Time is a stronger predictor of microbiome community composition than tissue in external mucosal surfaces of Atlantic salmon (Salmo salar) reared in a semi-natural freshwater environment

The mucosal surfaces provide the first line of defence to opportunistic pathogens in external environment as well other physiological functions including osmoregulation, gas exchange or nutrient absorption gut. Atlantic salmon is most valuable salmonid species cultured worldwide and its anadromous life cycle dictates periods growth both fresh seawater. transition fish between these two habitats often accompanied by high levels mortality. Communities commensal microbes inhabiting are vital health also subjected an abrupt change salinity temperature during seawater transfer salmon. In this study we followed a cohort through parr-smolt transformation open freshwater loch exposed natural decline water month post-transfer sea. Mucus swabs were taken from gill skin, hindgut collected n = 6 triplicate pens at four sampling points (FW) first- fourth-weeks post sea (n 18 total per sampling). Distinct temporal dynamics communities identified three surfaces. microbiome diversity was stable characterized inter-individual variability terms community composition. Microbiome decreased skin throughout FW rearing immediately but recovered pre-transfer after one Gill declined continued further due single dominant taxon Candidatus Clavichlamydia salmonicola, member phylum Chlamydiae. Mucosal all largely distinct surrounding water. This highlights importance considering impact time, conjunction with salinity, when determining composition urges caution inferring general functionality time point.