Mitigating salmon gill disease by integrating genotype-environment studies with host-gill microbiome associations

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Gill health is a priority area for salmon research with significantly increased UK salmon mortalities at sea being reported due to compromised gill performance. Up to 70% of mortalities reported between 2019-2022 have been attributed to gill health conditions with an upward trend reported where poor gill health is the most important driver for fish mortality in the UK. Fish mortalities across the UK salmon sector were 14.9 million in 2022 (Fish Health Inspectorate, Scotland). Environmental data indicates a warming of coastal water causing changes to the marine environment during the seawater production of salmon. As a result, gill health challenges have become a severe problem within the industry with increasing mortalities due to Amoebic gill Disease (AGD) and/or Complex Gill Disease (CGD) infections leading to impaired gas exchange, poor growth and severe morbidity and mortality being observed. Current treatments are limited and include hydrogen peroxide or freshwater bathing of affected fish throughout the production cycle. Changes to the production cycle of salmon by the recent incorporation of recirculating aquaculture system (RAS) based production in freshwater, that is independent to seasonal change, contributes significantly to off-season inputs into farming systems. This means that the farmed fish experience two full summer periods at sea leading to a doubling of exposure to pathogens therefore driving poor seawater performance and increased mortalities as observed within the industry in recent years. Poorer SW performance has not been exclusive to one salmon producer and has been observed across the industry. The gills represent the largest external surface of fish and are central to both gaseous exchange and are now also recognised as a site for pathogen entry and colonisation. The microbial communities colonising the gills collectively named as the gill microbiome are central to maintaining good gill health and are directly affected by aquaculture health management interventions such as freshwater treatment of AGD in seawater as demonstrated by the applicants. Importantly, current research has also shown a genetic component to resistance to infection by Neoparamoeba perurans, the causative agent of Amoebic Gill Disease (AGD). This indicates that host resistance to AGD is heritable and therefore can be targeted by selective breeding.Gill health is now regarded to be the highest health challenge within the industry and regarded as a priority area of research. A key area of research to promote improved fish welfare and survival is the identification of resistance to AGD within Atlantic salmon breeding programs. This project will directly demonstrate the relationships between genetic family background in salmon and aquaculture environment on the composition of the gill microbiome and how these interactions impact upon gill health during AGD infection and gill health during multiple health management interventions (freshwater treatments). The programme of work is assembled using current state of the art research freshwater and marine aquaria located at the Institute of Aquaculture combined with a suite of refined analytical methods including a suite of optimised molecular biology technologies including genotyping, 16SrRNA and metagenome DNA sequencing. This project will dramatically extend current knowledge highlighting the role of the gill microbiome in disease resistance and salmon robustness and importantly through our commercial partner will directly impact upon commercial selective breeding strategies to future proof sustainable salmon farming in the UK.