Pathogen and Gene Expression Profiles of Atlantic Salmon From an Endangered Population

ABSTRACT The role of pathogens in impacting the behaviour and fate of salmonids has been studied extensively for some selected pathogens such as sea lice. However, the whole pathobiome of the fish are seldom considered and may confound and influence the study species in situ. In this study, we investigated the presence of pathogens in returning adult wild and hatchery salmon in the river Vosso using gill samples analysed in high‐throughput PCR with a selection of assays targeting different fish pathogens. In addition, the samples were analysed for gene expressions that have been previously linked to imminent mortality, thermal stress, and inflammation related biomarkers. These data were linked to the behaviour of the individual fish collected from acoustic telemetry tags inserted in the abdomen of the fish. Previous analyses have suggested that the behaviour of the hatchery and wild salmon in this study area is different; however, there was no evidence that the pathobiome or the gene expression of the two groups of salmon (39 wild and 14 hatchery) could explain the behavioural differences between these two groups. Furthermore, neither pathogen profile nor gene expressions had a significant relationship between metrics of behaviour or survival of the fish. Results suggest that gene expression and pathogen screenings are insufficient to predict fates of migrating salmon. The Vosso salmon is a threatened population in Norway after collapsing in the 1980s; these data contribute to ongoing efforts to identify factors that are limiting the recovery of this population after decades of poor returns.