Full length articleSmoltification and seawater transfer of Atlantic salmon (Salmo salar L.) is associated with systemic repression of the immune transcriptome

•Smoltification of salmon is associated with profound endocrine alterations.•High incidence of infectious diseases in the sea indicate weakened protection.•Microarray analyses in head kidney, intestine and gill revealed immune suppression.•No recovery was observed after three weeks in seawater.•Duration and consequences of immune suppression need further exploration.

Smoltification and seawater adaptation of Atlantic salmon are associated with profound alterations in the endocrine status, osmoregulation and behaviour. Little is known about immunological changes during smoltification, although increased incidences of infectious diseases after seawater transfer (SWT) may indicate weakened protection. We report microarray gene expression analyses in farmed Atlantic salmon during smoltification stimulated with constant light and early seawater adaptation (one and three weeks after SWT). Gene expression changes were large, their magnitude in the head kidney and proximal intestine was greater than in the gill. Among 360 differentially expressed immune genes, 300 genes were down-regulated, and multiple functional groups were affected such as innate antiviral immunity, chemokines, cytokines and receptors, signal transducers, effectors of humoral and cellular innate immunity, antigen presentation and lymphocytes, especially T cells. No recovery was observed after three weeks in seawater. A notable exception was a transient up-regulation of immunoglobulin transcripts in the gill after SWT. Genes involved in stress responses and xenobiotic metabolism were up-regulated in respectively intestine and gill. The duration of this observed immune suppression and the possible consequences for susceptibility to infections and diseases need further exploration.