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

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.


Coral holobiont, Microbiota, Bacterial communities, Symbiodinium assemblages, Thermal adaptation, Scleractinian corals, Coral reefs, Pocillopora damicornis

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Table S1. Sample metadata including geographic and abiotic variables (temperature descriptors) as well as Pocillopora haplotype identification
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Figure S1. Maximum-likelihood tree of the mitochondrial ORF-defining Pocillopora types. Numbers are bootstraps (%) reflecting clade support.
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Table S2. Symbiodinium OTU table with sequence tag counts per sample and taxonomic affiliation
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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
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Table S3. Bacterial OTU table with sequence tag counts per sample and taxonomic affiliation.
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Table S4. Diversity indices calculated on bacterial diversity for each sample and statistical analyses of differences between regions
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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 ...
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Table S6. Variations in bacterial (16S rRNA gene) and Symbiodinium (ITS2) communities explained by the addition of significant variables for the reduced models identified using RDA and ...
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How to cite
Brener-Raffalli Kelly, Clerissi Camille, Vidal-Dupiol Jeremie, Adjeroud Mehdi, Bonhomme Francois, Pratlong Marine, Aurelle Didier, Mitta Guillaume, Toulza Eve (2018). Thermal regime and host clade, rather than geography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora damicornis sensu lato. Microbiome. 6 (39). 13p..,

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