Dynamique de l’holobionte corallien et plasticité transcriptomique : variabilité interindividuelle, interpopulationnelle et interspécifique

In the context of global warming, coral reefs are experiencing thermal stresses which are becoming more frequent and intense. In order to get a better understanding of the mechanisms of coral thermo­tolerance, I developed an integrative approach on the coral holobiont (meta­ organism composed of the coral host, its symbiotic algae and microbiota). For this, I performed an ecologically realistic thermal stress experiment on a coral species, Pocillopora damicornis. This species is widespread in the Indo­Pacific area. I compared the response of two populations whose thermotolerance is different since they are subjected to contrasting thermal regimes. I analyzed, for each of them, the response of the coral host (by RNAseq), as well as the structure and changes in the algal and bacterial microbiota (by metabarcoding). The results show that,while the structure of the microbiota is not influenced by stress, coral responds very differently depending on the population studied. The population from a more fluctuating environment displays a more effective and more plastic response, probably thanks to the involvement of epigenetic mechanisms. Another study carried out on different populations of P. damicornisshowed that the composition of the microbiota is influenced by the host genome and the thermal regime. One of the clades of the symbiotic algae, known to improve the heat­tolerance of the coral host, appears more sensitive to low temperatures than the others.Dans le contexte du réchauffement climatique, les récifs coralliens subissent des stress thermiques de plus en plus fréquents et intenses. Dans le but de mieux comprendre les mécanismes de la thermo­tolérance des coraux, j’ai développé une approche intégrative sur l’holobionte corallien (méta­organisme composé de l’hôte corallien, son algue symbiotique etson microbiote). Pour cela, j’ai réalisé une expérience de stress thermique écologiquement réaliste sur une espèce de corail, Pocillopora damicornis. Cette espèce étant présente dans l’ensemble de l’Indo­Pacifique, j’ai pu comparer la réponse de deux populations dont la thermotolérance est différente puisqu’elles sont soumises à des régimes thermiques contrastés. J’ai analysé, pour chacune d’entre­elles, la réponse de l’hôte corallien (par RNAseq), ainsi que la structure et les changements au niveau des microbiotes algaux et bactériens (par métabarcoding). Les résultats obtenus montrent qu’alors que la structure du microbiote n’est pas influencée par le stress, le corail y répond de façon très différente selon la population étudiée. La population issue d’un environnement plus fluctuant met en place une réponse plus efficace et plus plastique, probablement grâce à l’intervention de mécanismes épigénétiques. Une autre étude réalisée sur différentes populations de P. damicornis dans le cadre de cette thèse montre que la composition du microbiote est influencée par le génome de l’hôte ainsi que par le régime thermique. Un des clades de l’algue symbiotique connu pour améliorer la thermo­ tolérance de l’hôte corallien semble plus sensible aux basses températures que les autres

Dynamics of the coral holobionte and transcriptomic plasticity : variability inter individual, inter populational and interspecific

Dans le contexte du réchauffement climatique, les récifs coralliens subissent des stress thermiques de plus en plus fréquents et intenses. Dans le but de mieux comprendre les mécanismes de la thermo­tolérance des coraux, j’ai développé une approche intégrative sur l’holobionte corallien (méta­organisme composé de l’hôte corallien, son algue symbiotique etson microbiote). Pour cela, j’ai réalisé une expérience de stress thermique écologiquement réaliste sur une espèce de corail, Pocillopora damicornis. Cette espèce étant présente dans l’ensemble de l’Indo­Pacifique, j’ai pu comparer la réponse de deux populations dont la thermotolérance est différente puisqu’elles sont soumises à des régimes thermiques contrastés. J’ai analysé, pour chacune d’entre­elles, la réponse de l’hôte corallien (par RNAseq), ainsi que la structure et les changements au niveau des microbiotes algaux et bactériens (par métabarcoding). Les résultats obtenus montrent qu’alors que la structure du microbiote n’est pas influencée par le stress, le corail y répond de façon très différente selon la population étudiée. La population issue d’un environnement plus fluctuant met en place une réponse plus efficace et plus plastique, probablement grâce à l’intervention de mécanismes épigénétiques. Une autre étude réalisée sur différentes populations de P. damicornis dans le cadre de cette thèse montre que la composition du microbiote est influencée par le génome de l’hôte ainsi que par le régime thermique. Un des clades de l’algue symbiotique connu pour améliorer la thermo­ tolérance de l’hôte corallien semble plus sensible aux basses températures que les autres.In the context of global warming, coral reefs are experiencing thermal stresses which are becoming more frequent and intense. In order to get a better understanding of the mechanisms of coral thermo­tolerance, I developed an integrative approach on the coral holobiont (meta­ organism composed of the coral host, its symbiotic algae and microbiota). For this, I performed an ecologically realistic thermal stress experiment on a coral species, Pocillopora damicornis. This species is widespread in the Indo­Pacific area. I compared the response of two populations whose thermotolerance is different since they are subjected to contrasting thermal regimes. I analyzed, for each of them, the response of the coral host (by RNAseq), as well as the structure and changes in the algal and bacterial microbiota (by metabarcoding). The results show that,while the structure of the microbiota is not influenced by stress, coral responds very differently depending on the population studied. The population from a more fluctuating environment displays a more effective and more plastic response, probably thanks to the involvement of epigenetic mechanisms. Another study carried out on different populations of P. damicornisshowed that the composition of the microbiota is influenced by the host genome and the thermal regime. One of the clades of the symbiotic algae, known to improve the heat­tolerance of the coral host, appears more sensitive to low temperatures than the others

The tropical coral Pocillopora acuta displays an unusual chromatin structure and shows histone H3 clipping plasticity upon bleaching

Background: Pocillopora acuta is a hermatypic coral with strong ecological importance. Anthropogenic disturbances and global warming are major threats that can induce coral bleaching, the disruption of the mutualistic symbiosis between the coral host and its endosymbiotic algae. Previous works have shown that somaclonal colonies display different levels of survival depending on the environmental conditions they previously faced. Epigenetic mechanisms are good candidates to explain this phenomenon. However, almost no work had been published on the P. acuta epigenome, especially on histone modifications. In this study, we aim at providing the first insight into chromatin structure of this species. Methods: We aligned the amino acid sequence of P. acuta core histones with histone sequences from various phyla. We developed a centri-filtration on sucrose gradient to separate chromatin from the host and the symbiont. The presence of histone H3 protein and specific histone modifications were then detected by western blot performed on histone extraction done from bleached and healthy corals. Finally, micrococcal nuclease (MNase) digestions were undertaken to study nucleosomal organization. Results: The centri-filtration enabled coral chromatin isolation with less than 2% of contamination by endosymbiont material. Histone sequences alignments with other species show that P. acuta displays on average ~90% of sequence similarities with mice and ~96% with other corals. H3 detection by western blot showed that H3 is clipped in healthy corals while it appeared to be intact in bleached corals. MNase treatment failed to provide the usual mononucleosomal digestion, a feature shared with some cnidarian, but not all; suggesting an unusual chromatin structure. Conclusions: These results provide a first insight into the chromatin, nucleosome and histone structure of P. acuta. The unusual patterns highlighted in this study and partly shared with other cnidarian will need to be further studied to better understand its role in corals

Thermal regime and host clade, rather than geography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora damicornis sensu lato

Abstract Background Although the term holobiont has been popularized in corals with the advent of the hologenome theory of evolution, the underlying concepts are still a matter of debate. Indeed, the relative contribution of host and environment and especially thermal regime in shaping the microbial communities should be examined carefully to evaluate the potential role of symbionts for holobiont adaptation in the context of global changes. We used the sessile, long-lived, symbiotic and environmentally sensitive reef-building coral Pocillopora damicornis to address these issues. Results We sampled Pocillopora damicornis colonies corresponding to two different mitochondrial lineages in different geographic areas displaying different thermal regimes: Djibouti, French Polynesia, New Caledonia, and Taiwan. The community composition of bacteria and the algal endosymbiont Symbiodinium were characterized using high-throughput sequencing of 16S rRNA gene and internal transcribed spacer, ITS2, respectively. Bacterial microbiota was very diverse with high prevalence of Endozoicomonas, Arcobacter, and Acinetobacter in all samples. While Symbiodinium sub-clade C1 was dominant in Taiwan and New Caledonia, D1 was dominant in Djibouti and French Polynesia. Moreover, we also identified a high background diversity (i.e., with proportions < 1%) of A1, C3, C15, and G Symbiodinum sub-clades. Using redundancy analyses, we found that the effect of geography was very low for both communities and that host genotypes and temperatures differently influenced Symbiodinium and bacterial microbiota. Indeed, while the constraint of host haplotype was higher than temperatures on bacterial composition, we showed for the first time a strong relationship between the composition of Symbiodinium communities and minimal sea surface temperatures. Conclusion Because Symbiodinium assemblages are more constrained by the thermal regime than bacterial communities, we propose that their contribution to adaptive capacities of the holobiont to temperature changes might be higher than the influence of bacterial microbiota. Moreover, the link between Symbiodinium community composition and minimal temperatures suggests low relative fitness of clade D at lower temperatures. This observation is particularly relevant in the context of climate change, since corals will face increasing temperatures as well as much frequent abnormal cold episodes in some areas of the world

Additional file 7: of Thermal regime and host clade, rather than geography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora damicornis sensu lato

Table S5. Number of bacterial sequences and positive samples for each region at the family and genus levels. Taxa shared by at least 50% of samples in one population are colored in light gray, whereas taxa shared by at least 50% of the overall samples are colored in dark gray. We considered as core microbiota the taxa shared by 50% of samples for each of the four populations (regions) studied. (XLSX 128 kb

Additional file 6: of Thermal regime and host clade, rather than geography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora damicornis sensu lato

Table S4. Diversity indices calculated on bacterial diversity for each sample and statistical analyses of differences between regions. (XLSX 136 kb

Additional file 4: of Thermal regime and host clade, rather than geography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora damicornis sensu lato

Figure S2. Maximum-likelihood tree of the 53 Symbiodinium OTUs based on ITS2, together with GenBank representatives of each identified clade. Numbers are bootstraps (%) reflecting clade support. (PPTX 438 kb

Additional file 3: of Thermal regime and host clade, rather than geography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora damicornis sensu lato

Table S2. Symbiodinium OTU table with sequence tag counts per sample and taxonomic affiliation (XLSX 62 kb

Additional file 2 of Thermal regime and host clade, rather than geography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora damicornis sensu lato

Figure S1. Maximum-likelihood tree of the mitochondrial ORF-defining Pocillopora types. Numbers are bootstraps (%) reflecting clade support. (PPTX 307 kb