V. Barbosa-solomieu, R. T. Travers, and M. , Mass mortality in bivalves and the intricate case of the Pacific oyster, Crassostrea gigas, J Invertebr Pathol, vol.131, pp.2-10, 2015.

F. Pernet, C. Lupo, C. Bacher, and R. J. Whittington, Infectious diseases in oyster aquaculture require a new integrated approach, Philos Trans R Soc B Biol Sci, vol.371, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01483233

B. Petton, M. Bruto, A. James, Y. Labreuche, M. Alunno-bruscia et al., Crassostrea gigas mortality in France: the usual suspect, a herpes virus, may not be the killer in this polymicrobial opportunistic disease, Front Microbiol, vol.6, p.686, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01216445

J. De-lorgeril, A. Lucasson, B. Petton, E. Toulza, C. Montagnani et al., Immune-suppression by OsHV-1 viral infection causes fatal bacteraemia in Pacific oysters, Nat Commun, vol.9, p.4215, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01898110

P. Azéma, J. Lamy, P. Boudry, R. T. Travers, M. Dégremont et al., Genetic parameters of resistance to Vibrio aestuarianus, and OsHV-1 infections in the Pacific oyster, Crassostrea gigas, at three different life stages, Genet Sel Evol, vol.49, p.23, 2017.

F. Desriac, L. Chevalier, P. Brillet, B. Leguerinel, I. Thuillier et al., Exploring the hologenome concept in marine bivalvia: haemolymph microbiota as a pertinent source of probiotics for aquaculture, FEMS Microbiol Lett, vol.350, pp.107-123, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00948603

C. D. Becker and G. B. Pauley, An ovarian parasite (Protista incertae sedis) from the Pacific oyster, Crassostrea gigas, J Invertebr Pathol, vol.12, pp.425-462, 1968.

M. Comps, M. S. Park, and I. Desportes, Fine structure of Marteilioides chungmuensis n.g., n.sp., parasite of the oocytes of the oyster Crassostrea gigas, Aquaculture, vol.67, pp.264-269, 1987.

J. M. Grijalva-chon, R. Castro-longoria, T. L. Enríquez-espinoza, A. N. Maeda-martínez, and F. Mendoza-cano, Molecular evidence of the protozoan parasite Marteilia refringens in Crassostrea gigas and Crassostrea corteziensis from the Gulf of California, Lat Am J Aquat Res, vol.43, pp.776-80, 2015.

L. Arzeta-pino, A. Acosta, M. E. Sarmiento, M. Rojas-contreras, C. Rodríguez-jaramillo et al., Herpes virus OsHV-1 and the protist Perkinsus marinus modify the expression of the Down syndrome cell adhesion molecule gene in gill and mantle of Crassostrea spp, Aquac Res, vol.49, pp.3638-3684, 2018.

K. Tun, N. Itoh, Y. Shimizu, H. Yamanoi, T. Yoshinaga et al., Pathogenicity of the protozoan parasite Marteilioides chungmuensis in the Pacific oyster Crassostrea gigas, Int J Parasitol, vol.38, pp.211-218, 2008.

F. Berthe, L. Roux, F. Adlard, R. D. Figueras, and A. , Marteiliosis in molluscs: a review, Aquat Living Resour, vol.17, pp.433-481, 2004.

F. Robledo, J. A. Vasta, G. R. Record, and N. R. , Protozoan parasites of bivalve molluscs: literature follows culture, PLoS One, vol.9, p.100872, 2014.

J. Castrec, P. Soudant, L. Payton, D. Tran, P. Miner et al., Bioactive extracellular compounds produced by the dinoflagellate Alexandrium minutum are highly detrimental for oysters, Aquat Toxicol, vol.199, pp.188-98, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02324608

D. M. Anderson, A. D. Cembella, and G. M. Hallegraeff, Progress in understanding harmful algal blooms: paradigm shifts and new technologies for research, monitoring, and management, Annu Rev Mar Sci, vol.4, pp.143-76, 2012.

C. Bower-sm, . Rb, J. Goh-b, L. Sr, M. Gj et al., Preferential PCR amplification of parasitic protistan small subunit rDNA from metazoan tissues, J Eukaryot Microbiol, vol.51, pp.325-357, 2004.

J. Del-campo, M. J. Pons, M. Herranz, K. C. Wakeman, J. Del-valle et al., Validation of a universal set of primers to study animal-associated microeukaryotic communities, Environ Microbiol, vol.21, pp.3855-3861, 2019.

H. Vestheim and S. N. Jarman, Blocking primers to enhance PCR amplification of rare sequences in mixed samples -a case study on prey DNA in Antarctic krill stomachs, Front Zool, vol.5, p.12, 2008.

M. Leray, N. Agudelo, S. C. Mills, and C. P. Meyer, Effectiveness of annealing blocking primers versus restriction enzymes for characterization of generalist diets: unexpected prey revealed in the gut contents of two coral reef fish species, PLoS One, vol.8, p.58076, 2013.

C. Clerissi, S. Brunet, J. Vidal-dupiol, M. Adjeroud, P. Lepage et al., Protists within corals: the hidden diversity, Front Microbiol, vol.9, p.2043, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01887637

S. Tan and H. Liu, Unravel the hidden protistan diversity: application of blocking primers to suppress PCR amplification of metazoan DNA, Appl Microbiol Biotechnol, vol.102, pp.389-401, 2018.

T. Stoeck, D. Bass, M. Nebel, R. Christen, M. Jones et al., Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water, Mol Ecol, vol.19, pp.21-31, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00497208

M. Tragin, A. Zingone, and D. Vaulot, Comparison of coastal phytoplankton composition estimated from the V4 and V9 regions of the 18S rRNA gene with a focus on photosynthetic groups and especially Chlorophyta, Environ Microbiol, vol.20, pp.506-526, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01628365

R. Massana, J. Del-campo, M. E. Sieracki, S. Audic, and R. Logares, Exploring the uncultured microeukaryote majority in the oceans: reevaluation of ribogroups within stramenopiles, ISME J, vol.8, pp.854-66, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01258217

S. K. Hu, Z. Liu, A. Lie, P. D. Countway, D. Y. Kim et al., Estimating protistan diversity using high-throughput sequencing, J Eukaryot Microbiol, vol.62, pp.688-93, 2015.

J. Decelle, S. Romac, E. Sasaki, F. Not, and F. Mahé, Intracellular diversity of the V4 and V9 regions of the 18S rRNA in marine protists (radiolarians) assessed by high-throughput sequencing, PLoS One, vol.9, p.104297, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01100668

C. R. Giner, I. Forn, S. Romac, R. Logares, C. De-vargas et al., Environmental sequencing provides reasonable estimates of the relative abundance of specific picoeukaryotes, Appl Environ Microbiol, vol.82, pp.4757-66, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01332059

R. Piredda, M. P. Tomasino, D. 'erchia, A. M. Manzari, C. Pesole et al., Diversity and temporal patterns of planktonic protist assemblages at a mediterranean long term ecological research site, FEMS Microbiol Ecol, vol.93, p.200, 2017.

T. Kamiyama, Microzooplankton as a food source for the Pacific oyster Crassostrea gigas: seasonal variation in gut contents and food availability, Fish Sci, vol.77, pp.961-74, 2011.

C. De-vargas, S. Audic, N. Henry, J. Decelle, F. Mahé et al., Eukaryotic plankton diversity in the sunlit ocean, Science, vol.348, p.1261605, 2015.

F. Not, M. Latasa, M. D. Cariou, T. Vaulot, D. Simon et al., A single species, Micromonas pusilla (Prasinophyceae), dominates the eukaryotic picoplankton in the western English Channel, Appl Environ Microbiol, vol.70, pp.4064-72, 2004.

K. R. Theis, N. M. Dheilly, J. L. Klassen, R. M. Brucker, J. F. Baines et al., Getting the hologenome concept right: an eco-evolutionary framework for hosts and their microbiomes, mSystems, vol.1, pp.28-44, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01483722

N. García-lagunas, . De-jesús-r-gr, and N. Y. Hernández-saavedra, Changes in gene expression and histological injuries as a result of exposure of Crassostrea gigas to the toxic dinoflagellate Gymnodinium catenatum, J Molluscan Stud, vol.82, pp.193-200, 2016.

C. Quast, E. Pruesse, P. Yilmaz, J. Gerken, T. Schweer et al., The SILVA ribosomal RNA gene database project: improved data processing and webbased tools, Nucleic Acids Res, vol.41, pp.590-596, 2013.

P. Yilmaz, L. W. Parfrey, P. Yarza, J. Gerken, E. Pruesse et al., The SILVA and "all-species living Tree project (LTP)" taxonomic frameworks, Nucleic Acids Res, vol.42, pp.643-651, 2014.

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 Res, vol.30, pp.3059-66, 2002.

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.403-413, 1990.

C. Clerissi, J. De-lorgeril, B. Petton, A. Lucasson, J. Escoubas et al., Microbiota composition and evenness predict survival rate of oysters confronted to Pacific oyster mortality syndrome, Front Microbiol, vol.11, p.311, 2020.
URL : https://hal.archives-ouvertes.fr/hal-02551728

J. Wuyts, Y. Van-de-peer, T. Winkelmans, D. Wachter, and R. , The European database on small subunit ribosomal RNA, Nucleic Acids Res, vol.30, pp.183-188, 2002.

F. Escudie, L. Auer, M. Bernard, L. Cauquil, K. Vidal et al., FROGS: find rapidly OTU with galaxy solution, The environmental genomics Conference, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01886442

L. Guillou, D. Bachar, S. Audic, D. Bass, C. Berney et al., The Protist ribosomal reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy, Nucleic Acids Res, vol.41, pp.597-604, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01253994

J. Castresana, Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis, Mol Biol Evol, vol.17, pp.540-52, 2000.

L. Nguyen, H. A. Schmidt, V. Haeseler, A. Minh, and B. Q. , IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies, Mol Biol Evol, vol.32, pp.268-74, 2015.

B. Q. Minh, M. Nguyen, V. Haeseler, and A. , Ultrafast approximation for phylogenetic bootstrap, Mol Biol Evol, vol.30, pp.1188-95, 2013.

, R: a language and environment for statistical computing. R development Core team, 2008.

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