Longitudinal Analysis of the Gill microbiomes of Atlantic Salmon from four Scottish farms reveals dynamics in bacterial richness and seasonal trends in diversity.

Atlantic Salmon aquaculture in Scotland is a major industry being both Scotland, and the UK’s largest food export. Gill disease, in particular Complex Gill Disease, is a significant challenge of salmon production. It is increasingly understood that the microbiome can influence host health and immunity. Therefore, the objective of the study is to identify and characterise the gill microbiome from stocking to harvest from four sites in Scotland 2018-2020. At each site, mucosal gill swabs were collected fortnightly (sites A & C) or monthly (sites B & G) from eight fish in two pens (n=623 fish). Gill samples underwent 16S rRNA Illumina MiSeq amplicon library preparation and analysis to characterise changes in the gill mucosal communities. Complex Gill disease was identified in sampled fish from each site (A: 20%, B: 11%, C: 24%, G: 13%).
At the four sites we showed species richness (alpha diversity) varied over time ranging from 68 ±SD31 to 777 ±SD152 (average 353 ±SD 158). Interestingly, 1100–1500 degree-days after seawater transfer, a distinct decline in species richness and evenness was observed at three of the four sties (A:410 SD± 134 to 276 SD±86 , B:264 SD±67 to 156 SD±71 , C:356 SD±130 to 228 SD±89). In terms of community composition, 1) while there were similarities between all four sites, the communities were statistically different (R = 0.067, P<0.001) from each farm, indicating that sites contributes to differences seen in the microbiome. Within each farm, a seasonal pattern in the microbiome was seen, with community shifts through winter-spring-summer-autumn (A: R2 = 0.11, P<0.001, B: R2 = 0.30, P<0.001, C: R2 = 0.22, P<0.001, G: R2 = 0.11, P<0.001). Proteobacteria dominated the gills (average: 73.6%), with Bacteriodota (average: 18.2%) also highly abundant at all sites.
Overall, we have shown changes in the bacterial communities over time and between sites indicating both seasonal and temporal changes in the gill microbiome. Understanding this will help us to better understand the role of the gill microbiome and its role in fish health.