D. S. Mclusky, Marine and estuarine gradients -An overview, Netherlands Journal of Aquatic Ecology, vol.27, pp.489-493, 1993.

D. W. Pritchard, Estuarine classification -a help or a hindrance, Estuarine Circulation, pp.1-38, 1989.
DOI : 10.1007/978-1-4612-4562-9_1

J. M. Trigueros and E. Orive, Tidally driven distribution of phytoplankton blooms in a shallow, macrotidal estuary, J Plankton Res, vol.22, pp.969-986, 2000.

F. Azam, T. Fenchel, J. G. Field, J. S. Gray, and L. A. Meyer-reil, The ecological role of water-column microbes in the sea, Mar Ecol Prog Ser, vol.10, pp.257-263, 1983.

B. Díez, C. Pedrós-alió, and R. Massana, Study of genetic diversity of eukaryotic picoplankton in different oceanic regions by small-subunit rRNA gene cloning and sequencing, Appl Environ Microbiol, vol.67, pp.2932-2941, 2001.

S. Y. Moon-van-der-staay, D. Wachter, R. Vaulot, and D. , Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity, Nature, vol.409, pp.607-610, 2001.

V. P. Edgcomb, D. T. Kysela, A. Teske, D. Vera-gomez, A. Sogin et al., Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment, Proc Natl Acad Sci U S A, vol.99, pp.7658-7662, 2002.

R. Massana, V. Balagué, L. Guillou, and C. Pedrós-alió, Picoeukaryotic diversity in an oligotrophic coastal site studied by molecular and culturing approaches, FEMS Microbiol Ecol, vol.50, pp.231-243, 2004.

J. S-?-lapeta, D. Moreira, and P. López-garcía, The extent of protist diversity: insights from molecular ecology of freshwater eukaryotes, Proc Biol Sci/The Royal Society, vol.272, pp.2073-2081, 2005.

A. Behnke, K. J. Barger, J. Bunge, and T. Stoeck, Spatio-temporal variations in protistan communities along an O2/H2S gradient in the anoxic Framvaren Fjord (Norway), FEMS Microbiol Ecol, vol.72, pp.89-102, 2010.

D. Moreira and P. López-garcía, The molecular ecology of microbial eukaryotes unveils a hidden world, Trends Microbiol, vol.10, pp.31-38, 2002.

K. Muylaert, K. Sabbe, and W. Vyverman, Changes in phytoplankton diversity and community composition along the salinity gradient of the Schelde estuary, Estuar Coast Shelf Sci, vol.82, pp.335-340, 2009.

M. Lionard, K. Muylaert, A. Hanoutti, T. Maris, and M. Tackx, Interannual variability in phytoplankton summer blooms in the freshwater tidal reaches of the Schelde estuary (Belgium), Estuar Coast Shelf Sci, vol.79, pp.694-700, 2008.

P. Vigil, P. Countway, J. Rose, D. Lonsdale, and C. Gobler, Rapid shifts in dominant taxa among microbial eukaryotes in estuarine ecosystems, Aquat Microb Ecol, vol.54, pp.83-100, 2009.

L. Herfort, T. D. Peterson, L. Mccue, and P. Zuber, Protist 18S rRNA gene sequence analysis reveals multiple sources of organic matter contributing to turbidity maxima of the Columbia River estuary, Mar Ecol Prog Ser, vol.438, pp.19-31, 2011.

C. Klein, P. Claquin, V. Bouchart, L. Roy, B. Véron et al., Dynamics of Pseudonitzschia spp. and domoic acid production in a macrotidal ecosystem of the Eastern English Channel, Harmful Algae, vol.9, pp.218-226, 2010.

M. Ubertini, S. Lefebvre, A. Gangnery, K. Grangeré, L. Gendre et al., Spatial variability of benthic-pelagic coupling in an estuary ecosystem: consequences for microphytobenthos resuspension phenomenon, PloS ONE, vol.7, issue.8, p.44155, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00807556

F. Jouenne, S. Lefebvre, B. Véron, and Y. Lagadeuc, Phytoplankton community structure and primary production in small intertidal estuarine-bay ecosystem (eastern English Channel, France), Marine Biology, vol.151, pp.805-825, 2007.
DOI : 10.1007/s00227-006-0440-z

URL : https://hal.archives-ouvertes.fr/hal-00089992

F. Jouenne, S. Lefebvre, B. Véron, and Y. Lagadeuc, Biological and physicochemical factors controlling short-term variability in phytoplankton primary production and photosynthetic parameters in a macrotidal ecosystem (eastern English Channel), Estuar Coast Shelf Sci, vol.65, pp.421-439, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00014405

M. Desprez, J. Ducrotoy, and B. Sylvand, Fluctuations naturelles et e ´volution artificielle des biocenoses macrozoobenthiques intertidales de trois estuaires des côtes françaises de la Manche, vol.142, pp.249-270, 1986.
DOI : 10.1007/978-94-009-4049-9_22

A. Aminot and R. Kérouel, Dosage automatique des nutriments dans les eaux marines: méthodes en flux continu. Ifremer, vol.187, 2007.

N. Welschmeyer, Fluorometric analysis of chlorophyll chlorophyll b and pheopigments, Limnol Oceanogr, vol.39, pp.1985-1992, 1994.
DOI : 10.4319/lo.1994.39.8.1985

URL : https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.4319/lo.1994.39.8.1985

P. Bazin, F. Jouenne, A. F. Deton-cabanillas, A. Pérez-ruzafa, and B. Véron, Complex patterns in phytoplankton and microeukaryote diversity along the estuarine continuum, Hydrobiologia, vol.726, pp.155-178, 2014.
DOI : 10.1007/s10750-013-1761-9

P. Bourrelly, Les algues d'eau douce -Tome 1,2 et 3. Paris: Ed Boubée. 572, vol.606, p.577, 1981.

C. R. Tomas, Identifying Marine Phytoplankton, vol.858, 1997.

D. M. John, B. A. Whitton, and A. J. Brook, The Freshwater Algal Flora of the British Isles: An Identification Guide to Freshwater and Terrestrial Algae, vol.714, 2002.

H. Utermöhl-von, Neue Wege in der quantitativen Erfassung des Planktons, Mit besondere Beriicksichtigung des Ultrapanktons), vol.5, pp.567-595, 1931.

, Water quality -Guidance standard on the enumeration of phytoplankton using inverted microscopy (Utermöhl technique), vol.39, 2006.

J. Lund, C. Kipling, L. Cren, and E. D. , The Inverted Microscope method of estimating algal numbers and the statistical basis of estimations by counting, Hydrobiologia, vol.11, pp.143-170, 1958.

L. Medlin, H. J. Elwood, S. Stickel, and M. L. Sogin, The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions, Gene, vol.71, pp.491-499, 1988.

D. Hepperle and . Seqassem, A sequence analysis tool, contig assembler and trace data visualization for molecular sequences. Win32-Version. Distributed by the author, 2004.

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, J Mol Biol, vol.215, pp.403-410, 1990.

T. Huber, G. Faulkner, and P. Hugenholtz, Bellerophon: a program to detect chimeric sequences in multiple sequence alignments, Bioinformatics, vol.20, pp.2317-2319, 2004.

M. Viprey, L. Guillou, M. Ferréol, and D. Vaulot, Wide genetic diversity of picoplanktonic green algae (Chloroplastida) in the Mediterranean Sea uncovered by a phylum-biased PCR approach, Environ Microbiol, vol.10, pp.1804-1822, 2008.

K. Katoh, K. Kuma, H. Toh, and T. Miyata, MAFFT version 5: improvement in accuracy of multiple sequence alignment, Nucleic Acids Res, vol.33, pp.511-518, 2005.

P. D. Schloss, S. L. Westcott, T. Ryabin, J. R. Hall, and M. Hartmann, Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities, Appl Environ Microbiol, vol.75, pp.7537-7541, 2009.

K. Romari and D. Vaulot, Composition and temporal variability of picoeukaryote communities at a coastal site of the English Channel from 18S rDNA sequences, Limnol Oceanogr, vol.49, pp.784-798, 2004.

A. Chao, Non parametric estimation of the number of classes in a population, Scand J Statist, vol.11, pp.265-270, 1984.

Ø. Hammer, D. Harper, and P. D. Ryan, PAST: Paleontological statistics software package for education and data analysis, Paleontologia Electronica, vol.4, pp.1-9, 2001.

R. Massana, L. Guillou, B. Díez, and C. Pedro, Unveiling the organisms behind novel eukaryotic ribosomal DNA sequences from the Ocean, Appl Environ Microbiol, vol.68, pp.4554-4558, 2002.

R. Massana, J. Castresana, V. Balague, L. Guillou, and K. Romari, Phylogenetic and ecological analysis of Novel Marine Stramenopiles, Appl Environ Microbiol, vol.70, pp.3528-3534, 2004.

S. Charvet, W. F. Vincent, and C. Lovejoy, Chrysophytes and other protists in High Arctic lakes: molecular gene surveys, pigment signatures and microscopy, Polar Biol, vol.35, pp.733-748, 2011.

W. Luo, C. Bock, H. R. Li, J. Padisák, and L. Krienitz, Molecular and microscopic diversity of planktonic eukaryotes in the oligotrophic Lake Stechlin (Germany), Hydrobiologia, vol.661, pp.133-143, 2011.

K. Kolodziej and T. Stoeck, Cellular identification of a novel uncultured marine stramenopile (MAST-12 Clade) small-subunit rRNA gene sequence from a norwegian estuary by use of fluorescence in situ hybridization-scanning electron microscopy, Appl Environ Microbiol, vol.73, pp.2718-2726, 2007.

R. Massana, R. Terrado, I. Forn, C. Lovejoy, and C. Pedrós-alió, Distribution and abundance of uncultured heterotrophic flagellates in the world oceans, Environ Microbiol, vol.8, pp.1515-1522, 2006.

J. Del-campo and R. Massana, Emerging diversity within chrysophytes, choanoflagellates and bicosoecids based on molecular surveys, Protist, vol.162, pp.435-448, 2011.

R. A. Andersen, Y. Van-de-peer, D. Potter, J. P. Sexton, and M. Kawachi, Phylogenetic analysis of the SSU rRNA from members of the Chrysophyceae, Protist, vol.150, pp.71-84, 1999.

J. Boenigk, K. Pfandl, P. Stadler, and A. Chatzinotas, High diversity of the ''Spumella-like'' flagellates: an investigation based on the SSU rRNA gene sequences of isolates from habitats located in six different geographic regions, Environ Microbiol, vol.7, pp.685-697, 2005.

X. L. Shi, D. Marie, L. Jardillier, D. J. Scanlan, and D. Vaulot, Groups without cultured representatives dominate eukaryotic picophytoplankton in the oligotrophic South East Pacific Ocean, PloS ONE, vol.4, issue.10, p.7657, 2009.
DOI : 10.1371/journal.pone.0007657

URL : https://hal.archives-ouvertes.fr/hal-01254027

A. Zuendorf, J. Bunge, A. Behnke, K. J. Barger, and T. Stoeck, Diversity estimates of microeukaryotes below the chemocline of the anoxic Mariager Fjord, FEMS Microbiol Ecol, vol.58, pp.476-491, 2006.

T. R. Bachvaroff, S. Kim, L. Guillou, C. F. Delwiche, and D. W. Coats, Molecular diversity of the syndinean genus Euduboscquella based on single-cell PCR analysis, Appl Environ Microbiol, vol.78, pp.334-345, 2012.
DOI : 10.1128/aem.06678-11

URL : https://hal.archives-ouvertes.fr/hal-01254000

J. A. Deane, I. M. Strachan, G. W. Saunders, D. Hill, and G. I. Mcfadden, Cryptomonad evolution: nuclear 18S rDNA phylogeny versus cell morphology and pigmentation, J Phycol, vol.38, issue.6, pp.1236-1244, 2002.
DOI : 10.1046/j.1529-8817.2002.01250.x

F. Not, K. Valentin, K. Romari, C. Lovejoy, and R. Massana, Picobiliphytes: A marine picoplanktonic algal group with unknown affinities to other eukaryotes, Science, vol.315, pp.252-254, 2007.
DOI : 10.1126/science.1136264

S. Seoane, A. Laza, and E. Orive, Monitoring phytoplankton assemblages in estuarine waters: The application of pigment analysis and microscopy to sizefractionated samples, Estuar Coast Shelf Sci, vol.67, pp.343-354, 2006.

P. J. Harrison, K. Yin, J. Lee, J. Gan, and H. Liu, Physical-biological coupling in the Pearl River Estuary, Cont Shelf Res, vol.28, pp.1405-1415, 2008.
DOI : 10.1016/j.csr.2007.02.011

B. L. Clay and P. Kugrens, Characterization of Hemiselmis amylosa sp. nov. and phylogenetic placement of the blue-green Cryptomonads H. amylosa and Falcomonas daucoides, Protist, vol.150, pp.297-310, 1999.

M. C. Savin, J. L. Martin, M. Legresley, M. Giewat, and J. Rooney-varga, Plankton diversity in the Bay of Fundy as measured by morphological and molecular methods, Microb Ecol, vol.48, pp.51-65, 2004.

A. Laza-martínez, Urgorri complanatus gen. et sp. nov. (Cryptophyceae), a red-tide-forming species in brackish waters, J Phycol, vol.48, pp.423-435, 2012.

K. Shalchian-tabrizi, J. Bråte, R. Logares, D. Klaveness, and C. Berney, Diversification of unicellular eukaryotes: cryptomonad colonizations of marine and fresh waters inferred from revised 18S rRNA phylogeny, Environ Microbiol, vol.10, pp.2635-2644, 2008.

A. Alpine and J. Cloern, Phytoplankton growth rates in a light-limited environment, Mar Ecol Prog Ser, vol.44, pp.167-173, 1988.

C. Wylezich and K. Jürgens, Protist diversity in suboxic and sulfidic waters of the Black Sea, Environ Microbiol, vol.13, pp.2939-2956, 2011.

J. M. Trigueros and E. Orive, Tidally driven distribution of phytoplankton blooms in a shallow, macrotidal estuary, J Plankton Res, vol.22, pp.969-986, 2000.

E. L. Quinlan and E. J. Phlips, Phytoplankton assemblages across the marine to low-salinity transition zone in a blackwater dominated estuary, J Plankton Res, vol.29, pp.401-416, 2007.

D. A. Caron, P. D. Countway, and M. V. Brown, The growing contributions of molecular biology and immunology to protistan ecology: molecular signatures as ecological tools, J Eukaryot Microbiol, vol.51, pp.38-48, 2004.

J. S-?-lapeta, P. López-garcía, and D. Moreira, Global dispersal and ancient cryptic species in the smallest marine eukaryotes, Mol Biol Evol, vol.23, pp.23-29, 2006.

H. Liu, I. Probert, J. Uitz, H. Claustre, and S. Aris-brosou, Extreme diversity in noncalcifying haptophytes explains a major pigment paradox in open oceans, Proc Natl Acad Sci U S A, vol.106, pp.12803-12808, 2009.
URL : https://hal.archives-ouvertes.fr/hal-01258271

T. Stoeck, B. Hayward, G. T. Taylor, R. Varela, and S. S. Epstein, A multiple PCRprimer approach to access the microeukaryotic diversity in environmental samples, Protist, vol.157, pp.31-43, 2006.
DOI : 10.1016/j.protis.2005.10.004

F. Zhu, R. Massana, F. Not, D. Marie, and D. Vaulot, Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene, FEMS Microbiol Ecol, vol.52, pp.79-92, 2005.
URL : https://hal.archives-ouvertes.fr/hal-01651691

K. Muylaert, R. Van-mieghem, K. Sabbe, M. Tackx, and W. Vyverman, Dynamics and trophic roles of heterotrophic protists in the plankton of a freshwater tidal estuary, Hydrobiologia, vol.432, pp.25-36, 2000.

M. Potvin and C. Lovejoy, PCR-based diversity estimates of artificial and environmental 18S rRNA gene libraries, J Eukaryot Microbiol, vol.56, pp.174-181, 2009.

D. A. Caron, P. D. Countway, P. Savai, R. J. Gast, and A. Schnetzer, Defining DNA-based operational taxonomic units for microbial eukaryote ecology, Appl Environ Microbiol, vol.75, pp.5797-5808, 2009.
DOI : 10.1128/aem.00298-09

URL : https://aem.asm.org/content/75/18/5797.full.pdf