Photoperiod manipulation is routinely used in salmon aquaculture to control life history events and ensure maximal growth, especially during the freshwater stages of development where light is often provided 24 hours per day. However, there is limited information available concerning how this may impact fish immune competence and disease resistance. In human and animal models, there is growing evidence that disruption of circadian rhythms can have negative impacts on health and immune responsiveness. For the sustainable scaling up of recirculating aquaculture systems (RAS) for salmon and other finfish farming, the establishment of photoperiod regimes that maintain both productivity and fish health and welfare are critical. This has been highlighted as a research priority by the sector, including our industry partners, and the representative body, Salmon Scotland. This project will combine experimental and functional genomic approaches with industry-relevant pathology and welfare measures to address how early-life photoperiods impact immune resilience in key salmon developmental stages. This project will: 1) examine immune and molecular clock transcriptional rhythmicity in freshwater Atlantic salmon under contrasting photoperiods and pathogen challenges, 2) assess the impact of photoperiod on the transition of freshwater salmon stages to seawater acclimated smolts, vaccination efficacy, and disease resistance during marine growth. Together, this will deliver a fundamental understanding of the importance of light environments on fish immunity, provide evidence for improved salmon rearing practices to promote circadian health, and lay the foundation for the development of chronotherapeutic approaches in aquaculture.

Amoebic gill disease (AGD), caused by Neoparamoeba perurans, is as a major disease in salmonid aquaculture. Treatment options are currently extremely limited. Using an existing state-of the-art drug discovery pipeline at the University of Glasgow, we propose to test the potency of existing licensed and experimental drugs used against the kinetoplastid diseases (Chagas Disease, Sleeping Sickness, Leishmania) for activity against N. perurans in vitro in Scotland prior to in vivo testing of the drug candidates at a unique trial site in Ireland. Crucially N. perurans has an endosymbiotic kinetoplastid (a kinetoplastid living inside every N. perurans cell) on which it relies for essential metabolic processes. Working on the hypothesis that killing the endosymbiont will lead to death of its host, our approach promises to deliver new drugs to address an intractable problem in aquaculture. In doing so it may even drive the costs of these drugs down for medical and veterinary applications in the tropics.

Farmed Atlantic Salmon is the UK's biggest food export with an annual turnover exceeding £ 1 billion. This mainstay of our blue economy is principally located on the Scottish west coast and islands where it improves livelihoods, economic prosperity, social inclusion and wellbeing in remote communities, as well as providing a low carbon sustainable food. Elevated abundances of naturally occurring planktonic organisms (harmful phytoplankton, jellyfish and hydrozoans (hereafter collectively termed "plankton")) are increasingly understood to deteriorate the health of farmed salmon, negatively affecting fish welfare and the economic and environmental sustainability of the industry. Historically, most concern has been over harmful phytoplankton, but there is increasing evidence that hydrozoans and other jellyfish are also a major problem. The recent Scottish Government fish farm production survey (Munro, 2023) highlighted micro-jellyfish as the cause of a significant drop in salmon production. Harmful algal blooms (HABs) have long posed a risk to the survival of farmed fish (Bruno et al., 1989). Different taxa may be harmful through a) physical irritation of the gills, b) reduced levels of dissolved oxygen and hypoxia, c) toxicity, d) production of reactive oxygen species. Through modification of physical and chemical oceanographic conditions that drive blooms, climate change is influencing their spatial and temporal dynamics and increasing risk to aquaculture (Hallegraeff et al., 2021; Wells et al., 2020). The economic impacts of HAB events can be significant, e,g. a recent major farmed fish kill in Chile killed 29 million salmon at a cost of USD 800M (Anderson and Rensel 2017). Hydrozoans and jellyfish pose a great threat to aquaculture with effects including mass mortality events and damage to skin, eyes and gills, which in turn can trigger or exacerbate other infections, such as amoebic gill disease (Kintner and Brierley 2018). Ingestion can damage fish digestive systems and cause negative behavioural responses. The economic impacts of jellyfish blooms on marine finfish aquaculture were brought into public awareness by a massive bloom of Pelagia noctiluca that killed more than 100,000 farmed fish in Northern Ireland in 2007. The bloom extended into Scottish waters, covering hundreds of square kilometers (Doyle et al. 2008). In addition to such high-profile events, mortalities are a recurrent problem with the literature indicating that jellyfish blooms are increasing in frequency and size (Richardson et al., 2009) due to a range of factors including climate change (Richardson and Gibbons 2008), food-web changes caused by over-fishing (Lynam et al., 2006), changing nutrient profiles (Arai, 2001) and increases in marine litter, which may provide settlement sites for benthic stages (Holst and Jarms, 2007). Industry observations indicate that the problem has been acute in recent years (https://www.heraldscotland.com/news/23748545.tiny-jellyfish-big-threat-salmon-farming/). To achieve sustainable development in a changing climate (Scottish Government, 2023) the aquaculture industry urgently requires better understanding of the environmental conditions that promote plankton blooms, and enhanced methods for monitoring, forecasting and rapidly disseminating the occurrence of these events to allow sufficient time to undertake mitigation. Our consortium will therefore address plankton impact on aquaculture through 1) The combination of farm-based microscope plankton monitoring with novel automated imaging approaches, 2) AI based classification and enumeration of automatically imaged plankton, 3) Mathematical model-based assessment and forecast of plankton risk 4) Data synthesis, interpretation and real time web-based reporting to the aquaculture industry of plankton risk.

Atlantic Salmon aquaculture in the UK is facing an existential threat in the form of poor gill health. Losses are mounting every year, threatening the viability of an industry that is worth >£1Billion to the UK economy and represented the largest UK food export during 2021 but has decreased due to ongoing health challenges. Gills are vital organs, with functions in gas exchange, water balance and excretion of nitrogenous waste. Salmon gills are in constant and direct contact with the constantly changing marine environment, the 'Achilles heel' of this economically important fish. Organisms in the plankton such as harmful algae and micro-jellyfish are the principal cause of gill damage and inflammation, but little is known about which plankton species are detrimental to fish health. Warming surface waters are causing these planktonic agents to bloom more frequently and in greater numbers. Other parasitic organisms, for example amoeba causing amoebic gill disease, exacerbate gill damage. At present, aquaculture producers have few tools at their disposal to predict, avoid or treat the gill damage that occurs. New approaches are required to fully understand the biology of this system and to enable salmon producers to mitigate losses. For example, to understand which planktonic organisms are causing gill damage a systematic approach is required to reveal the hidden diversity of plankton communities. The University of Glasgow has recently shown 'proof of concept' at two aquaculture sites that daily environmental DNA metabarcoding direct from salmon pens, alongside rigorous statistical analysis, can reveal plankton diversity and provide 'early warning' for damaging bloom events. Meanwhile, the University of Aberdeen has developed a panel of gene expression biomarkers that has the potential to detect early gill damage before it becomes irreversible. Selective breeding of more resilient salmon is the ultimate tool to mitigate against salmon losses due to planktonic challenge. Working with Benchmark Genetics, the Roslin Institute has shown that salmon can be bred have resistance to amoebic gill disease. Progress can also be made towards breeding salmon more resilient to gill challenge from harmful plankton if the complexity of these planktonic communities can be simulated under laboratory conditions. The current project is an Industrial Partnership Award which includes contributions and involvement from Scotland's three largest salmon producers (MOWI, Scottish Sea Farms, Bakkafrost), Benchmark Genetics (a salmon selective breeding company) and EsoxBio (a molecular diagnostics start-up). Academic partners are the Universities of Glasgow, Aberdeen, Stirling, and Edinburgh. In a first objective, the project will undertake systematic sampling of planktonic communities and salmon gill biomarkers over three years at nine sites to rigorously identify which planktonic species and which gill biomarkers predict gill damage. Secondly, via in-house marine aquaria and in vitro cellular models, the role that cleaning biofouling from net pens has in releasing harmful organisms into the plankton will be explored in the context of acute gill inflammation. Thirdly, using innovative mobile experimental aquaria at three shore-side aquaculture sites, complex planktonic challenges will be simulated to enable a replicated genome wide association study (GWAS) for salmon resilience to gill damage as well as to trial multiple interventions to mitigate gill damage. The GWAS represents a first step towards a selective breeding program; the intervention study will inform aquaculture producers on immediate steps that can be taken to combat losses. In a final objective, data streams from across the project will flow into an integrated mathematical model that will reveal the environmental and molecular mechanisms that underpin salmon responses to harmful plankton as well as predict the likely success of gill health interventions in the future.

The disease saprolegniosis is a major problem in the aquaculture industry with losses of up to 10% of fish caused by the oomycete pathogen Saprolegnia parasitica. As with all pathogens new genetic variations emerge within a species. Indeed, we isolated several distinct S. parasitica phylotypes (strains) from 14 Scottish fish farms in collaboration with our aquaculture partners in a recent study, and we have now established that there are six distinct phylotypes of S. parasitica with different levels of heterozygosity, that can be found across Europe. But we also found that although there were 5 different phylotypes present in the Scottish fish farms, essentially only one particular S. parasitica phylotype was infecting Atlantic salmon. The phylotype of a S. parasitica isolate is defined by its internal transcribed spacer sequence (ITS). The ITS sequence of the six phylotypes are very similar (i.e. one or two base pair differences), indicative of the extent of whole genome similarities of these S. parasitica phylotypes. We therefore propose to exploit this to determine what is unique in the whole genome sequence of the pathogenic strains in comparison to the non-pathogenic strains. We have already recently performed Illumina sequencing of a total of 41 Saprolegnia isolates. These genomes cover the six phylotypes from S. parasitica, as well as isolates from Saprolegnia australis, Saprolegnia diclina and Saprolegnia ferax, all found in Scottish aquaculture sites. This resource is now available to search for unique target genes that are distinct for the individual phylotypes, in particular for the pathogenic phylotype. Therefore, our main objective is to perform a comparative analysis of the whole genome sequences of all phylotypes found in the farms and determine what unique genes the pathogenic isolates have that can be used to develop a quantitative detection test initially via a PCR based test but ultimately with a more-preferred handheld antigen testing kit. Furthermore, the current approach to develop and use a quantification method that does not discriminate between the phylotypes is essentially futile because only one phylotype is relevant for the outbreaks we see in the farms. Moreover, an outbreak with Saprolegnia is usually a rapid overnight event. Thus, the development of a rapid and accurate quantitative diagnostic kit for only the pathogenic phylotype would greatly facilitate our industrial partners in making informed decisions as to treat or not to treat, based on various parameters including the spore load of the pathogenic phylotype in the water and would provide a focused and sustainable disease management approach that will ultimately reduce the use of chemicals in aquaculture.