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.

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.

By 2050 it is estimated that the global population will exceed 9 billion. This is expected to result in a 100% increase in demand for food. The world needs more high-quality protein, produced in a responsible manner. This challenge is addressed by UN Sustainable Development Goals SDG2 (Zero hunger) and SDG12 (Responsible Consumption and Production). Expansion of marine fish aquaculture has been highlighted as a key route to increase food production. It is also an important area for the blue economy with high potential for new jobs and revenue. In the UK, marine aquaculture is worth over £2 billion to the economy, supports 2300 jobs and has ambitions to double production by 2030. But climate change is a threat as fish production is highly sensitive to the environment. Climate change assessments are often only available for large areas, e.g. global or regional, and do not capture the local conditions that influence fish production. They focus on long-term decadal averages which miss the daily environmental variability and multiple stressors that fish experience. Impacts on growth, health and welfare of the farmed fish are determined by these environment-biological complexities at farm level, and are also influenced by production strategies and industry decisions which may be based on social or economic factors. Robust, industry-relevant, climate impact assessment must include the complexities, relationships and trade-offs between different natural processes and human interventions. Thus, a more comprehensive approach which uses systems thinking to capture the interlinking interdisciplinary components is urgently needed. Precision aquaculture, where vast amounts of data are collected and analysed, offers a framework to provide the detail required to understand the complex farm system, evaluate how the environment is changing and assess implications for future production. In this FLF, I will deliver a rigorous scientific framework for assessing impact of climate change on marine aquaculture using systems thinking and precision-based information. I will create an approach which integrates detailed knowledge of what is happening in the complex farm system now, with future projections of climate change and potential stakeholder response. This will involve collecting high resolution data, analysing complex datasets, developing farm-level models, simulating future climate scenarios, and determining the adaptive capacity of the sector. I will work closely with my network of key industry partners, research organisations, regulators and policy makers to maximise translation and transfer of knowledge and approaches to industry and associated stakeholders. Atlantic salmon (Salmo salar) aquaculture in the Northeast Atlantic (Scotland and Norway) is used as a case study. Salmon leads marine fish production, with over 2 million tonnes produced each year, the equivalent of 17.5 billion meals. Norway and Scotland are responsible for 60% of production. The latitudinal range of farms extends across the thermal tolerance of the salmon, from temperate conditions in Scotland and south Norway, to arctic conditions in the north of Norway. This allows assessment of the spatio-temporal heterogeneity of climate change and a thorough analysis of how impact may vary between locations and different responses required. Beyond aquaculture, the positioning of marine fish farms offers an exceptional opportunity to gain deeper insight into the rate, magnitude and variability of climate change in coastal areas. This FLF will deliver vital new knowledge, data and approaches to understand how the environment is changing. This research is highly interdisciplinary, covering aspects of climate, environmental, biological and social science. The innovative techniques and transformative approaches will allow aquaculture to respond to the climate emergency, enhance blue economy opportunities and maximise its contribution to global food security.