J. Jackson, M. K. Donovan, K. L. Cramer, and V. V. Lam, Status and Trends of Caribbean Coral Reefs, Global Coral Reef Monitoring Network, pp.1970-2012, 2014.

J. F. Bruno and E. Selig, Regional Decline of Coral Cover in the Indo-Pacific: Timing, Extent, and Subregional Comparisons, PLoS ONE, vol.360, issue.8, p.711, 2007.
DOI : 10.1371/journal.pone.0000711.s010

C. Wilkinson, Status of Coral Reefs of the World: 2008 (Global Coral Reef Monitoring Network and Reef and Rainforest Research Centre, 2008.

J. F. Bruno, Thermal Stress and Coral Cover as Drivers of Coral Disease Outbreaks, PLoS Biology, vol.3, issue.6, pp.1220-1227, 2007.
DOI : 10.1371/journal.pbio.0050124.t003

C. M. Eakin, Caribbean Corals in Crisis: Record Thermal Stress, Bleaching, and Mortality in 2005, PLoS ONE, vol.6, issue.12, p.13969, 2010.
DOI : 10.1371/journal.pone.0013969.s005

M. M. Littler, D. S. Littler, and B. L. Brooks, Herbivory, nutrients, stochastic events, and relative dominances of benthic indicator groups on coral reefs: a review and recommendations, Smithsonian Contributions to the Marine Sciences, vol.38, issue.38, pp.401-414, 2009.
DOI : 10.5479/si.01960768.38.401

J. E. Smith, C. L. Hunter, and C. M. Smith, The effects of top???down versus bottom???up control on benthic coral reef community structure, Oecologia, vol.51, issue.2, pp.497-507, 2010.
DOI : 10.1007/s00442-009-1546-z

D. E. Burkepile and M. E. Hay, HERBIVORE VS. NUTRIENT CONTROL OF MARINE PRIMARY PRODUCERS: CONTEXT-DEPENDENT EFFECTS, Ecology, vol.87, issue.12, pp.3128-3139, 2006.
DOI : 10.1890/0012-9658(2006)87[3128:HVNCOM]2.0.CO;2

T. P. Hughes, Phase Shifts, Herbivory, and the Resilience of Coral Reefs to Climate Change, Current Biology, vol.17, issue.4, pp.360-365, 2007.
DOI : 10.1016/j.cub.2006.12.049

C. L. Birrell, L. J. Mccook, B. L. Willis, and G. A. Diaz-pulido, Effects Of Benthic Algae On The Replenishment Of Corals And The Implications For The Resilience Of Coral Reefs, Oceanogr. Mar. Biol. Annu. Rev, vol.46, pp.25-63, 2008.
DOI : 10.1201/9781420065756.ch2

N. A. Graham, S. Jennings, M. A. Macneil, D. Mouillot, and S. K. Wilson, Predicting climate-driven regime shifts versus rebound potential in coral reefs, Nature, vol.9, issue.7537, pp.94-97, 2015.
DOI : 10.1038/nature14140

O. Hoegh-guldberg, Coral Reefs Under Rapid Climate Change and Ocean Acidification, Science, vol.318, issue.5857, pp.1737-1742, 2007.
DOI : 10.1126/science.1152509

M. P. Lesser, C. H. Mazel, M. Y. Gorbunov, and P. G. Falkowski, Discovery of Symbiotic Nitrogen-Fixing Cyanobacteria in Corals, Science, vol.305, issue.5686, pp.997-1000, 2004.
DOI : 10.1126/science.1099128

K. B. Ritchie, Regulation of microbial populations by coral surface mucus and mucus-associated bacteria, Marine Ecology Progress Series, vol.322, pp.1-14, 2006.
DOI : 10.3354/meps322001

J. Maynard, Projections of climate conditions that increase coral disease susceptibility and pathogen abundance and virulence, Nature Climate Change, vol.224, issue.7, pp.688-694, 2015.
DOI : 10.1007/s00338-009-0502-z
URL : https://hal.archives-ouvertes.fr/hal-01162335

J. Tout, Increased seawater temperature increases the abundance and alters the structure of natural Vibrio populations associated with the coral Pocillopora damicornis, Frontiers in Microbiology, vol.5, issue.e67745, p.432, 2015.
DOI : 10.1007/BF02919216

J. Smith, Indirect effects of algae on coral: algae-mediated, microbe-induced coral mortality, Ecology Letters, vol.268, issue.7, pp.835-845, 2006.
DOI : 10.1007/BF00354620

M. J. Vermeij, J. E. Smith, C. M. Smith, R. Vega-thurber, and S. A. Sandin, Survival and settlement success of coral planulae: independent and synergistic effects of macroalgae and microbes, Oecologia, vol.206, issue.2, pp.325-336, 2009.
DOI : 10.1007/s00442-008-1223-7

R. Vega-thurber, Macroalgae Decrease Growth and Alter Microbial Community Structure of the Reef-Building Coral, Porites astreoides, PLoS ONE, vol.7, issue.9, p.44246, 2012.
DOI : 10.1371/journal.pone.0044246.s006

K. Morrow, V. Paul, M. Liles, and N. Chadwick, Allelochemicals produced by Caribbean macroalgae and cyanobacteria have species-specific effects on reef coral microorganisms, Coral Reefs, vol.32, issue.2, pp.309-320, 2011.
DOI : 10.1007/s00338-011-0747-1

C. Jessen, In-situ Effects of Eutrophication and Overfishing on Physiology and Bacterial Diversity of the Red Sea Coral Acropora hemprichii, PLoS ONE, vol.56, issue.1, p.62091, 2013.
DOI : 10.1371/journal.pone.0062091.s005

F. Rohwer, M. Breitbart, J. Jara, F. Azam, and N. Knowlton, Diversity of bacteria associated with the Caribbean coral Montastraea franksi, Coral Reefs, vol.20, pp.85-91, 2001.

J. Frias-lopez, A. L. Zerkle, G. T. Bonheyo, and B. W. Fouke, Partitioning of Bacterial Communities between Seawater and Healthy, Black Band Diseased, and Dead Coral Surfaces, Applied and Environmental Microbiology, vol.68, issue.5, pp.2214-2228, 2002.
DOI : 10.1128/AEM.68.5.2214-2228.2002

R. V. Thurber, Metagenomic analysis of stressed coral holobionts, Environmental Microbiology, vol.69, issue.8, pp.2148-2163, 2009.
DOI : 10.1111/j.1462-2920.2009.01935.x

J. Mao-jones, K. B. Ritchie, L. E. Jones, and S. P. Ellner, How Microbial Community Composition Regulates Coral Disease Development, PLoS Biology, vol.21, issue.3, p.1000345, 2010.
DOI : 10.1371/journal.pbio.1000345.s005

D. I. Kline, N. M. Kuntz, M. Breitbart, N. Knowlton, and F. Rohwer, Role of elevated organic carbon levels and microbial activity in coral mortality, Marine Ecology Progress Series, vol.314, pp.119-125, 2006.
DOI : 10.3354/meps314119

F. Rohwer, M. Youle, and D. Vosten, Coral Reefs In The Microbial Seas, 2010.

A. F. Haas, Effects of Coral Reef Benthic Primary Producers on Dissolved Organic Carbon and Microbial Activity, PLoS ONE, vol.247, issue.11, p.27973, 2011.
DOI : 10.1371/journal.pone.0027973.s003

A. Gregg, Biological oxygen demand optode analysis of coral reef-associated microbial communities exposed to algal exudates, PeerJ, vol.71, issue.2, p.107, 2013.
DOI : 10.7717/peerj.107/supp-2

K. Barott, Hyperspectral and Physiological Analyses of Coral-Algal Interactions, PLoS ONE, vol.4, issue.11, p.8043, 2009.
DOI : 10.1371/journal.pone.0008043.s002

D. Wangpraseurt, In Situ Oxygen Dynamics in Coral-Algal Interactions, situ oxygen dynamics in coral-algal interactions, p.31192, 2012.
DOI : 10.1371/journal.pone.0031192.s001
URL : https://hal.archives-ouvertes.fr/hal-00722760

N. M. Kuntz, D. I. Kline, S. A. Sandin, and F. Rohwer, Pathologies and mortality rates caused by organic carbon and nutrient stressors in three Caribbean coral species, Marine Ecology Progress Series, vol.294, pp.173-180, 2005.
DOI : 10.3354/meps294173

M. M. Nugues, G. W. Smith, R. J. Hooidonk, M. I. Seabra, and R. P. Bak, Algal contact as a trigger for coral disease, Ecology Letters, vol.2, issue.10, pp.919-923, 2004.
DOI : 10.1111/j.1461-0248.2004.00651.x

M. Garren, A bacterial pathogen uses dimethylsulfoniopropionate as a cue to target heat-stressed corals, The ISME Journal, vol.46, issue.5, pp.999-1007, 2014.
DOI : 10.1046/j.1462-2920.2001.00196.x

N. E. Kimes, Temperature regulation of virulence factors in the pathogen Vibrio coralliilyticus, The ISME Journal, vol.8, issue.4, pp.835-846, 2012.
DOI : 10.1038/ismej.2011.154

J. Vidal-dupiol, Thermal Stress Triggers Broad Pocillopora damicornis Transcriptomic Remodeling, while Vibrio coralliilyticus Infection Induces a More Targeted Immuno-Suppression Response, PLoS ONE, vol.10, issue.1, p.107672, 2014.
DOI : 10.1371/journal.pone.0107672.s004
URL : https://hal.archives-ouvertes.fr/hal-01134257

K. L. Rypien, J. R. Ward, and F. Azam, Antagonistic interactions among coral-associated bacteria, Environmental Microbiology, vol.173, issue.1, pp.28-39, 2010.
DOI : 10.1111/j.1462-2920.2009.02027.x

S. J. Box and P. J. Mumby, Effect of macroalgal competition on growth and survival of juvenile Caribbean corals, Marine Ecology Progress Series, vol.342, pp.139-149, 2007.
DOI : 10.3354/meps342139

D. B. Rasher and M. E. Hay, Chemically rich seaweeds poison corals when not controled by herbivores, Proc. Natl Acad. Sci. USA, pp.9683-9688, 2010.

M. G. Langille, Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences, Nature Biotechnology, vol.51, issue.9, pp.814-821, 2013.
DOI : 10.1093/nar/gkr1178

C. E. Nelson, Coral and macroalgal exudates vary in neutral sugar composition and differentially enrich reef bacterioplankton lineages, The ISME Journal, vol.174, issue.5, pp.962-979, 2013.
DOI : 10.3354/ab00269

A. H. Moeller, SIV-Induced Instability of the Chimpanzee Gut Microbiome, Cell Host & Microbe, vol.14, issue.3, pp.340-345, 2013.
DOI : 10.1016/j.chom.2013.08.005

R. H. Whittaker, Evolution and Measurement of Species Diversity, Taxon, vol.21, issue.2/3, pp.213-251, 1972.
DOI : 10.2307/1218190

C. Roder, C. Arif, C. Daniels, E. Weil, and C. R. Voolstra, Bacterial profiling of White Plague Disease across corals and oceans indicates a conserved and distinct disease microbiome, Molecular Ecology, vol.45, issue.4, pp.965-974, 2014.
DOI : 10.1111/mec.12638

E. P. Chassignet, The HYCOM (HYbrid Coordinate Ocean Model) data assimilative system, Journal of Marine Systems, vol.65, issue.1-4, pp.60-83, 2007.
DOI : 10.1016/j.jmarsys.2005.09.016

G. Liu, A. E. Strong, and W. Skirving, Remote sensing of sea surface temperatures during 2002 Barrier Reef coral bleaching, Eos, Transactions American Geophysical Union, vol.1, issue.15, pp.137-141, 2003.
DOI : 10.1029/2003EO150001

R. D. Rotjan and S. M. Lewis, Impact of coral predators on tropical reefs, Marine Ecology Progress Series, vol.367, pp.73-91, 2008.
DOI : 10.3354/meps07531

D. E. Burkepile, Context-dependent corallivory by parrotfishes in a Caribbean reef ecosystem, Coral Reefs, vol.301, issue.1, pp.111-120, 2012.
DOI : 10.1007/s00338-011-0824-5

L. J. Raymundo, A. R. Halford, A. P. Maypa, and A. M. Kerr, Functionally diverse reef-fish communities ameliorate coral disease, Proc. Natl Acad. Sci. USA, pp.17067-17070, 2009.
DOI : 10.1073/pnas.0900365106

P. J. Mumby, Herbivory versus corallivory: are parrotfish good or bad for Caribbean coral reefs?, Coral Reefs, vol.222, issue.3, pp.683-690, 2009.
DOI : 10.1007/s00338-009-0501-0

R. Vega-thurber, Chronic nutrient enrichment increases prevalence and severity of coral disease and bleaching, Global Change Biology, vol.85, issue.2, pp.544-554, 2014.
DOI : 10.1111/gcb.12450

E. S. Charlson, Disordered Microbial Communities in the Upper Respiratory Tract of Cigarette Smokers, PLoS ONE, vol.73, issue.12, p.15216, 2010.
DOI : 10.1371/journal.pone.0015216.s004

P. Nithyanand, S. Manju, and S. Karutha-pandian, Phylogenetic characterization of culturable actinomycetes associated with the mucus of the coral Acropora digitifera from Gulf of Mannar, FEMS Microbiology Letters, vol.314, issue.2, pp.112-118, 2011.
DOI : 10.1111/j.1574-6968.2010.02149.x

H. J. Edwards, How much time can herbivore protection buy for coral reefs under realistic regimes of hurricanes and coral bleaching?, Global Change Biology, vol.19, issue.6, pp.2033-2048, 2011.
DOI : 10.1111/j.1365-2486.2010.02366.x

K. Anthony, Ocean acidification and warming will lower coral reef resilience, Global Change Biology, vol.19, issue.5, pp.1798-1808, 2011.
DOI : 10.1111/j.1365-2486.2010.02364.x

R. R. Ruzicka, Temporal changes in benthic assemblages on Florida Keys reefs 11 years after the 1997/1998 El Ni??o, Marine Ecology Progress Series, vol.489, pp.125-141, 1997.
DOI : 10.3354/meps10427

D. Green, P. J. Edmunds, and R. C. Carpenter, Increasing relative abundance of Porites astreoides on Caribbean reefs mediated by an overall decline in coral cover, Marine Ecology Progress Series, vol.359, pp.1-10, 2008.
DOI : 10.3354/meps07454

J. Lokrantz, M. Nyström, M. Thyresson, and C. Johansson, The non-linear relationship between body size and function in parrotfishes, Coral Reefs, vol.222, issue.4, pp.967-974, 2008.
DOI : 10.1007/s00338-008-0394-3

P. J. Mumby, Fishing, Trophic Cascades, and the Process of Grazing on Coral Reefs, Science, vol.311, issue.5757, pp.98-101, 2006.
DOI : 10.1126/science.1121129

D. R. Bellwood, A. S. Hoey, and T. P. Hughes, Human activity selectively impacts the ecosystem roles of parrotfishes on coral reefs, Proceedings of the Royal Society B: Biological Sciences, vol.12, issue.4, p.20111906, 2011.
DOI : 10.1371/journal.pone.0005239

M. M. Littler, D. S. Littler, B. L. Brooks, and B. Lapointe, Nutrient manipulation methods for coral reef studies: A critical review and experimental field data, Journal of Experimental Marine Biology and Ecology, vol.336, issue.2, pp.242-253, 2006.
DOI : 10.1016/j.jembe.2006.05.014

J. W. Fourqurean and J. C. Zieman, Nutrient content of the seagrass Thalassia testudinum reveals regional patterns of relative availability of nitrogen and phosphorus in the Florida Keys USA, Biogeochemistry, vol.61, issue.3, pp.229-245, 2002.
DOI : 10.1023/A:1020293503405

J. Bohnsack and D. Harper, NOAA Technical Memorandum (NMFSSEFC-215, 1988.

J. G. Caporaso, QIIME allows analysis of high-throughput community sequencing data, Nature Methods, vol.8, issue.5, pp.335-336, 2010.
DOI : 10.1038/nmeth.f.303

D. Mcdonald, An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea, The ISME Journal, vol.180, issue.3, pp.610-618, 2012.
DOI : 10.1038/nature08656

C. A. Lozupone, M. Hamady, S. T. Kelley, and R. Knight, Quantitative and Qualitative ?? Diversity Measures Lead to Different Insights into Factors That Structure Microbial Communities, Applied and Environmental Microbiology, vol.73, issue.5, pp.1576-1585, 2007.
DOI : 10.1128/AEM.01996-06

J. R. Zaneveld and R. L. Thurber, Hidden state prediction: a modification of classic ancestral state reconstruction algorithms helps unravel complex symbioses, Frontiers in Microbiology, vol.38, issue.1203, p.431, 2014.
DOI : 10.1093/nar/gkq066