Host Species and Body Site Explain the Variation in the Microbiota Associated to Wild Sympatric Mediterranean Teleost Fishes

Abstract

Microorganisms are an important component shaping the evolution of hosts and as such, the study of bacterial communities with molecular techniques is shedding light on the complexity of symbioses between bacteria and vertebrates. Teleost fish are a heterogeneous group that live in a wide variety of habitats, and thus a good model group to investigate symbiotic interactions and their influence on host biology and ecology. Here we describe the microbiota of thirteen teleostean species sharing the same environment in the Mediterranean Sea, and compare bacterial communities among different species and body sites (external mucus, skin, gills and intestine). Our results show that Proteobacteria is the dominant phylum present in fish and water. However, the prevalence of other bacterial taxa differs between fish and the surrounding water. Significant differences in bacterial diversity are observed among fish species and body sites, with higher diversity found in the external mucus. No effect of sampling time nor species individual were found. The identification of indicator bacterial taxa further supports that each body site harbours its own characteristic bacterial community. These results improve current knowledge and understanding of symbiotic relationships among bacteria and their fish hosts in the wild, since the majority of previous studies focused on captive individuals.

Ecological Specialization Within a Carnivorous Fish Family Is Supported by a Herbivorous Microbiome Shaped by a Combination of Gut Traits and Specific Diet

“…(Sullam et al, 2012;Egerton et al, 2018), i.e., a dominance of Proteobacteria, Bacteroidetes, and Firmicutes, with these three phyla representing more than 84% of the sequences. Our results also confirm that the genus Vibrio, albeit dominant on the mucus, skin and gills of teleost (Chiarello et al, 2018;Ruiz-Rodríguez et al, 2020), represents only a small proportion of their gut microbiome. Regarding Sparidae' microbiome, the literature is highly skewed toward one species, Sparus aurata, which is used as a model in aquaculture (Dimitroglou et al, 2010;Estruch et al, 2015;Nikouli et al, 2019;Rosado et al, 2019), while microbiomes of most other Sparidae have not been described in the wild, with the exception of a recent study (Ruiz-Rodríguez et al, 2020).…”

“…Our results also confirm that the genus Vibrio, albeit dominant on the mucus, skin and gills of teleost (Chiarello et al, 2018;Ruiz-Rodríguez et al, 2020), represents only a small proportion of their gut microbiome. Regarding Sparidae' microbiome, the literature is highly skewed toward one species, Sparus aurata, which is used as a model in aquaculture (Dimitroglou et al, 2010;Estruch et al, 2015;Nikouli et al, 2019;Rosado et al, 2019), while microbiomes of most other Sparidae have not been described in the wild, with the exception of a recent study (Ruiz-Rodríguez et al, 2020). To our knowledge, our study provides the first report of the gut microbiome composition for five species: B. boops, D. puntazzo, Diplodus sargus, Lithognathus mormyrus, and Pagellus acarne.…”

“…The structure of the gut microbiome significantly differed between the 12 studied species, with no genus and only four families (Rikenellaceae, Lachnospiraceae, Desulfovibrionaceae, and Vibrionaceae) representing more than 10% of the sequences in more than two host species. Species-specific gut microbiomes have been reported for other marine fishes both within and between families (Miyake et al, 2015;Ruiz-Rodríguez et al, 2020), but some studies also reported the absence of inter-specific difference because of high inter-individual variability in the gut microbiome (Nikouli et al, 2020).…”

“…Marine teleost fishes gather >10,000 species and >100 families, and a large range of ecological strategies, with for instance diet ranging from herbivory to top-predators even within some families (e.g., Labridae, Sparidae). However, to date only a few studies have assessed the microbiome of several fish species from a single ecosystem using sequencingbased approaches (Givens et al, 2015;Miyake et al, 2015;Sullam et al, 2015;Sylvain et al, 2019;Ruiz-Rodríguez et al, 2020). Consequently, the presence or absence of gut phylosymbiosis in the gut microbiome of marine fishes has never been tested.…”

Characterization of ecto- and endoparasite communities of wild Mediterranean teleosts by a metabarcoding approach

“…In this study, we characterized the parasitic communities associated to skin mucus, gill mucus and intestine of several wild Mediterranean teleost fish species, by analyzing the non-specific reads obtained during a metabarcoding survey of the bacterial communities. In a global study of fish associated microbiota [42], we employed 16S rDNA primers biased towards bacteria and archaea [43]. However, these primers that can also amplify the 18S rDNA from eukaryotic organisms [43–44], also yielded several thousand reads that corresponded to eukaryotes.…”