Microbiology, vol.40, issue.5, pp.606-609, 1993.
DOI : 10.1016/S0959-437X(05)80192-3

J. Carrias, C. Quiblier-lloberas, and G. Bourdier, Seasonal dynamics of free and attached heterotrophic nanoflagellates in an oligomesotrophic lake, Freshwater Biology, vol.35, issue.1, pp.91-101, 1998.
DOI : 10.1046/j.1365-2427.1998.00263.x

B. Auer and H. Arndt, Taxonomic composition and biomass of heterotrophic flagellates in relation to lake trophy and season, Freshwater Biology, vol.53, issue.7, pp.959-972, 2001.
DOI : 10.1046/j.1365-2427.1998.00263.x

E. Cleven and T. Weisse, Seasonal succession and taxon-specific bacterial grazing rates of heterotrophic nanoflagellates in Lake Constance, Aquatic Microbial Ecology, vol.23, pp.147-161, 2001.
DOI : 10.3354/ame023147

I. Domaizon, S. Viboud, and D. Fontvieille, Taxon-specific and seasonal variations in flagellates grazing on heterotrophic bacteria in the oligotrophic Lake Annecy ?????? importance of mixotrophy, FEMS Microbiology Ecology, vol.46, issue.3, pp.317-329, 2003.
DOI : 10.1016/S0168-6496(03)00248-4

J. Comte, S. Jacquet, S. Viboud, D. Fontvieille, and A. Millery, Microbial Community Structure and Dynamics in the Largest Natural French Lake (Lake Bourget), Microbial Ecology, vol.31, issue.1, pp.72-89, 2006.
DOI : 10.1007/s00248-004-0230-4

B. Sonntag, T. Posch, S. Klammer, K. Teubner, and R. Psenner, Phagotrophic ciliates and flagellates in an oligotrophic, deep, alpine lake: contrasting variability with seasons and depths, Aquatic Microbial Ecology, vol.43, pp.193-207, 2006.
DOI : 10.3354/ame043193

C. Wieltschnig, A. Kirschner, A. Steitz, and B. Velimirov, Weak coupling between heterotrophic nanoflagellates and becteria in a eutrophic freshwater environment, Microb Ecol, vol.42, pp.159-167, 2001.

B. Diez, C. Pedros-alio, and R. Massana, Study of Genetic Diversity of Eukaryotic Picoplankton in Different Oceanic Regions by Small-Subunit rRNA Gene Cloning and Sequencing, Applied and Environmental Microbiology, vol.67, issue.7, pp.2932-2941, 2001.
DOI : 10.1128/AEM.67.7.2932-2941.2001

P. Lopez-garcia, F. Rodriguez-valera, C. Pedro-alio, 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

S. Moon-van-der-staay, D. Wachter, R. Vaulot, and D. , Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity, Nature, vol.409, issue.6820, pp.607-610, 2001.
DOI : 10.1038/35054541

D. Moreira and P. Lopez-garcia, The molecular ecology of microbial eukaryotes unveils a hidden world, Trends in Microbiology, vol.10, issue.1, pp.31-38, 2002.
DOI : 10.1016/S0966-842X(01)02257-0

R. Massana, V. Balagué, and L. Guillou, Picoeukaryotic diversity in an oligotrophic coastal site studied by molecular and culturing approaches, FEMS Microbiology Ecology, vol.50, issue.3, pp.231-243, 2004.
DOI : 10.1016/j.femsec.2004.07.001

K. Romari and D. Vaulot, Composition and temporal variability of picoeukaryote communities at a coastal site of the English Channel from 18S rDNA sequences, Limnology and Oceanography, vol.49, issue.3, pp.784-798, 2004.
DOI : 10.4319/lo.2004.49.3.0784

F. Not, R. Gausling, F. Azam, J. Heidelberg, and A. Worden, Vertical distribution of picoeukaryotic diversity in the Sargasso Sea, Environmental Microbiology, vol.43, issue.5, pp.1233-1252, 2007.
DOI : 10.1016/j.ejop.2005.06.001

E. Lefèvre, C. Bardot, C. Noël, J. Carrias, and E. Viscogliosi, Unveiling fungal zooflagellates as members of freshwater picoeukaryotes: evidence from a molecular diversity study in a deep meromictic lake, Environmental Microbiology, vol.49, issue.1, pp.61-71, 2007.
DOI : 10.1016/j.femsle.2004.09.030

J. Slapeta, D. Moreira, and P. Lopez-garcia, The extent of protist diversity: insights from molecular ecology of freshwater eukaryotes, Proceedings of the Royal Society B: Biological Sciences, vol.81, issue.1-4, pp.2073-2081, 2005.
DOI : 10.1023/A:1020547517255

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. 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

W. Lee and D. Patterson, Diversity and Geographic Distribution of Free-Living Heterotrophic Flagellates ??? Analysis by PRIMER, Protist, vol.149, issue.3, pp.229-244, 1998.
DOI : 10.1016/S1434-4610(98)70031-8

J. Hughes, J. Hellmann, T. Ricketts, and B. Bohannan, Counting the Uncountable: Statistical Approaches to Estimating Microbial Diversity, Applied and Environmental Microbiology, vol.67, issue.10, pp.4399-4406, 2001.
DOI : 10.1128/AEM.67.10.4399-4406.2001

M. Sleigh, Trophic strategies In The flagellates: Unity, diversity and evolution, pp.147-165, 2000.

B. Leander, O. Kuvardina, V. Aleshin, A. Mylnikov, and P. Keeling, Molecular Phylogeny and Surface Morphology of Colpodella edax (Alveolata): Insights into the Phagotrophic Ancestry of Apicomplexans, The Journal of Eukaryotic Microbiology, vol.6, issue.5, pp.334-340, 2003.
DOI : 10.1017/S0031182097001157

F. Gleason and G. Gordon, Anaerobic Growth and Fermentation in Blastocladia, Mycologia, vol.81, issue.5, pp.811-815, 1989.
DOI : 10.2307/3759889

V. Edgcomb, D. Kysela, A. Teske, V. De, A. Gomez et al., Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment, Proceedings of the National Academy of Sciences, vol.99, issue.11, pp.7658-7662, 2002.
DOI : 10.1073/pnas.062186399

S. Dawson and N. Pace, Novel kingdom-level eukaryotic diversity in anoxic environments, Proceedings of the National Academy of Sciences, vol.99, issue.12, pp.8324-8329, 2002.
DOI : 10.1073/pnas.062169599

K. Takishita, H. Miyake, M. Kawato, and T. Maruyama, Genetic diversity of microbial eukaryotes in anoxic sediment around fumaroles on a submarine caldera floor based on the small-subunit rDNA phylogeny, Extremophiles, vol.31, issue.3, pp.185-196, 2005.
DOI : 10.1007/s00792-005-0432-9

A. Zettler, L. Gomez, F. Zettler, E. Keenan, B. Amils et al., Microbiology: Eukaryotic diversity in Spain's River of Fire, Nature, vol.151, issue.6885, p.137, 2002.
DOI : 10.1038/417137a

E. Burreson, K. Reece, and C. Dungan, Molecular, Morphological, and Experimental Evidence Support the Synonymy of Perkinsus chesapeaki and Perkinsus andrewsi, Journal of Eukaryotic Microbiology, vol.14, issue.3, pp.258-270, 2005.
DOI : 10.1111/j.1550-7408.2005.05-00035.x

G. Brugerolle, Cryptophagus subtilis: a new parasite of cryptophytes affiliated with the Perkinsozoa lineage, European Journal of Protistology, vol.37, issue.4, pp.379-390, 2002.
DOI : 10.1078/0932-4739-00837

M. Park, S. Cooney, W. Yih, and D. Coats, Effects of two strains of the parasitic dinoflagellate Amoebophrya on growth, photosynthesis, light absorption, and quantum yield of bloom-forming dinoflagellates, Marine Ecology Progress Series, vol.227, pp.281-292, 2002.
DOI : 10.3354/meps227281

H. Arndt, D. Dietrich, B. Auer, E. Cleven, and T. Grä-fenhan, Functional diversity of heterotrophic flagellates in aquatic ecosystems In The flagellates: Unity, diversity and evolution, Leadbeater BSC, pp.240-268, 2000.

E. Sherr and B. Sherr, Heterotrophic dinoflagellates: a significant component of microzooplankton biomass and major grazers of diatoms in the sea, Marine Ecology Progress Series, vol.352, pp.187-197, 2008.
DOI : 10.3354/meps07161

P. Letcher, M. Powell, P. Churchill, and J. Chambers, Ultrastructural and molecular phylogenetic delineation of a new order, the Rhizophydiales (Chytridiomycota), Mycological Research, vol.110, issue.8, pp.898-915, 2006.
DOI : 10.1016/j.mycres.2006.06.011

T. James, D. Porter, C. Leander, R. Vilgalys, and J. Longcore, Molecular phylogenetics of the Chytridiomycota supports the utility of ultrastructural data in chytrid systematics, Can J Bot, vol.78, pp.336-350, 2000.

D. Bass and T. Cavalier-smith, Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa), INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.54, issue.6, pp.2393-2404, 2004.
DOI : 10.1099/ijs.0.63229-0

K. Shalchian-tabrizi, W. Eikrem, D. Klaveness, D. Vaulot, and M. Minge, Telonemia, a new protist phylum with affinity to chromist lineages, Proceedings of the Royal Society B: Biological Sciences, vol.99, issue.6, pp.1833-1842, 2006.
DOI : 10.1126/science.1071196

D. Klaveness, K. Shalchian-tabrizi, H. Thomsen, W. Eikrem, and K. Jakobsen, Telonema antarcticum sp. nov., a common marine phagotrophic flagellate, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.55, issue.6, 2005.
DOI : 10.1099/ijs.0.63652-0

J. Carrias, A. Thouvenot, C. Amblard, and T. Sime-ngando, Dynamics and growth estimates of planktonic protists during early spring in Lake Pavin, France, Aquatic Microbial Ecology, vol.24, pp.163-174, 2001.
DOI : 10.3354/ame024163
URL : https://hal.archives-ouvertes.fr/hal-00527673

P. Soudant, F. Chu, and E. Lund, , Using SYBRgreen-Propidium Iodide Double Staining and Flow Cytometry, Journal of Eukaryotic Microbiology, vol.52, issue.6, pp.492-499, 2005.
DOI : 10.1111/j.1550-7408.2005.00058.x

C. Dugan, K. Reece, J. Moss, R. Hamilton, and B. Diggles, Perkinsus olseni in vitro Isolates from the New Zealand Clam Austrovenus stutchburyi, The Journal of Eukaryotic Microbiology, vol.17, issue.3, pp.263-270, 2007.
DOI : 10.1093/nar/22.22.4673

C. Gestal, B. Novoa, D. Posada, A. Figueras, and C. Azevedo, Perkinsoide chabelardi n. gen., a protozoan parasite with an intermediate evolutionary position: possible cause of the decrease of sardine fisheries?, Environmental Microbiology, vol.87, issue.6, pp.1105-1114, 2006.
DOI : 10.1093/nar/25.24.4876

M. Park, W. Yih, and D. Coats, 132 Parasites and Phytoplankton, with a Special Emphasis on Dinoflagellate Infections, Journal of Phycology, vol.39, issue.s1, pp.145-155, 2004.
DOI : 10.1111/j.0022-3646.2003.03906001_132.x

D. Coats, E. Adam, C. Gallegos, and S. Hedrick, Parasitism of photosynthetic dinoflagellates in a shallow subestuary of Chesapeake Bay, USA, Aquatic Microbial Ecology, vol.11, pp.1-9, 1996.
DOI : 10.3354/ame011001

G. Brugerolle and J. Mignot, Observations sur le cycle, l'ultrastructure et la position systématique de Spiromonas perforans (Bodo perforans Hollande 1938), flagellé parasite de Chilomonas paramecium : ses relations avec les dinoflagellés et sporozoaires, Protistologica, vol.2, pp.183-196, 1979.

M. Siddall, K. Reece, T. Nerad, and E. Buresson, Molecular Determination of the Phylogenetic Position of a Species in the Genus Colpodella (Alveolata), American Museum Novitates, vol.3314, pp.1-10, 2001.
DOI : 10.1206/0003-0082(2001)314<0001:MDOTPP>2.0.CO;2

A. Alster and T. Zohary, Interactions between the bloom-forming dinoflagellate Peridinium gatunense and the chytrid fungus Phlyctochytrium sp., Hydrobiologia, vol.49, issue.1, pp.131-139, 2007.
DOI : 10.1007/s10750-006-0439-y

B. Ibelings, D. Bruin, A. Kagami, M. Rijkeboer, M. Brehm et al., ), Journal of Phycology, vol.6, issue.3, pp.437-453, 2004.
DOI : 10.1111/j.1529-8817.2004.03117.x

G. Hausner, A. Belkhiri, and G. Klassen, Phylogenetic analysis of the small subunit ribosomal RNA gene of the hyphochytrid <i>Rhizidiomyces apophysatus</i>, Canadian Journal of Botany, vol.78, issue.1, pp.124-128, 2000.
DOI : 10.1139/cjb-78-1-124

S. Nikolaev, C. Berney, J. Fahrni, A. Mylnikov, and V. Aleshin, Gymnophrys cometa and Lecythium sp. are core Cercozoa: Evolutionary implications, Acta Protozool, vol.42, pp.183-190, 2003.

A. Mil-'nikov and S. Karpov, Review of diversity and taxonomy of cercomonads, Protistology, vol.3, pp.201-217, 2004.

E. Schnepf and S. Kühn, Food uptake and fine structure of Cryothecomonas longipes sp. nov., a marine nanoflagellate incertae sedis feeding phagotrophically on large diatoms, Helgoland Marine Research, vol.54, issue.1, pp.18-32, 2000.
DOI : 10.1007/s101520050032

G. Debres, S. Kühn, A. Gmelch, and E. Schnepf, Cryothecomonas aestivalis sp. nov., a colourless nanoflagellate feeding on the marine centric diatom Guinardia delicatula (Cleve) Hasle, Helgol Mar Res, vol.50, pp.497-515, 1996.

K. Vickerman, L. Ray, D. Hoef-emden, K. , D. Jonckheere et al., The Soil Flagellate Proleptomonas faecicola: Cell Organisation and Phylogeny Suggest that the only Described Free-Living Trypanosomatid is not a Kinetoplastid but has Cercomonad Affinities, Protist, vol.153, issue.1, pp.9-24, 2002.
DOI : 10.1078/1434-4610-00079

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

A. Hagström, F. Azam, A. Andersson, J. Wikner, and F. Rassoulzadegan, Microbial loop in an oligotrophic pelagic marine ecosystem: possible roles of cyanobacteria and nanoflagellates in the organic fluxes, Marine Ecology Progress Series, vol.49, pp.171-178, 1988.
DOI : 10.3354/meps049171

L. Pomeroy and W. Wiebe, Energetics of microbial food webs, Hydrobiologia, vol.10, issue.1, pp.7-18, 1988.
DOI : 10.1007/BF00007363

E. Sherr and B. Sherr, Role of microbes in pelagic food webs: A revised concept, Limnology and Oceanography, vol.33, issue.5, pp.1225-1227, 1988.
DOI : 10.4319/lo.1988.33.5.1225

M. Kagami, E. Van-donk, A. De-bruin, M. Rijkeboer, and B. Ibelings, can protect diatoms from fungal parasitism, Limnology and Oceanography, vol.49, issue.3, pp.680-685, 2004.
DOI : 10.4319/lo.2004.49.3.0680

M. Kagami, D. Bruin, A. Ibelings, B. Van-donk, and E. , Parasitic chytrids: their effects on phytoplankton communities and food-web dynamics, Hydrobiologia, vol.13, issue.1, pp.113-129, 2007.
DOI : 10.1007/s10750-006-0438-z

M. Kagami, E. Von-alert, B. Ibelings, A. De-bruin, and E. Van-donk, The parasitic chytrid, Zygorhizidium, facilitates the growth of the cladoceran zooplankter, Daphnia, in cultures of the inedible alga, Asterionella, Proceedings of the Royal Society B: Biological Sciences, vol.270, issue.1520, pp.1561-1566, 2007.
DOI : 10.1098/rspb.2003.2357