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A multi-population study of the intestinal microbiota of wild fishes in the Mediterranean Sea: Focus on the impact of geographic origin, local habitat and host-related factors on bacterial community structure and potential functionality

par Lilli, Ginevra
Président du jury Danis, Bruno
Promoteur George, Isabelle
Co-Promoteur Flot, Jean-François
Publication Non publié, 2024-06-04

Thèse de doctorat

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Résumé :

The Mediterranean Sea is renowned for its heterogeneity of habitats and endemism, to the point that it is considered a miniature ocean and a hotspot of biodiversity. Since the last century, the human pressure in this basin has increased drastically with serious consequences to the different ecosystems and species occurring within it. The study of microbial communities, including those living freely and those associated with hosts, can provide support for monitoring and preserving ecosystem and organism health. The microbial communities associated with the intestinal mucosa of fishes are described to influence greatly host’s homeostasis and metabolism. Yet, limited information is available for wild fish species, and in the Mediterranean Sea only a handful of studies have explored this subject.We investigated the gut microbiota of wild Mediterranean demersal fishes to determine if its variability across the Mediterranean Sea is related to the habitat heterogeneity in this basin. Demersal fishes are a good model to evaluate this relationship since they strongly rely on the type of sea bottom during their life. Hence, we have selected multiple populations of four demersal species (Scorpaena notata, Scorpaena porcus, Scorpaena scrofa, Diplodus vulgaris) living across the Mediterranean Sea to address our question.The gut mucosa microbiota of fishes is described in the literature to be rather homogenous taxonomically, with host species being one of the factors predicting its taxonomic composition. Although we observed a significant influence of the host species on the taxonomical composition of the gut microbiota, we mostly highlighted a spatial variability of the taxonomical and functional features of the microbial communities at both small and large geographical scales. Furthermore, we relied on a single population of D. vulgaris to define the correlation between the features of the gut microbiota and those of the benthic substratum occurring in the home range of the fish. We observed a significant effect of the presence and abundance of Posidonia oceanica meadows in the fish home range on the taxonomical structure and diversity of its gut bacterial community.Nevertheless, although we observed significant differences in the gut mucosa microbiota across the Mediterranean Sea for the four species, certain bacterial taxa were consistently found in the majority of the specimens investigated, regardless of the geographic origin of the host. The analysis of the genome of one of those bacterial taxa (i.e. Aliivibrio) highlighted the presence of specific genomic features that allow it to colonize, survive and establish a mutualistic relationship with the host such as the ability to create biofilms, resist bile salts activity and degrade undigestible diet components (e.g. chitin).The perspectives of this research are twofold: first it will provide a methodology for future studies focused on analyzing the gut microbiota of wild fish species; second, by establishing microbiological baseline data for these four species, it will support future research aimed at monitoring their health and homeostasis in a changing Mediterranean Sea.