Mucosal and digesta microbiota of Atlantic salmon farmed in Tasmania during the summer of 2018

To understand bacterial colonisation of the Atlantic salmon farmed in Tasmania the microbial communities from gut sections were assessed using 16S rRNA gene amplicon sequencing, network analysis and annotated genome sequences of isolates. Samples comprised digesta, washed mucosa from gut sections (fore-, mid- and hindgut) as well as stripped faeces. Samples analysed in the study included historical data and new data involving fish surveyed between 2010 to 2018. Bacteria considered colonisers were observed to become much more abundant after smolt had been in sea cages for 3 months or more and also tended to be abundant in the mucosa compared to the digesta. Feed/water non-coloniser relative abundances tended to decline between the foregut to the hindgut and were less abundant in the mucosal layer overall. Network analysis confirmed these observations. The results also confirm the consistent colonisers of the farmed Atlantic salmon included only Aliivibrio, Vibrio, uncultured members of the Mycoplasmatales and potentially Photobacterium, virtually all other taxa are transients from water or are diet-associated artifacts. The data suggests Aliivibrio is a major consistent and predominant coloniser of the Atlantic salmon gut. Aliivibrio spp. take 6-9 months to reach maximum hindgut populations and are mostly non-bioluminescent, halophilic, mesophiles preferring summer conditions. These growth responses were confirmed by 6 month seawater tank temperature-based trials. The tank experiments indicated only one or a few species of Aliivibro and/or Vibrio become predominate and do not fully replicate responses seen with sea cage fish where a suite of gut colonisers typically occur. Genome sequencing revealed Aliivibrio colonisers include a number of genetic groups related to Aliivibrio finisterresis and genome annotation revealed that colonisation is enabled by many traits similar to that of Aliivibrio fischeri, a major coloniser of squid light organs. Though none of the strains studied can be considered to cause disease in salmon some of the abundant colonising Aliivibrio strains possess genes coding for cytolethal distending toxin, which has unknown ramifications for fish health, in particular dysbiosis.