Cleaning the cleaner fish: managing the microbiome of lumpfish in hatcheries

The salmon farming industry is worth almost £2 billion in Scotland alone, but in recent years the salmon louse (Lepeophtheirus salmonis) has become a widespread commercial problem leading to a 10% reduction in salmon production in 2016. The ectoparasites cause damage to fins, gills, and skin, and can disrupt ionic homeostasis in smolts, leaving the fish vulnerable to secondary infections. The salmon louse can lay thousands of eggs during its brief lifespan which increases the risk of infection to both farmed salmon and wild stock. Increasing resistance to pesticides and the misuse of Thermolicers, causing mass mortality events in salmon farms, has led the industry to turn to biocontrol. In particular cleaner fish have been successfully deployed to salmon cages to remove the lice from the salmon. The species most commonly used as cleaner fish are wrasse (Labridae) and lumpsuckers (Cyclopterus lumpus L.). Wrasse have been used to delouse salmon for almost thirty years and consequently commercial production is well developed. However, in recent years attention has moved to lumpfish as they continue to feed at temperatures as low as 4 degrees C and are ready for deployment to cages much earlier than wrasse. Lumpfish have traditionally been caught from the wild but this is an unsustainable approach and there is now a push to develop lumpfish as an aquaculture species in the UK. There has been a high mortality rate of lumpfish both pre- and post- deployment to salmon farms which is largely due to bacterial pathogens, including Pasteurella spp., Aeromonas salmonicida and other common aquaculture pathogens. A mounting body of evidence points to a central role for the microbiome in the development of the immune system and in providing direct protection against pathogens. An understanding of these interactions therefore holds great promise for improving fish husbandry. Currently, however, the microbiome of C. lumpus is completely uncharacterised. The main aim of the PhD is to characterise the microbiome of C. lumpus during the vulnerable early life stages (eggs, larvae, fry). By combining both genotypic (metagenomic) and phenotypic (experimental) approaches the project will aim to further understand the role of the microbiome in lumpsucker development, immunity and general health, and ultimately develop novel probiotics or prebiotics. Whole genome sequencing will be used to profile the bacterial communities at the level of species abundance and down to the level of individual genes. This will inform on community structure and function and give an insight into how different conditions the lumpfish are exposed to e.g. diet, water temperature and stocking density can impact on the microbiome. Antagonistic interactions will be examined between individual isolates and whole communities to identify likely pathogenic or protective species and the genes underpinning these reactions. Recent studies in other organisms have shown the microbiome can influence host behavior, including feeding patterns, which can be manipulated to increase the salmon cleaning efficiency. This project fits with the BBSRCs strategic research priority of agricultural and food security as the overall aim is to reduce the sea lice burden of salmon, thus increasing salmon production.