Assessment of gill microbiome of two strains of Atlantic salmon reared in flowthrough and recirculation hatcheries and following seawater transfer

The gill mucosal microbiome of Atlantic salmon has a significant impact on mucosal health and physiology under homeostatic conditions, but the microbial community may itself be influenced by host genetics, the culture system and seawater transfer. In this study, the impact of two commercial strains of Atlantic salmon, reared in two parallel hatchery systems (flow-through -FT and recirculation -RAS) on the gill microbiome was investigated. Samples of gill mucosal microbiome, tank biofilm and water were collected from the fish cohorts at the hatcheries and following seawater transfer. Though the gill microbiome of fish from the two commercially equivalent FT and RAS hatcheries had similar beta and alpha diversity, the alpha diversity indicators of bacterial communities of gills significantly increased after seawater input. Ultimately, no effect of the genetic strain on the gill microbiome was detected. Our results showed that under commercially equivalent FT or RAS hatchery systems with a common water source, two strains of Atlantic salmon had comparable gill microbiomes.