Gill infections, gill pathology and gill-related mortality in farmed Atlantic salmon

Last year (2021) 54 million Atlantic salmon died at Norwegian food producing sea sites. This constitutes a loss of 15,5% of the fish that were transferred to sea. Gill diseases are among the health issues that causes considerable mortality, economic loss, and reduced fish welfare in salmonid mariculture. The overall aim of the Ph.D. work was to investigate the impact and interactions of selected microorganisms, environmental and managerial factors on gill health of farmed Atlantic salmon. To determine if variation in pathogen prevalence and load, and zoo- and phytoplankton levels had an impact on gill health we performed a prospective cohort study. Groups of Atlantic salmon in Western Norway were followed with repeated sampling and data collection from the hatchery phase and throughout the 1st year at sea. A secondary goal was to describe the temporal development of selected gill infections. Neoparamoeba perurans appeared to be the most important cause of gill pathology in the study cohorts. No consistent covariation and no or weak associations were observed between the extent of gill pathology and prevalence or load of SGPV, Ca. B. cysticola and D. lepeophtherii. The only exception was an association between epithelial necrosis/apoptosis and SGPV, and to a lesser extent Ca. B. cysticola. At sea, D. lepeophtherii and Ca. B. cysticola persistently infected all fish-groups, while N. perurans and SGPV infection showed a seasonal variation. There was no impact of zoo- and phytoplankton on gill health or overall mortality in our cohorts. Co-infection with three or more putative gill pathogens was common across all sites. To determine if in situ net cleaning, thermal and mechanical delousing had an impact on gill health, we performed three separate historical control field trials. Exposure to biofouling debris during a single in situ net cleaning event of moderately fouled net pens was associated with an increase in the number of salmon with thrombi in the gills. There was an increase in vascular and hyperplastic gill lesions observed post-treatment after a single thermal or mechanical delousing treatment, though the overall percentage of gill tissue with pathology was generally low. An increased pathogen load of Ca. B. cysticola and differential expression of genes involved in pathways of cell stress, inflammation, repair, and proliferation was detected in the gill tissue after the thermal delousing event. Furthermore, there was an increase in the number of fish with microorganisms and lesions possibly associated with pathogens observed in the gill tissue after both treatments