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

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Gill health is now regarded to be the highest health challenge across the UK salmon industry and regarded as a priority area of research to support industry sustainability. Fish mortalities across the UK salmon sector were 14.9 million in 2022 (Fish Health Inspectorate, Scotland) with >70% being related to compromised gill function since 2019. State of the art research is required to promote improved fish welfare in the UK industry with the identification of resistance to amoebic gill disease (AGD) within commercial Atlantic salmon breeding programs a priority. This project will directly demonstrate the relationships between genetic family background in salmon and aquaculture environment on the composition and function of the gill microbiome and how these interactions impact upon gill health and survival during both AGD infection and multiple health management interventions for AGD in the seawater phase of salmon culture (freshwater treatments). 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. The programme of work assembled uses 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, normalised 16SrRNA analyses for low-biomass (gill) samples 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.