Concurrent analysis of histomorphology and immune-related gene expression in gills of Atlantic salmon (Salmo salar) from recirculating aquaculture systems

Gill health is crucial in aquaculture but remains difficult to define because the gills are dynamic organs with nonspecific responses to environmental and biological stressors. This descriptive, exploratory study examined histological changes and gene expression patterns in selected apparently healthy Atlantic salmon from two commercial recirculating aquaculture systems (RAS), encompassing freshwater and saltwater production phases. The two systems also differed in facility, fish size, and life stage. Using a semiquantitative histology scoring system and RT-qPCR, we assessed associations between mild gill alterations, including increased mucous cell numbers, lamellar clubbing, and inflammation, and the expression of selected immunological and physiological markers. The selected material included fish with and without apparent morphological changes, allowing exploratory examination of gene-morphology relationships across the included spectrum, but not estimation of the population prevalence of gill alterations. Within this material, mucous cell, lamellar clubbing, and lamellar inflammation scores were higher among fish from the saltwater production system. Associations that remained significant after correction for multiple testing included lamellar clubbing with IFN-α and IgT, lamellar inflammation with IgT, mucous cell numbers with IgM, and mucous cell numbers with NKA α-1a. Ca. Branchiomonas cysticola was the only pathogen detected and coincided with increased lamellar inflammation at subclinical loads. These exploratory findings characterize morphological and transcriptional variation within the selected sample and demonstrate the value of combining histology, gene expression, and pathogen detection when assessing gill health in RAS-reared salmon.