Abstract
Closed cages offer the potential to address significant challenges associated with large-scale marine farming of Atlantic salmon (Salmo salar). Notably, they can effectively prevent sea lice infestations, thereby reducing reliance on intensive delousing procedures that can compromise fish welfare. However, the effects of production intensity within closed confinement systems (CCS) on fish welfare remain insufficiently understood. In this study, we investigated the effects of moderate (2–34 kg/m3) and high (4–44 kg/m3) stocking densities on salmon welfare in commercial-scale CCS over seven months. Fish were sampled during the hatchery phase, one month post-sea transfer, and seven months post-sea transfer. At each sampling, external welfare indicators were assessed. In addition, 60 fish were euthanized for collection of whole blood, gill and heart tissues for cortisol screening, histopathological assessment, and gene expression analyses. Mortality remained low across both density groups. However, progressive gill and heart pathologies were observed for seven months post-sea transfer. These patterns varied across cages and could not be attributed to differences in stocking density alone. Early welfare decline was linked to stress and physical trauma during sea transfer, and infection by salmonid gill pox virus (SGPV). At the later production phase, co-infection with piscine orthoreovirus-1 (PRV-1) and Moritella viscosa was detected, alongside high cortisol levels and significant transcriptional changes in genes involved in stress signaling, immune response, and apoptosis. These findings indicate that reduced welfare in closed cages may arise from an interplay between prolonged, cumulative stress and high infection pressure under dynamic, cage-specific environmental conditions.