Integrative microbiome surveillance for effective management of gill health in Atlantic salmon, Salmo salar

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 health management treatment options are limited although efficacious when applied to non-compromised populations. Critically, poor health surveillance data availability impacts the efficacy of successive health management interventions throughout the seawater growth phase and significantly impedes the development of data-driven health surveillance management strategies resulting in limited capacity to improve the health and welfare of the farmed populations.

Furthermore, 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, has led to off-season inputs into farming systems. This means that farmed fish can experience two full summer periods at sea leading to a doubling of exposure to pathogens therefore driving poorer seawater performance as observed in recent years 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.

Previously, we validated a refined methodology for 16S-based amplicon sequencing using titration to normalise library construction that provides higher resolution than current methods and guarantees a statistically robust analytical methodology. This advance sets the standard for normalisation and comparison across 16S studies. Using this approach, we demonstrated that variation in gill microbiome reflects animal welfare in sea cages and appears related to health management intervention frequency.

No other methods applied, including pathogen screening and immunological assessment were able to identify significant changes and therefore be related to observed increases in mortality and decreased welfare conditions. Using this method we have shown that the frequency of husbandry interventions including net cleaning, freshwater treatments and de-lousing procedures (thermolicer) directly impacts gill microbiome diversity and abundance.The main objective of this proposal is to capture critical longitudinal gill microbiome data and integrate all other data elements including pathogen screening and production and environmental data to develop an informed data-driven foundation for effective health and welfare management of salmon gill health.