The skin and gill microbiome of diploid and triploid Atlantic salmon before and after experimental salmonid alphavirus infection

The microbial communities that live in symbiosis with the mucosal surfaces of animals provide the host with defense strategies against other microbes. These microbial communities are largely shaped by the environment and the host genetics. Triploid Atlantic salmon are being considered for aquaculture as they are reproductively sterile and thus cannot contaminate the natural gene pool. It has not been previously investigated how the microbiome of triploid salmon compares to that of their diploid counterparts. In this study, we compare the steady-state skin and gill microbiome of both diploid and triploid salmon, and determine the effects of salmonid alphavirus 3 experimental infection on the microbial composition of diploid and triploid salmon. Our results show limited differences in the skin-associated microbiome between triploid and diploid salmon, irrespective of infection. In the gills, we observed a high incidence of the bacterial pathogen Candidatus Branchiomonas, with higher abundance in diploid compared to triploid control fish. Diploid salmon infected with SAV3 showed greater histopathological signs of epitheliocystis compared to controls, a phenomenon not observed in triploid fish. Together, these results show a limited effect of ploidy on the salmon microbial community composition, and provide insights into co-infection with SAV3 and C. Branchiomonas in Atlantic salmon.