A. Alberti, J. Poulain, S. Engelen, K. Labadie, S. Romac et al., Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition, Scientific Data, vol.531, 2017.
DOI : 10.1101/gr.5969107

URL : https://hal.archives-ouvertes.fr/hal-01771844

C. Arif, C. Daniels, T. Bayer, E. Banguera-hinestroza, A. Barbrook et al., diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region, Molecular Ecology, vol.10, issue.17, pp.4418-4433, 2014.
DOI : 10.1006/mpev.1998.0546

N. Boulotte, S. Dalton, A. Carroll, P. Harrison, H. Putnam et al., Exploring the Symbiodinium rare biosphere provides evidence for symbiont switching in reef-building corals, The ISME Journal, vol.530, issue.53, pp.2693-2701, 2016.
DOI : 10.1007/s00338-010-0649-7

D. Bourne, K. Morrow, and N. Webster, Insights into the Coral Microbiome: Underpinning the Health and Resilience of Reef Ecosystems, Annual Review of Microbiology, vol.70, issue.1, pp.317-340, 2016.
DOI : 10.1146/annurev-micro-102215-095440

A. Coleman, A. Suarez, and L. Goff, MOLECULAR DELINEATION OF SPECIES AND SYNGENS IN VOLVOCACEAN GREEN ALGAE (CHLOROPHYTA)1, Journal of Phycology, vol.30, issue.1, 1994.
DOI : 10.1111/j.0022-3646.1994.00080.x

R. Cunning, R. Gates, and P. Edmunds, communities within and between shores., PeerJ, vol.25, issue.9, pp.3472-3482, 2017.
DOI : 10.7717/peerj.3472/table-2

T. Hughes, M. Barnes, D. Bellwood, J. Cinner, G. Cumming et al., Coral reefs in the Anthropocene, Nature, vol.352, issue.7656, pp.82-90, 1038.
DOI : 10.1126/science.aac7125

B. Hume, Are specific coral-Symbiodinium partnerships associated with survival in extreme temperature environments of the Persian/Arabian Gulf?, 2013.

B. Hume, D. Angelo, C. Burt, J. Baker, A. Riegl et al., Corals from the Persian/Arabian Gulf as models for thermotolerant reef-builders: Prevalence of clade C3 Symbiodinium, host fluorescence and ex situ temperature tolerance, Marine Pollution Bulletin, vol.72, issue.2, pp.313-322, 2013.
DOI : 10.1016/j.marpolbul.2012.11.032

B. Hume, D. Angelo, C. Smith, E. Stevens, J. Burt et al., Symbiodinium thermophilum sp. nov., a thermotolerant symbiotic alga prevalent in corals of the world's hottest sea, the Persian/Arabian Gulf, Scientific Reports, vol.61, issue.1, pp.8562-8572, 2015.
DOI : 10.1093/sysbio/sys029

B. Hume, C. Voolstra, C. Arif, D. Angelo, C. Burt et al., Ancestral genetic diversity associated with the rapid spread of stress-tolerant coral symbionts in response to Holocene climate change, Proceedings of the National Academy of Sciences, vol.29, issue.2, pp.4416-4421, 2016.
DOI : 10.7717/peerj.394

D. Kemp, X. Hernandez-pech, R. Iglesias-prieto, W. Fitt, and G. Schmidt, spp. before, during, and after a coral bleaching event, Limnology and Oceanography, vol.59, issue.3, pp.788-797, 2014.
DOI : 10.4319/lo.2014.59.3.0788

T. 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, Journal of Phycology, vol.37, issue.5, 2001.
DOI : 10.1046/j.1529-8817.2001.01031.x

T. Lajeunesse, Diversity and community structure of symbiotic dinoflagellates from Caribbean coral reefs, Marine Biology, vol.141, issue.2, pp.387-400, 2002.

T. Lajeunesse, D. Wham, D. Pettay, J. Parkinson, S. Keshavmurthy et al., Ecologically differentiated stress-tolerant endosymbionts in the dinoflagellate genus Symbiodinium (Dinophyceae) Clade D are different species, Phycologia, vol.531, issue.4, pp.305-319, 2014.

R. Levin, C. Voolstra, K. Weynberg, and M. Van-oppen, Evidence for a role of viruses in the thermal sensitivity of coral photosymbionts, The ISME Journal, vol.164, issue.3, pp.808-812, 2017.
DOI : 10.1016/j.protis.2013.04.002

F. Moberg and C. Folke, Ecological goods and services of coral reef ecosystems, Ecological Economics, vol.29, issue.2, pp.215-233, 1999.
DOI : 10.1016/S0921-8009(99)00009-9

S. Mordret, S. Romac, N. Henry, C. S. Carmichael, M. Berney et al., The symbiotic life of Symbiodinium in the open ocean within a new species of calcifying ciliate (Tiarina sp.), The ISME Journal, vol.58, issue.6, pp.1424-1436, 2016.
DOI : 10.1111/j.1365-3040.2008.01802.x

URL : https://hal.archives-ouvertes.fr/hal-01258214

L. Muscatine, The role of symbiotic algae in carbon and energy flux in reef corals, Ecosystems of the World Coral Reefs, vol.25, pp.75-87, 1990.

M. Nitschke, S. Davy, and S. Ward, Horizontal transmission of Symbiodinium cells between adult and juvenile corals is aided by benthic sediment, Coral Reefs, vol.9, issue.1, pp.335-344, 2016.
DOI : 10.1371/journal.pone.0097003

A. Norstrom, M. Nystrom, J. Jouffray, C. Folke, N. Graham et al., Guiding coral reef futures in the Anthropocene, Frontiers in Ecology and the Environment, vol.38, issue.9, pp.490-498, 2016.
DOI : 10.1111/ecog.01353

J. Pandolfi, S. Connolly, D. Marshall, and A. Cohen, Projecting Coral Reef Futures Under Global Warming and Ocean Acidification, Science, vol.17, issue.3, pp.418-422, 2011.
DOI : 10.1890/06-2079.1

R. Peixoto, P. Rosado, D. Leite, A. Rosado, and D. Bourne, Beneficial Microorganisms for Corals (BMC): Proposed Mechanisms for Coral Health and Resilience, Frontiers in Microbiology, vol.32, issue.14213, 2017.
DOI : 10.1111/j.1574-6976.2008.00123.x

URL : http://journal.frontiersin.org/article/10.3389/fmicb.2017.00341/pdf

S. Pesant, F. Not, M. Picheral, S. Kandels-lewis, L. Bescot et al., Open science resources for the discovery and analysis of Tara Oceans data, Scientific Data, vol.2, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01253984

L. Plaisance, M. Caley, R. Brainard, and N. Knowlton, The Diversity of Coral Reefs: What Are We Missing?, PLoS ONE, vol.318, issue.10, 2011.
DOI : 10.1371/journal.pone.0025026.t002

URL : https://doi.org/10.1371/journal.pone.0025026

X. Pochon and R. Gates, A new Symbiodinium clade (Dinophyceae) from soritid foraminifera in Hawai???i, Molecular Phylogenetics and Evolution, vol.56, issue.1, pp.492-497, 2010.
DOI : 10.1016/j.ympev.2010.03.040

X. Pochon, J. Pawlowski, L. Zaninetti, and R. Rowan, High genetic diversity and relative specificity among Symbiodinium-like endosymbiotic dinoflagellates in soritid foraminiferans, Marine Biology, vol.139, issue.6, pp.1069-1078, 2001.

X. Pochon, H. Putnam, and R. Gates, dinoflagellates: a perspective on rarity, symbiosis, and evolution, PeerJ, vol.41, pp.394-404, 2014.
DOI : 10.7717/peerj.394/supp-2

URL : https://peerj.com/articles/394.pdf

X. Pochon, M. Stat, M. Takabayashi, L. Chasqui, L. Chauka et al., COMPARISON OF ENDOSYMBIOTIC AND FREE-LIVING SYMBIODINIUM (DINOPHYCEAE) DIVERSITY IN A HAWAIIAN REEF ENVIRONMENT1, Journal of Phycology, vol.298, issue.1, pp.53-65, 2010.
DOI : 10.4319/lo.2008.53.5.1853

. Hume, , 2018.

C. Pogoreutz, N. Radecker, A. Cardenas, A. Gardes, C. Voolstra et al., Sugar enrichment provides evidence for a role of nitrogen fixation in coral bleaching, Global Change Biology, vol.8, issue.2017, pp.3838-3848, 2017.
DOI : 10.1038/ncomms14213

N. Radecker, C. Pogoreutz, C. Voolstra, J. Wiedenmann, and C. Wild, Nitrogen cycling in corals: the key to understanding holobiont functioning?, Trends in Microbiology, vol.23, issue.8, pp.490-497, 2015.
DOI : 10.1016/j.tim.2015.03.008

R. Rowan, N. Knowlton, A. Baker, and J. Jara, Landscape ecology of algal symbionts creates variation in episodes of coral bleaching, Nature, vol.365, issue.6639, pp.265-269, 1997.
DOI : 10.1038/365836a0

P. Schloss, S. Westcott, T. Ryabin, J. Hall, M. Hartmann et al., 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, 1128.
DOI : 10.1128/AEM.01541-09

R. Silverstein, R. Cunning, and A. Baker, Change in algal symbiont communities after bleaching, not prior heat exposure, increases heat tolerance of reef corals, Global Change Biology, vol.96, issue.433, pp.236-249, 2015.
DOI : 10.1073/pnas.96.4.1463

E. Smith, R. Ketchum, and J. Burt, Host specificity of Symbiodinium variants revealed by an ITS2 metahaplotype approach, The ISME Journal, vol.11, issue.6, pp.1500-1503, 2017.
DOI : 10.1111/evo.12270

M. Stat, X. Pochon, R. Cowie, and R. Gates, Specificity in communities of Symbiodinium in corals from Johnston Atoll, Marine Ecology Progress Series, vol.386, pp.83-96, 2009.
DOI : 10.3354/meps08080

L. Thomas, G. Kendrick, W. Kennington, Z. Richards, and M. Stat, corals from geographical extremes of Western Australia with 454 amplicon pyrosequencing, Molecular Ecology, vol.51, issue.12, pp.3113-3126, 2014.
DOI : 10.1007/s002390010064

D. Thornhill, E. Howells, D. Wham, T. Steury, and S. Santos, , Dinophyceae), Molecular Ecology, vol.44, issue.10, pp.2640-2659, 2017.
DOI : 10.1111/jbi.12913

G. Torda, J. Donelson, M. Aranda, D. Barshis, L. Bay et al., Rapid adaptive responses to climate change in corals, Nature Climate Change, vol.18, issue.9, pp.627-636, 1038.
DOI : 10.1111/j.1365-2486.2011.02520.x

URL : https://hal.archives-ouvertes.fr/hal-01598493

D. Wham, G. Ning, and T. Lajeunesse, Symbiodinium glynnii sp. nov., a species of stresstolerant symbiotic dinoflagellates from pocilloporid and montiporid corals in the Pacific Ocean, Phycologia, vol.561, issue.4, pp.396-409, 2017.

M. Ziegler, C. Arif, J. Burt, S. Dobretsov, C. Roder et al., around the Arabian Peninsula, Journal of Biogeography, vol.533, issue.3, pp.674-686, 2017.
DOI : 10.3354/meps11365

M. Ziegler, V. Eguíluz, C. Duarte, and C. Voolstra, Rare symbionts may contribute to the resilience of coral???algal assemblages, The ISME Journal, vol.44, issue.1, pp.161-172, 2017.
DOI : 10.1111/jbi.12913

M. Ziegler, F. Seneca, L. Yum, S. Palumbi, and C. Voolstra, Bacterial community dynamics are linked to patterns of coral heat tolerance, Nature Communications, vol.31, pp.14213-14223, 1038.
DOI : 10.1038/nbt.2676

URL : http://www.nature.com/articles/ncomms14213.pdf