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Assessment of immune competence of farmed Atlantic salmon is especially important during smoltification and the first several months in the sea. Recently developed tools were applied to salmon raised in a traditional flow-through facility (FT, cohort 1) and in a recirculation aquaculture system (RAS, cohort 2). Fish were sampled at four time-points: parr, smolt, and at three weeks and three months after seawater transfer (SWT); expression of 85 selected immune and stress genes, IgM transcripts (Ig-seq), and circulating antibodies were analyzed. A steady increase in gene expression was seen over time in gill and spleen in both cohorts, and especially in antiviral and inflammatory genes in the gill. Differences between the cohorts were greatest in the dorsal fin but later leveled off. Comparison with a gill reference dataset found a deviation in only three of 85 fish, suggesting a good immune status in both cohorts. Levels of both specific and nonspecific antibodies were higher in cohort 2 in smolts and in growers three weeks after SWT; however, levels evened out after three months in the sea. Ig-seq indicated association between antibody production, expansion of the largest clonotypes, and massive migration of B cells from spleen to gill in smolts. The results suggested greater agitation and higher reactivity of the immune system in RAS-produced salmon, but the difference between the cohorts leveled off over time.

Evaluation of Immune Status in Two Cohorts of Atlantic Salmon Raised in Different Aquaculture Systems (Case Study)