M. Adjeroud, A. Guérécheau, J. Vidal-dupiol, J. Flot, S. Arnaud-haond et al., Genetic diversity, clonality and connectivity in the scleractinian coral Pocillopora damicornis: a multi-scale analysis in an insular, fragmented reef system, Mar. Biol, vol.161, pp.531-541, 2014.
URL : https://hal.archives-ouvertes.fr/halsde-01007685

T. D. Ainsworth, A. J. Fordyce, and E. F. Camp, The other microeukaryotes of the coral reef microbiome, Trends Microbiol, vol.25, pp.980-991, 2017.

T. D. Ainsworth, L. Krause, T. Bridge, G. Torda, J. Raina et al., The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts, ISME J, vol.9, pp.2261-2274, 2015.

A. S. Amend, D. J. Barshis, and T. A. Oliver, Coral-associated marine fungi form novel lineages and heterogeneous assemblages, ISME J, vol.6, pp.1291-1301, 2012.

C. Arif, C. Daniels, T. Bayer, E. Banguera-hinestroza, A. Barbrook et al., Assessing Symbiodinium diversity in scleractinian corals via nextgeneration sequencing-based genotyping of the ITS2 rDNA region, Mol. Ecol, vol.23, pp.4418-4433, 2014.

T. Bayer, M. J. Neave, A. Alsheikh-hussain, M. Aranda, L. K. Yum et al., The microbiome of the Red Sea coral Stylophora pistillata is dominated by tissue-associated Endozoicomonas bacteria, Appl. Environ. Microbiol, vol.79, pp.4759-4762, 2013.

H. M. Bik, W. Sung, P. De-ley, J. G. Baldwin, J. Sharma et al., Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments, Mol. Ecol, vol.21, pp.1048-1059, 2012.

M. Bo, A. Baker, E. Gaino, H. Wirshing, F. Scoccia et al., First description of algal mutualistic endosymbiosis in a black coral (Anthozoa: Antipatharia), Mar. Ecol. Prog. Ser, vol.435, pp.1-11, 2011.

K. Brener-raffalli, C. Clerissi, J. Vidal-dupiol, M. Adjeroud, F. Bonhomme et al., Thermal regime and host clade, rather than geography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora damicornis sensu lato, vol.6, p.39, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01729372

M. A. Coffroth and S. R. Santos, Genetic diversity of symbiotic dinoflagellates in the genus Symbiodinium, Protist, vol.156, pp.19-34, 2005.

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.

R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, vol.32, pp.1792-1797, 2004.

F. Escudié, L. Auer, M. Bernard, M. Mariadassou, L. Cauquil et al., FROGS: find, rapidly, OTUs with galaxy solution, Bioinformatics, vol.34, pp.1287-1294, 2017.

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, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01253994

M. Harel, E. Ben-dov, D. Rasoulouniriana, N. Siboni, E. Kramarsky-winter et al., A new Thraustochytrid, strain Fng1, isolated from the surface mucus of the hermatypic coral Fungia granulosa, FEMS Microbiol. Ecol, vol.64, pp.378-387, 2008.

D. S. Hibbett, After the gold rush, or before the flood? Evolutionary morphology of mushroom-forming fungi (Agaricomycetes) in the early 21st century, Mycol. Res, vol.111, pp.1001-1018, 2007.

R. A. Hutagalung, A. E. Sukoco, D. Soedharma, L. M. Goreti, I. Andrean et al., Isolation, identification and growth optimization of microalgae derived from soft coral Dendronephthya sp, APCBEE Proc, vol.10, pp.305-310, 2014.

J. Janou?kovec, A. Horák, K. L. Barott, F. L. Rohwer, and P. J. Keeling, Global analysis of plastid diversity reveals apicomplexan-related lineages in coral reefs, Curr. Biol, vol.22, pp.518-519, 2012.

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.3059-3066, 2002.

N. L. Kirk, D. J. Thornhill, D. W. Kemp, W. K. Fitt, and S. R. Santos, Ubiquitous associations and a peak fall prevalence between apicomplexan symbionts and reef corals in Florida and the Bahamas, Coral Reefs, vol.32, pp.847-858, 2013.

E. Kramarsky-winter, M. Harel, N. Siboni, E. B. Dov, I. Brickner et al., Identification of a protist-coral association and its possible ecological role, Mar. Ecol. Prog. Ser, vol.317, pp.67-73, 2006.

T. C. Lajeunesse, Investigating the biodiversity, ecology, and phylogeny of endosymbiotic dinoflagellates in the genus Symbiodinium using the ITS region: in search of a "species" level marker, J. Phycol, vol.37, pp.866-880, 2001.

T. C. Lajeunesse, Diversity and community structure of symbiotic dinoflagellates from Caribbean coral reefs, Mar. Biol, vol.141, 2002.

T. C. Lajeunesse, D. T. Pettay, E. M. Sampayo, N. Phongsuwan, B. Brown et al., Long-standing environmental conditions, geographic isolation and host-symbiont specificity influence the relative ecological dominance and genetic diversification of coral endosymbionts in the genus Symbiodinium, J. Biogeogr, vol.37, pp.785-800, 2010.

L. Campion-alsumard, T. Golubic, S. Hutchings, and P. , Microbial endoliths in skeletons of live and dead corals: Porites lobata, vol.117, pp.149-157, 1995.

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.

T. Magoc and S. L. Salzberg, FLASH: fast length adjustment of short reads to improve genome assemblies, Bioinformatics, vol.27, pp.2957-2963, 2011.

F. Mahé, T. Rognes, C. Quince, C. De-vargas, and M. Dunthorn, Swarm v2: highly-scalable and high-resolution amplicon clustering, PeerJ, vol.3, p.1420, 2015.

N. Mantel, The detection of disease clustering and a generalized regression approach, Cancer Res, vol.27, p.209, 1967.

M. Martin, Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet J, vol.17, p.10, 2011.

J. M. Mcdevitt-irwin, J. K. Baum, M. Garren, and R. L. Vega-thurber, Responses of coral-associated bacterial communities to local and global stressors, Front. Mar. Sci, vol.4, p.262, 2017.

P. J. Mcmurdie and S. Holmes, phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data, PLoS One, vol.8, p.61217, 2013.

B. Q. Minh, M. A. Nguyen, and A. Haeseler, Ultrafast approximation for phylogenetic bootstrap, Mol. Biol. Evol, vol.30, pp.1188-1195, 2013.

A. R. Mohamed, V. R. Cumbo, S. Harii, C. Shinzato, C. X. Chan et al., Deciphering the nature of the coral-Chromera association, ISME J, vol.12, pp.776-790, 2018.

R. B. Moore, M. Oborník, J. Janou?kovec, T. Chrudimský, M. Vancová et al., A photosynthetic alveolate closely related to apicomplexan parasites, Nature, vol.451, pp.959-963, 2008.

M. J. Neave, A. Apprill, C. Ferrier-pagès, and C. R. Voolstra, Diversity and function of prevalent symbiotic marine bacteria in the genus Endozoicomonas, 2016.

, Appl. Microbiol. Biotechnol, vol.100, pp.8315-8324

M. J. Neave, R. Rachmawati, L. Xun, C. T. Michell, D. G. Bourne et al., Differential specificity between closely related corals and abundant Endozoicomonas endosymbionts across global scales, ISME J, vol.11, pp.186-200, 2017.

L. Nguyen, H. A. Schmidt, A. Von-haeseler, M. , and B. Q. , IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies, Mol. Biol. Evol, vol.32, pp.268-274, 2015.

R. S. Peixoto, P. M. Rosado, D. C. Leite, A. S. Rosado, and D. G. Bourne, Beneficial microorganisms for corals (BMC): proposed mechanisms for coral health and resilience, Front. Microbiol, vol.8, p.341, 2017.

D. Pica, A. Tribollet, S. Golubic, M. Bo, C. G. Di-camillo et al., Microboring organisms in living stylasterid corals (Cnidaria. Hydrozoa), Mar. Biol. Res, vol.12, pp.573-582, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01497841

X. Pochon, J. I. Montoya-burgos, B. Stadelmann, and J. Pawlowski, Molecular phylogeny, evolutionary rates, and divergence timing of the symbiotic dinoflagellate genus Symbiodinium, Mol. Phylogenet. Evol, vol.38, pp.20-30, 2006.

M. N. Price, P. S. Dehal, and A. P. Arkin, FastTree 2-approximately maximum-likelihood trees for large alignments, PLoS One, vol.5, p.9490, 2010.

H. M. Putnam, M. Stat, X. Pochon, and R. D. Gates, Endosymbiotic flexibility associates with environmental sensitivity in scleractinian corals, Proc. R. Soc. B Biol. Sci, vol.279, pp.4352-4361, 2012.

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

K. M. Quigley, S. W. Davies, C. D. Kenkel, B. L. Willis, M. V. Matz et al., Deep-sequencing method for quantifying background abundances of Symbiodinium types: exploring the rare Symbiodinium biosphere in reefbuilding corals, vol.9, p.94297, 2014.

. R-core-team, R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing, 2018.

A. Ramette and P. L. Buttigieg, The R package otu2ot for implementing the entropy decomposition of nucleotide variation in sequence data, Front. Microbiol, vol.5, p.601, 2014.

K. B. Ritchie, Regulation of microbial populations by coral surface mucus and mucus-associated bacteria, Mar. Ecol. Prog. Ser, vol.322, pp.1-14, 2006.

M. Rodriguez-lanetty, S. Chang, and J. Song, Specificity of two temperate dinoflagellate-anthozoan associations from the north-western Pacific Ocean, Mar. Biol, vol.143, pp.1193-1199, 2003.

T. Rognes, T. Flouri, B. Nichols, C. Quince, and F. Mahé, VSEARCH: a versatile open source tool for metagenomics, PeerJ, vol.4, p.2584, 2016.

F. Rohwer, V. Seguritan, F. Azam, and N. Knowlton, Diversity and distribution of coral-associated bacteria, Mar. Ecol. Prog. Ser, vol.243, pp.1-10, 2002.

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

J. Schrével, A. Valigurová, G. Prensier, A. Chambouvet, I. Florent et al., Ultrastructure of Selenidium pendula, the type species of archigregarines, and phylogenetic relations to other marine Apicomplexa, Protist, vol.167, pp.339-368, 2016.

M. Shnit-orland and A. Kushmaro, Coral mucus-associated bacteria: a possible first line of defense, FEMS Microbiol. Ecol, vol.67, pp.371-380, 2009.

N. Siboni, D. Rasoulouniriana, E. Ben-dov, E. Kramarsky-winter, A. Sivan et al., Stramenopile microorganisms associated with the massive coral Favia sp, J. Eukaryot. Microbiol, vol.57, pp.236-244, 2010.

R. Silverstein, A. Correa, T. Lajeunesse, and A. Baker, Novel algal symbiont (Symbiodinium spp.) diversity in reef corals of Western Australia, Mar. Ecol. Prog. Ser, vol.422, pp.63-75, 2011.

J. ?lapeta and M. C. Linares, Combined amplicon pyrosequencing assays reveal presence of the Apicomplexan "type-N" (cf. Gemmocystis cylindrus) and Chromera velia on the great Barrier Reef, Australia. PLoS One, vol.8, p.76095, 2013.

T. Stoeck, D. Bass, M. Nebel, R. Christen, M. D. 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

L. Su, Q. Zhang, and J. Gong, Development and evaluation of specific PCR primers targeting the ribosomal DNA-internal transcribed spacer (ITS) region of peritrich ciliates in environmental samples, Chin. J. Oceanol. Limnol, vol.36, pp.818-826, 2017.

M. Sweet and J. Bythell, Ciliate and bacterial communities associated with White syndrome and brown band disease in reef-building corals, Environ. Microbiol, vol.14, pp.2184-2199, 2012.

M. J. Sweet, J. Craggs, J. Robson, and J. C. Bythell, Assessment of the microbial communities associated with white syndrome and brown jelly syndrome in aquarium corals, J. Zoo Aquar. Res, vol.1, pp.20-27, 2013.

M. J. Sweet and M. G. Séré, Ciliate communities consistently associated with coral diseases, J. Sea Res, vol.113, pp.119-131, 2016.

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.

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

T. F. Thingstad, R. G. Bellerby, G. Bratbak, K. Y. Børsheim, J. K. Egge et al., Counterintuitive carbon-to-nutrient coupling in an Arctic pelagic ecosystem, Nature, vol.455, pp.387-390, 2008.

D. J. Thornhill, E. J. Howells, D. C. Wham, T. D. Steury, and S. R. Santos, Population genetics of reef coral endosymbionts (Symbiodinium, Dinophyceae), Mol. Ecol, vol.26, pp.2640-2659, 2017.

R. V. Thurber, J. P. Payet, A. R. Thurber, and A. M. Correa, Virus-host interactions and their roles in coral reef health and disease, Nat. Rev. Microbiol, vol.15, pp.205-2016, 2017.

W. Toller, R. Rowan, and N. Knowlton, Genetic evidence for a protozoan (phylum Apicomplexa) associated with corals of the Montastraea annularis species complex, Coral Reefs, vol.21, pp.143-146, 2002.

L. Tonk, P. Bongaerts, E. M. Sampayo, and O. Hoegh-guldberg, SymbioGBR: a web-based database of Symbiodinium associated with cnidarian hosts on the Great Barrier Reef, BMC Ecol, vol.13, p.7, 2013.

M. Tragin, . Lopes, A. Santos, R. Christen, and D. Vaulot, Diversity and ecology of green microalgae in marine systems: an overview based on 18S rRNA gene sequences, Perspect. Phycol, vol.3, pp.141-154, 2016.

A. Tribollet, Dissolution of dead corals by euendolithic microorganisms across the Northern Great Barrier Reef (Australia), Microb. Ecol, vol.55, pp.569-580, 2008.

A. Tribollet, The boring microflora in modern coral reef ecosystems: a review of its roles, Current Developments in Bioerosion Erlangen Earth Conference Series, pp.67-94, 2008.

A. Tribollet and C. Payri, Bioerosion of the coralline alga hydrolithon onkodes by microborers in the coral reefs of Moorea, French polynesia, Oceanol. Acta, vol.24, pp.329-342, 2001.

S. J. Upton and E. C. Peters, A new and unusual species of coccidium (Apicomplexa: Agamococcidiorida) from Caribbean scleractinian corals, J. Invertebr. Pathol, vol.47, pp.184-193, 1986.

M. J. Van-oppen, J. C. Mieog, C. A. Sanchez, and K. E. Fabricius, Diversity of algal endosymbionts (zooxanthellae) in octocorals: the roles of geography and host relationships, Mol. Ecol, vol.14, pp.2403-2417, 2005.

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. 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.

L. Wegley, R. Edwards, B. Rodriguez-brito, H. Liu, and F. Rohwer, Metagenomic analysis of the microbial community associated with the coral Porites astreoides, Environ. Microbiol, vol.9, pp.2707-2719, 2007.

L. Wegley, Y. Yu, M. Breitbart, V. Casas, D. I. Kline et al., , 2004.

, Mar. Ecol. Prog. Ser, vol.273, pp.89-96

L. C. Wicks, E. Sampayo, J. P. Gardner, and S. K. Davy, Local endemicity and high diversity characterise high-latitude coral-Symbiodinium partnerships, Coral Reefs, vol.29, pp.989-1003, 2010.

B. Winnepenninckx, T. Backeljau, and R. Wachter, Extraction of high molecular weight DNA from molluscs, Trends Genet, vol.9, issue.93, p.90102, 1993.

J. Wuyts, P. De-rijk, Y. Van-de-peer, G. Pison, P. Rousseeuw et al., Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA, Nucleic Acids Res, vol.28, pp.4698-4708, 2000.

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.183-185, 2002.

P. Yilmaz, L. W. Parfrey, P. Yarza, J. Gerken, E. Pruesse et al., , 2014.

S. The, All-species Living Tree Project (LTP)" taxonomic frameworks, Nucleic Acids Res, vol.42, pp.643-648

M. Ziegler, F. O. Seneca, L. K. Yum, S. R. Palumbi, and C. R. Voolstra, Bacterial community dynamics are linked to patterns of coral heat tolerance, Nat. Commun, vol.8, p.14213, 2017.