LAUSR

AIMS To investigate the relationship between microbial community profiles and gill pathology during a production cycle of Atlantic salmon in two commercial hatcheries. METHODS AND RESULTS Relationships between gill histology, environmental conditions and microbiome were determined using high-throughput data including 16S rDNA amplicon sequencing data, histopathology data and water quality parameters. Hatchery A used riverine water and operated a mixed system of recirculation aquaculture system (RAS) and flowthrough. Hatchery B was used bore water and operated a RAS. Melanin deposits, hyperplastic, inflammatory lesions were observed histologically in the gills. A higher prevalence of melanin deposits was detected and correlated to a change in beta diversity of bacterial communities in early time points (fingerling and parr stages). High abundance of Sphaerotilus sp., Pseudomonas sp., Nitrospira sp., Exiguobacterium sp., Deinococcus sp., and Comamonas sp. was correlated with high prevalence of melanin in filaments. Bacterial diversity increased as the fish cohort transitioned from RAS to flowthrough in hatchery A. CONCLUSIONS Under commercial conditions, the commensal community of gill bacteria was related to melanin prevalence.