Evaluating the variation in fish skin microbiomes among hierarchical levels

The skin microbiome of fish is part of the protecting barrier between the host and its environment, and it can impact host fitness. Microbiome community members of fish skin may highly vary among populations and species. Still, studies that investigate the factors shaping this variation, particularly among and within host individuals, are rare. In this study, we investigated patterns of variation in fish skin microbiomes among hierarchical levels by comparing samples from different body sites, individuals, and source populations of Perca fluviatilis. We performed replicate sampling on dorsal and ventral body sites of 39 perch individuals from two distinct populations along the Baltic Sea Swedish coast. We characterized the variation of fish skin microbiome and bacterioplankton communities in the surrounding water with metabarcoding of the V3-V4 regions of the 16S rRNA gene. Specifically, we explored: (i) Do species richness or community composition of microbiome communities vary among different fish host individuals and different body parts within hosts? (ii) Do microbiome community diversity and composition differ between different host populations? (iii) Does a single sample from each host individual reliably characterise the fish skin microbiome community composition?