Active colonisers of the gastrointestinal tract of Atlantic salmon farmed in a warm water region

Abstract Background. Atlantic salmon (Salmo salar) farmed in seawater in Tasmania (lutruwita) can experience temper-atures close to their thermotolerance limit during summer and Vibrionaceae are a major component of their gut microbiome. This study focuses on understanding the microbiome of the Atlantic salmon gastrointestinal tract via the taxonomy, population dynamics, and traits of the main colonists. Results. Multiyear survey and co-occurrence network analyses confirmed novel members of Aliivibrio reliably colonise the gut microbiome in Atlantic salmon farmed in marine pens in Tasmania when the confounding influences of DNA and bacteria from feed and water was considered. Aliivibrio and Mycoplasma were the main taxa found to colonise the gut mucosal layers. Warm water temperature(19°C) experiments performed in seawater tanks indicated Aliivibrio and Vibrio rapidly become predominant in the digesta of Atlantic salmon that had reduced feeding and high faecal cast production while Mycoplasma were found to be mostly absent. Salmon-associated Aliivibrio isolates were found to share many genes required for host colonisation with that of the faunal mutualist Aliivibrio fischeri. Though most salmon digesta isolates seem to lack obvious virulence factors, strains of two abundant novel colonising Aliivibriostrain groups possessed the genes for cytolethal distending toxin (CDT). Conclusions. Multiyear surveys confirm Atlantic salmon farmed in the relatively warm conditions of Tasmania are persistently colonised by the same, largely novel, Aliivibrio species and a restricted range of other Vibrionaceae. Some of these species were found to be particularly adept at colonising salmon in warm water conditions. Though some Aliivibrio coloniser strains possessed CDT-genes it is yet unknown whether CDT-gene-positive Aliivibrio negatively impact Atlantic salmon . Since the strains studies possess a range of different colonization enabling mechanisms, interactions between Vibrionaceae in the gut of Atlantic salmon could be important for overall fish health, especially when they are exposed to stressful conditions, such as elevated sea surface temperatures.