The rapid expansion of the global Atlantic salmon industry has been made possible through the adoption of new farming technologies (land based Recirculating Aquaculture Systems, RAS) and husbandry regimes to manipulate animal physiology. This includes the parr-smolt transformation (the process by which salmon become seawater tolerant) and early maturation impacting on fish welfare and product quality. Salmon producers in the UK have either already built or are in the process of building such large production units. These systems have clear advantages over land-based or open water loch systems, including a reduction in water usage, improved management of waste, a better control of disease and the ability to manipulate environmental conditions for year round salmon production. However, questions about robustness of these fish when exposed to challenging natural conditions in open seawater cages have been emerging over recent years, especially for gill pathologies and a new anaemic syndrome. While the Industry and Government have strong aspirations for growth of the salmon sector to meet increasing market demands, considerable pressures are being experienced by the farming companies and production, at best, has stagnated over recent years and even decreased since 2015. This is mainly due to fish health challenges at sea resulting in emergency harvests and unsustainable losses at sea. From results obtained by the consortium research teams over the past 4 years, it appears very clearly that conditions experienced by fish early during freshwater development can impact on long-term performance and robustness at sea. The current project aims to characterise the impacts of freshwater environmental conditions including water chemistry, temperature, photoperiod and nutrition, between RAS and open water loch systems, on fish performance and overall health. The main hypothesis tested by the project is that early life history of salmon produced in freshwater RAS impacts on immune barriers (mainly gill, gut and skin), which may predispose fish to gill pathologies at sea. The project will investigate how RAS microbiota (e.g. microbe populations living in the fish intestine, gill and skin) and water chemistry (especially carbon dioxide) impact on fish immune function and performance. The effects of altered environmental regimes (photoperiod, temperature and diet) and vaccines that provide active protection against particular diseases at sea, will be tested on smolt immune function, performance and health following transfer to sea. Finally, the relationship between fish development in freshwater RAS and its impact upon commercial performance and overall health will be studied including the effects of the fish genetic makeup, the characterisation of the new anaemic syndrome and a large-scale epidemiological study. To ensure the success of the project, the consortium brings together world leading scientists from four of the main UK research Institutions working on aquaculture and sustainable livestock development in conjunction with the four leading salmon farming, feed manufacturing and pharmaceutical companies. The project has also a strong support from governmental research centres and industry led organisations. The research will enable the development of practical methods for the production of high quality salmon with benefits for animal welfare and the sustainability and profitability of the industry. Since farmed salmon are a major food source in the UK diet, with more than 1.2 million salmon meals eaten per day, this project also has great significance to the health and well-being of the population in the UK. By supporting the sustainable development of the salmon farming industry, this project will contribute to protect more than 9,000 directly employed and industry-associated jobs in largely rural areas of Scotland and will help create new jobs.

The salmon louse, Lepeophtheirus salmonis, is a crustacean ectoparasite infecting wild and farmed salmonid fishes, which causes significant problems in marine Atlantic salmon aquaculture. Salmon louse infections on farms require control to maintain good fish health and welfare, and to minimise potential impacts of farm-origin parasites on wild fish populations. Currently, salmon louse control on fish farms depends heavily upon the use of drugs, supplemented by farm management measures. A number of non-chemical control strategies are currently under development, and these include the biological control of lice through cleaner fish and attempts to render salmon resistant to lice through vaccination and selective breeding programmes. However, these and other alternative control strategies are presently not sufficiently developed to allow full implementation at an industrial scale. While anti-parasitic drugs offer efficient salmon louse control, relatively few types of delousing agents are available. It is known from other pests and parasites that the repeated use of the same or similar chemicals increases the risk that parasites may develop drug resistances, driven by the mechanisms of natural selection discovered by Charles Darwin. Certain genetic features, called "resistance alleles", are usually rare in organisms as they provide no benefits to their carriers under normal conditions. Parasites possessing resistance alleles, however, are able to survive drug treatments better than those without, hence if the same drug is over-used, resistance alleles can increase their frequency in treated parasite populations as susceptible individuals are killed by treatment. This may ultimately result in drug resistance of the entire population. Very little is known about the mechanisms responsible for drug resistance in salmon lice. In the proposed project, drug-resistant strains of salmon lice generated in the laboratory will be used to investigate potential resistance mechanisms. Two strategies will be followed to find out how these lice have managed to become drug resistant. Firstly, breeding crosses will be made between resistant and drug-susceptible salmon lice, and genetic sequences that are associated with resistance will be identified using the latest DNA sequencing methodologies. Secondly, differences in gene expression between resistant and drug-susceptible salmon lice will be determined, which will provide new insights into the involvement of particular molecular pathways in development of resistance to particular drugs. Such knowledge will be extremely useful in the identification of drugs which can break the resistance mechanism. Choices among available treatment options on salmon farms are currently based on the results of "bioassays", which are small-scale laboratory treatments of salmon lice used to establish susceptibility to treatment. However, salmon louse bioassays are error-prone and regularly fail to correctly predict the success of subsequent farm treatments. The present project will develop fast tests to detect genetic susceptibility to treatment that are expected to be more specific and accurate than bioassays in identifying the best treatment choice for a given farm situation. Using the best available treatment has obvious economic and environmental benefits, and can help to prevent resistance development. New, unexploited drug classes represent a limited natural resource of high value for future food security. By helping to combat the development of drug resistance, this project will help to extend the life of current and novel delousing agents, and thus improve the sustainability of intensive salmon farming.

The sudden 'en masse' appearance of jellyfish has serious consequences for coastal power stations through biofouling of cooling water systems. The reduction in water flow caused by jellyfish has forced power plants to run at reduced efficiency or temporarily shut down as a precautionary measure to prevent overheating, which impacts the provision of electricity to customers at a significant financial cost to the electricity supplier. A persistent difficulty lies in identifying the origin of blooms and when they will appear at a coastal facility and water intake. The main project partner for this proposal is EDF (nuclear), however the methodology is intentionally generic to allow adaptation to other sensitive coastal sites and therefore our project has the support of both SSE (gas energy) and SSPO (Scottish Salmon Producers Organisation). The aim of this proposal is to provide a robust tool for rapid evaluation of the likelihood and scale of jellyfish ingress at EDF's Torness Nuclear Power Station based on simulated patterns of historic bloom dispersal within the North Sea from the last 20 years. To achieve this we will translate our previously NERC-funded research with the state-of-the-art marine Connectivity Modelling System to simulate dispersal of individuals within blooms incorporating specific biological behaviours of jellyfish (e.g. vertical migration, rough surface conditions avoidance and buoyancy-related effects of aging). We have two objectives which will be completed within 18 months at a cost of £161,618 (80% fEC): (1) to provide gridded maps, specific to the time of the year or oceanographic conditions, giving the probability of jellyfish arriving at Torness, as well as minimum and peak arrival times, for blooms arising at any given source location within the North Sea. (2) to test the suitability of the tool for providing an early warning of potential ingress threat from jellyfish blooms, including validation with historic and satellite-based observational data. This tool will allow rapid risk evaluation and inform operational response by EDF when a jellyfish bloom is located in the future or during specific weather events. The tool will also identify critical locations in the North Sea where ongoing monitoring is essential for an early warning system for Torness Nuclear Facility.

ShellEye-DEMO aims to translate novel satellite-informed techniques for early warning of harmful algae blooms (HABs) and microbiological risks into a unique and viable service to support the sustainability of UK aquaculture. This exploits existing research to identify certain HABs using satellite ocean colour, and the fusion of Earth observation, meteorological and in situ data to infer increased risk of E. coli. The objectives are: 1. [D]omain expansion: to involve pilot aquaculture farms in two additional UK regions, and consultation with the largest salmon farms in Scotland, as a route to wider exploitation of the potential benefits of ShellEye's approach. 2. [E]nhanced resolution of HAB detection, from 1km to 300m, to improve precision of near-coast and near-farm HAB risk estimation (using latest Sentinel-3 satellite). 3. [M]arine insurance: to develop long-term HAB probability maps to assist in insurance risk assessment, and encourage clients to take up satellite early warning to reduce losses. 4. [O]ther types of aquaculture, using a customised version of the ShellEye methods to protect the emerging potential of offshore lobster farming. This will be achieved through activities organised into 5 work packages: Stakeholder engagement; Enhanced HAB warning; Microbiological hazard warning for new domains and types; Quantifying HAB risk for marine insurance; and Advanced pilot trial. Partners from the insurance industry, aquaculture farms in three regions, and regulatory organisations, will contribute their time, expertise and data to support the application of our novel methods and engage in real-time trials. Outputs will comprise pilot risk-warning services to address the challenges of satellite monitoring and modelling of dynamic near-coastal environments; and a long-term HAB probability to inform the challenge of assessing insurance risk. Impact will be realised through development and protection of UK aquaculture industries, the quantification of reduced stock losses and recalls, and improved insurance risk assessment enabling lower premiums. All of which will help to boost the UK aquaculture industry and the quality of its produce, and contribute to increased economic gains and food security impacts for the UK. Keywords: Sustainable aquaculture; shellfish; finfish; salmon; harmful algal blooms; E coli; satellite Earth observation; ocean colour; modelling of microbiological hazards. Secured project partner stakeholders: Sunderland Marine Insurance (SMI) National Lobster Hatchery (NLH) Westcountry Mussels Ltd (WCM) Morecambe Bay Oysters Bangor Mussel Producers Ltd Centre for Environment, Fisheries and Aquaculture Science (CEFAS) Food Standards Agency (FSA) Shellfish Association of Great Britain (SAGB) Scottish Salmon Producers' Organisation (SSPO)