Microbial and histopathological insights into gill health of Atlantic salmon (Salmo salar) across Scottish aquaculture sites

Abstract

The increasing prevalence of gill diseases in sea-farmed Atlantic salmon (Salmo salar) poses significant challenges to the aquaculture industry, affecting both fish welfare and economic productivity. This study investigates the association between gill microbiota and histopathological health in Atlantic salmon across three Scottish marine production sites. Gill mucus samples were collected and analysed using 16S rRNA sequencing to profile microbial communities, in parallel with histopathological examinations of gill tissue. The findings reveal rich and diverse microbial communities in gills with low histopathology, with a notable decrease in microbial diversity associated with increased prevalence of histopathological markers. Genera including Candidatus Branchiomonas and Candidatus Rubidus were more prevalent in gills with higher pathology scores, implicating these genera as potential microbial indicators of gill disease. These results suggest that specific microbial profiles could serve as potential measurable biological indicators or biomarkers for early detection and management of gill diseases in aquaculture. This study enhances our understanding of gill microbiome dynamics and their implications for fish health management in marine aquaculture environments.