How transfer to seawater from hatchery and different hatchery system types influence the gill microbiome of seven cohorts of farmed Atlantic salmon

Background: Salmon aquaculture involves a number of different stages in the production cycle as fish are moved from freshwater hatcheries to sea. In recent times there has been an increase in gill disease during the seawater phase which has led to an urgent need to understand the gill microbiome. Despite recent interest there is still a lack of understanding on the what drives its composition, and the influence various stages of the production cycle have on it. We characterise the gill microbiome from seven cohorts of Atlantic Salmon raised in six different hatcheries under three different operational systems - recirculating aquaculture system (RAS), flowthrough (FT) and loch-based system, prior to and after transfer to seven seawater farms, over two different input seasons, S0 (2018) and S1 (2019). Results: Using the V1-V2 region of the 16S rRNA gene, we produced amplicon libraries with no salmon reads. We show that hatchery system influenced the gill microbiome (PERMAOVA R2=0.226, P<0.001) with loch and FT systems more similar to each other than the three RAS systems, which clustered together. On transfer to sea, the gill microbiomes of all fish changed and became more similar irrespective of initial hatchery system, seawater farm location or season of input. Nevertheless, the gill microbiome among seawater farm locations was different (PERMAOVA R2=0.528, P<0.001) but yet, even at sea, clustering of the gill microbiome by hatchery system of origin was observed (PERMAOVA R=0.164, P<0.001). Finally, we show that the gill microbiome and surrounding water at each hatchery was highly similar, and have more shared ASVs than in seawater. Conclusion: We show that hatchery type significantly impacts the gill microbiome clustering by system - Loch, FT or RAS. On transfer to sea, the microbiomes change and become more similar, with site the fish are transferred to a significant driver, however interestingly a signature from the hatchery operation system remains. With more shared ASVs present between water and gill at hatchery, this may offer an opportunity to influence the gill microbiome.