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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.; Le microbiome entérique est aujourd’hui considéré comme un organe à part entière pour son rôle bénéfique apporté à l’hôte. Bien que les poissons représentent le plus vieux et diversifié groupe de vertébrés sur Terre, son microbiome entérique et les fonctions associées restent peu documentés en comparaison de leurs pairs terrestres. Ceci est d'autant plus vrai concernant les > 6 000 espèces coralliennes de plus en plus menacées par le changement climatique et les activités humaines. Cette thèse vise à caractériser et à quantifier la biodiversité microbienne intestinale des poissons coralliens pour identifier ses déterminants afin de mieux comprendre (i) comment les poissons et leurs symbiotes ont co-évolué au cours de leur histoire mutuelle, et (ii) quelle est en retour l’influence de cette relation sur les flux de matière vers le milieu marin.Dans un premier temps, nous avons pu démontrer que les archées, et principalement les méthanogènes, sont en présence de trace dans le microbiome entérique des poissons marins, suggérant une contribution négligeable dans les émissions de méthane. Cette absence semble être liée à l’abondance de bactéries sulfato-réductrices, plus compétitives dans l’utilisation d’un substrat commun (e.g. l’acétate). Nous intéressant aux mécanismes expliquant l'assemblage du bactériome intestinal des poissons au cours de leur évolution, nos résultats apportent la première preuve d'un modèle cohérent de phylosymbiose chez les poissons coralliens et soulignent l'effet combiné de la phylogénie de l'hôte et du régime alimentaire. Bien que jouant un rôle moins influent, le régime alimentaire structure les compositions bactériennes et leurs fonctions associées, avec une richesse et une variabilité du bactériome corrélée à la position trophique de l’hôte. Enfin, nous avons pu démontrer que la transition d’une couverture corallienne à une domination macroalgale dans les récifs influence les compositions entériques bactériennes des poissons, notamment des herbivores, avec une augmentation significative de bactéries et de métabolismes fermenteurs. Compte tenu de l’érosion croissante des systèmes coralliens, inventorier la biodiversité microbienne récifale et comprendre sa vulnérabilité face au changement climatique et aux pressions anthropiques est une problématique de conservation urgente pour le maintien des processus écologiques dans les systèmes coralliens.

Replacement of coral by macroalgae in post-disturbance reefs, also called a “coral-macroalgal regime shift”, is increasing in response to climate-driven ocean warming. Such ecosystem change is known to impact planktonic and benthic reef microbial communities but few studies have examined the effect on animal microbiota. In order to understand the consequence of coral-macroalgal shifts on the coral reef fish enteric bacteriome, we used a metabarcoding approach to examine the gut bacteriomes of 99 individual fish representing 36 species collected on reefs of the Inner Seychelles islands that, following bleaching, had either recovered to coral domination, or shifted to macroalgae. While the coral-macroalgal shift did not influence the diversity, richness or variability of fish gut bacteriomes, we observed a significant effect on the composition (R2 = 0.02, p = 0.001), especially in herbivorous fishes (R2 = 0.07, p = 0.001). This change is accompanied by a significant increase in the proportion of fermentative bacteria (Rikenella, Akkermensia, Desulfovibrio, Brachyspira) and associated metabolisms (carbohydrates metabolism, DNA replication, and nitrogen metabolism) in relation to the strong turnover of Scarinae and Siganidae fishes. Predominance of fermentative metabolisms in fish found on macroalgal dominated reefs indicates that regime shifts not only affect the taxonomic composition of fish bacteriomes, but also have the potential to affect ecosystem functioning through microbial functions.

Environmental DNA (eDNA) analysis is a revolutionary method to monitor marine biodiversity from animal DNA traces. Examining the capacity of eDNA to provide accurate biodiversity measures in species‐rich ecosystems such as coral reefs is a prerequisite for their application in long‐term monitoring. Here, we surveyed two Colombian tropical marine reefs, the island of Providencia and Gayraca Bay near Santa Marta, using eDNA and underwater visual census (UVC) methods. We collected a large quantity of surface water (30 L per filter) above the reefs and applied a metabarcoding protocol using three different primer sets targeting the 12S mitochondrial DNA, which are specific to the vertebrates Actinopterygii and Elasmobranchii. By assigning eDNA sequences to species using a public reference database, we detected the presence of 107 and 85 fish species, 106 and 92 genera, and 73 and 57 families in Providencia and Gayraca Bay, respectively. Of the species identified using eDNA, 32.7% (Providencia) and 18.8% (Gayraca) were also found in the UVCs. We further found congruence in genus and species richness and abundance between eDNA and UVC approaches in Providencia but not in Gayraca Bay. Mismatches between eDNA and UVC had a phylogenetic and ecological signal, with eDNA detecting a broader phylogenetic diversity and more effectively detecting smaller species, pelagic species and those in deeper habitats. Altogether, eDNA can be used for fast and broad biodiversity surveys and is applicable to species‐rich ecosystems in the tropics, but improved coverage of the reference database is required before this new method could serve as an effective complement to traditional census methods., Environmental DNA, 3 (1), ISSN:2637-4943