Rearing system type affects baseline and post-vaccination immune gene expression in Atlantic salmon gills during smoltification.

Atlantic salmon undergo critical development before sea transfer, and vaccination during this stage is routine to build protective immunity. This study compared immune responses to vaccination in smolt-stage salmon reared in flow-through (FT) versus recirculating (REC) aquaculture systems. Ten clinically healthy fish per facility were collected one week before and two weeks after intraperitoneal vaccination with commercial multivalent vaccines. Using qPCR, we compared immune gene expression in the fish gills. Before the vaccination, REC fish exhibited higher relative expression of genes coding cathelicidin-1 (cath-1), interleukin-1β (il-1β), and tumour necrosis factor-α (tnf-α) than FT fish. Fourteen days after vaccination, REC fish showed increased expression of gene coding defensin (def) and decreased expression of gene for transforming growth factorβ (tgf-β), while in FT fish, vaccination was associated with increased relative gene expression of tnf-α, tgf-β, and il-10. Within REC, cath-1 expression declined postvaccination, concurrent with an increase in il-10, suggesting a possible counter-regulatory response; in FT, the coordinated rise of pro-inflammatory (tnf-α) and anti-inflammatory (tgf-β, il-10) transcripts is consistent with an activation followed by regulatory signalling. These transcriptomic patterns imply that baseline immune gene expression and post-vaccination gill transcriptomic responses differ between rearing water systems used during smoltification in Atlantic salmon.