Abstract
Oceans contain thousands of microbial species playing crucial roles for the functioning of the marine ecosystem. These microorganisms are present everywhere in the water column. Some microorganisms also colonize the surface and the digestive tract of marine macro-organisms, forming communities called microbiomes. These microbiomes have positive effects for their host’s fitness. The diversity of these marine animal surface microbiome is still largely understudied, despite recent progress in molecular biology that now permits to fully assess its different facets of biodiversity, i.e. taxonomic, phylogenetic and functional. The goal of this thesis is therefore to describe the diversity of the surface microbiome of marine animals, to assess its variability at different levels, as well as its determinants, and the significance of such diversity at the ecosystem’s scale. Firstly, I have assessed the efficiency of various diversity indices to detect ecological signals in the specific case of microbial communities. Secondly, I have described the surface microbiome of major marine animal clades (teleostean fishes, cetaceans and several classes of invertebrates). I found that these microbiomes are highly distinct from the surrounding planktonic communities. I demonstrated that these microbiomes are variable both between individuals from the same species and between species, but do not show a phylosymbiosis pattern. Last, I assessed the contribution of surface microbiomes to the global microbial community at the scale of a coral reef ecosystem. I demonstrated that marine animal surfaces host almost twenty times more microbial species than the water column, and 75% of the phylogenetic richness present in the ecosystem. In a context of massive erosion of marine macroscopic organisms, it is therefore urgent to exhaustively assess marine microbial biodiversity and its vulnerability facing anthropic pressures.