Microbiota associated with the skin, gills, and gut of the fish Parachondrostoma toxostoma from five sites in the Durance and Ardeche rivers

We used high throughput sequencing of 16S rRNA gene to investigate on a total of 54 specimens of the sofie fish Parachrontoma toxostoma (Pt) the composition, taxonomic and functional, of microbiota associated with the skin, gills and gut tissues of Parachondrostoma toxostoma species (Pt), within and between five wild populations from the Ardeche and Durance river basins in the Mediterranean part of the large watershed of the Rhône (Southern France). We found that the skin microbiota was more diverse and variable in bacterial composition than the gut microbiota. These differences suggest that different deterministic factors underlie the composition of these bacterial communities, resulting in tissue-specific phenotypic plasticity of the microbiota in response to the external environment. Microbiota diversity and composition differed between wild Pt populations at both regional and local spatial scales. The taxonomic variation of the microbiota in the river fish populations was associated using the Picrust molecular tool to the enrichment of predicted metabolic pathways. In particular, carbohydrate metabolism was more represented and xenobiotic biodegradation pathways less represented in the gut microbiota of Pt populations from the Ardeche than in those from the Durance. This result suggests variability in the ability to acclimate to environmental features through the assimilation of food resources from plants and the detoxification of xenobiotic components. Across the various spatial scales and tissues explored in wild populations, this study highlights new perspectives in biodiversity preservation combining our capacity to detect subtle shifts in abiotic and biotic environmental features with the potential of species to functionally respond and acclimate.