Abstract
Microbes residing in the intestinal tract of fish provide a range of essential functions for their host. Although fishes represent the most diverse and oldest group of vertebrates, our understanding of their gut microbiome and its functional significance is scarce in contrast to their terrestrial counterparts. This is particularly true for the >6 000 fish species living in coral reefs, whose status are severly threatened by climate change and human pressures. This thesis aims to characterise and quantify the microbial biodiversity associated to the gastro-intestinal tract of coral reef fish in order to identify its determinants to undersand (i) how fish and their microbes coevolved, and (ii) what is the influence of this interaction on material flows into marine environments.First, we demonstrated than archaea, of which methanogens, are in trace abundances in the gut microbiome of marine fishes, sugegsting their negligible contribution to methane emission. This abcense seems to be explained by the abundance of sulfato-reducting bacteria which competite for the utilization of common substrat (e.g. actetate). Investigating the mecanisms underlying the bacterial assembly associated to reef fish guts, our results showed for the first time a phylosymbiosis pattern in reef fish, supporting the combined effect of the host phylogeny and of the diet, which involves horizontal acquisition since first evolutionary steps of fish. Even if its influence is lower, the diet structures bacterial compositions and their associated functions, with a richness and a bacterial variability which correlates with the host trophic positions. Finally, we investigated the influence of an environmental shift in a post-disturbed reef and demonstrated that macroalgal dominance in reefs influenced the enteric bacterial composition of coral fishes, mainly in herbivores, with a significant increase in the proportion of fermentative bacteria and associated metabolisms. Because of the ongoing erosion of coral systems, assessing the marine microbial biodiversity and its vulnerability under climatic and anthropogenic pressures is an imperative issue for their conservation.