Microbiota associated with the skin, gills, and gut of the fish Parachondrostoma toxostoma from the Rhône basin

Abstract

1. The close relationships between hosts and their microbiota underlie the current concept of holobionts. This biological entity enlarges our perception of the genomic diversity supported by individuals/species and the potential abilities of hosts to respond to the environment.2. We investigated a total of 54 specimens of the sofie fish Parachrondrostoma toxostoma (Pt) for the taxonomic and functional composition of microbiota associated with the skin, gills, and gut tissues. Five wild populations from the Ardèche and Durance river basins in the Mediterranean part of the large catchment of the Rhône (southern France) were compared.3. We found that the skin microbiota was more diverse and variable in bacterial community composition than the gut microbiota. These differences suggest that different deterministic factors underlie the composition of these bacterial communities, resulting in tissue-specific variation of the microbiota composition between wild fish populations inhabiting two rivers. Microbiota diversity and composition differed between wild Pt populations at both regional and local spatial scales. 4. Using the Picrust tool, the taxonomic variation of the microbiota composition in the river fish populations could be associated with 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 Ardèche than of 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.5. This study opens perspectives in the detection of subtle shifts in environmental features through the description of the microbiota composition, and in the potential prediction of the functional capacities of species to acclimate. K E Y W O R D Sbacterial communities, cyprinid species, holobiont, mucosal tissues, predicted functional pathways | 447 GUIVIER Et al. S U PP O RTI N G I N FO R M ATI O NAdditional supporting information may be found online in the Supporting Information section.

Diversity and structure of sparids external microbiota (Teleostei) and its link with monogenean ectoparasites

“…Regarding diversity, gill mucus harbored a lower alpha diversity, compared to skin mucus and water bacterial communities. Other freshwater or seawater fish species display a similar trend, with a lower diversity in gill mucus compared to the skin mucus [ 15 , 64 , 88 ]. Moreover, we found that sparid skin and gill mucus are also highly species-specific, both in terms of diversity and composition, as previously reported in several other fish families such as Chaetodontidae, Serranidae, Labridae or Mullidae [ 23 , 24 , 64 , 82 , 89 ].…”

The gills and skin microbiota of five pelagic fish species from the Atlantic Ocean

“…gills that had increased total AA biosynthesis. Enrichment of AA metabolism in sh skin has been related to metabolic pathways involved in the activation of immune responses (Guivier et al 2020) and, thus, could of relevance to defence mechanisms against pathogens colonising the skin. The highest relative abundances of AA biosynthesis were observed for isoleucine, methionine, lysine, and arginine.…”

Shark Provisioning Influences the Gut Microbiota of the Black-Tip Reef Shark in French Polynesia

“…Indeed, gut microbiota play a central role in digestion and the health status of their host [8]. Studies on fish microbiota have increased these last years, showing that individual factors may affect the bacterial community, such as host sex [9] or development stage [10]. Environmental factors may also influence microbiota [11], and diet seems to be one of the major factors affecting its composition [9,[12][13][14][15][16].…”

“…Studies on fish microbiota have increased these last years, showing that individual factors may affect the bacterial community, such as host sex [9] or development stage [10]. Environmental factors may also influence microbiota [11], and diet seems to be one of the major factors affecting its composition [9,[12][13][14][15][16]. Indeed, Fishes 2022, 7, 312 2 of 14 several studies have shown that in rearing conditions, the intestinal microbiota is fooddependent, and this could be in terms of both alpha (i.e., within each sample) and beta diversity (i.e., between samples) [17,18].…”