Distinct microbial dynamics in three mucosal surfaces of Atlantic salmon (Salmo salar) during rearing in a semi-natural freshwater environment and following transfer to sea.

Atlantic salmon is a valuable aquaculture species that requires both fresh and seawater to complete its life cycle and the transition of fish between these two habitats is often accompanied by high levels of mortality. Communities of commensal microbes inhabiting mucosal surfaces are vital in fish health and are also subjected to an abrupt change in salinity during seawater transfer of Atlantic salmon. Here we analyse the temporal dynamics of the distal intestine, skin and gill mucus associated microbiome of Atlantic salmon across smolt production in an open loch system and in the first weeks post-seawater-transfer. Water and diet samples were also analysed.