ROBUST-SMOLT Impact of early life history in freshwater Recirculation Aquaculture Systems on A. salmon robustness and susceptibility to disease at sea

Lead Research Organisation: University of Stirling
Department Name: Institute of Aquaculture


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.

Technical Summary

The adoption of Recirculation Aquaculture Systems for freshwater salmon production has clear benefits however, fish transferred from RAS systems are not performing equally to fish reared in open water loch systems. In the current project, we hypothesise that RAS rearing conditions, especially water chemistry and microbiology, nutrition, photoperiod and temperature, affect early life history traits of salmon and impact on microbiomes, immune barriers, osmoregulation, and robustness at sea especially for gill pathologies and new anaemic syndrome. The proposed research is multidisciplinary and will develop basic knowledge on RAS, photo-thermal history, diet and vaccine effects on fish physiology that may predispose fish to disease at sea. Two large-scale trials will be performed to test RAS vs. open water lochs in a commercial setting and the interaction between photoperiod, diet and vaccine in a controlled experiment. In addition, small-scale experiments will test the effects of increased CO2 on salmon physiology, the effects of freshwater history on smolt immune function (using double stranded RNA challenge) and post-smolt amoebic gill disease susceptibility when challenged with infectious agent N. Peruvans. A toolbox will be used to study fish health biomarkers including blood chemistry, haematopoietic indexes, endocrine status and immune function including leukocyte inflammatory markers, anti-viral response in erythrocytes and plasma prostaglandins. The genotype by environment interaction will also be studied. Experimental and production data will be combined in a meta-analysis to produce a unique large-scale epidemiological study and identify risk factors for disease at sea. Major outcomes will be industry recommendations, protocols and tools for early freshwater conditioning that promote enhanced immune function and health at sea. The ROBUST-SMOLT project will contribute to boost the competitiveness and sustainability of the UK aquaculture sector.

Planned Impact

The project will have significant economic, social and environmental impacts by furthering our understanding and improving inconsistences in smolt quality supply and subsequent seawater performance and losses. Thus, the overarching goal is to provide new knowledge and tools to monitor and enhance farming system (RAS) efficiency and reliability, fish robustness and health, and sector productivity and sustainability. Furthermore, the project aims to improve our basic understanding of mechanisms of the gut microbiome, mucosal integrity, physiological regulation of smoltification and interaction with water chemistry under closed RAS systems to enhance immunocompetence and post-sea transfer performance. By gaining an insight into molecular regulation and phenotypic development under closed containment systems, the salmon producers will also benefit from development of new tools and markers to aid improving smolt health and consistency, thus ensuring that fish produced are in optimum condition and meeting welfare standards. Such knowledge will help reduce losses and increase viability, competitiveness and sustainability of the UK aquaculture production sectors. The UK is the world's second largest salmon producer with ex-farm value of £400 million, worldwide retail value of over £1 billion, and contributes over £500 million to the UK economy. Salmon comprises 40% of Scottish food exports, a 500% increase in the last 20 years, and exports to 55 countries. Most importantly, fish farming supports employment for over 8,000 people in rural areas in which jobs otherwise are few, and injects £5m every week into these communities as wages and local expenditure. Furthermore, the UK salmon industry has been tasked to farm 70,000 extra tonnes by 2020 (market value of £280M+) and >100,000t by 2030. This can only come from opening new locations and improving production efficiency - requiring a significant "paradigm" shift in public perception of the sustainability and welfare of farmed salmon. Losses at sea in 2016 accounted for ~36,000T (16.8% of smolts put to sea), 50% of the desired UK production target for 2020. Thus collaboration between the industry and academic research in this area is vital as aquaculture is not supported by any Government research institute, as in other areas of agriculture. As such, the primary economic beneficiaries will be the UK aquaculture industry, specifically through producers (MHS, SSF, SSC & Cooke), Biomar Ltd. and Pharmaq Ltd., allowing them to strength UK competitiveness in the global market, by keeping pace with, and refining operative efficiency, as part of the progressive nature of global aquaculture. The project benefits will therefore get passed directly to the UK salmon producers through the generation of new husbandry protocols, health management strategies, feed and vaccines. The project will directly benefit the competitiveness of the entire UK salmon industry chain. This project will also contribute to UK policies for sustainability and environmentally sound food production, whilst ensuring health and welfare of fish. Improved control will also support the Renewed Strategic Framework for Scottish Aquaculture (2010) and the Future of European aquaculture (EATiP, 2012). The data will also aid the industry portray a more pro-active approach to addressing the public concerns of welfare of farmed salmon. Finally, there will also be direct public health benefits by increasing productivity. Since farmed salmon are a major source of long-chain omega-3 in the UK diet, with more than 1.2m salmon meals eaten per day, this project can also make a significant contribution to the health and well-being of the human population. Overall, the major outcome of this project will be to provide data to industry in order to optimise practical methods for the routine production of high quality smolts in RAS systems and maximise robustness of farmed stocks during seawater ongrowing.


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Bolton C (2021) Rhythmic Clock Gene Expression in Atlantic Salmon Parr Brain in Frontiers in Physiology

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Chalmers L (2020) Response of triploid Atlantic salmon (Salmo salar) to commercial vaccines in Fish & Shellfish Immunology

Description 1. Research has demonstrated that salmon smolts produced in Recirculating Aquaculture Systems (RAS) display differences in osmoregulatory status (ATPase, chloride) compared to smolt produced in ambient loch systems.
2. Microbiome communities at skill, gill and gut are highly variable, time-dependent and appear to be impacted by freshwater histories. This may impact upon health and welfare status.
3. Immunological variables, with particular reference to anti-viral responses, are impacted by freshwater conditions those being natural versus recirculating systems.
4. The health status of all fish in both freshwater and sea was generally too high to detect any impact of the early rearing environment on health in later life.
5. The blood biochemistry of salmon parr is altered to a level that could impact on their chronic health for water physico-chemistry conditions experienced in commercial RAS.
6. Measurement of markers of immune function give no indication for adverse impact on their health chronic health for water physico-chemistry conditions experienced in commercial RAS.
7. Analyses on the histopathology of the gills and skin and gill microbiomes of salmon parr under the water physico-chemistry conditions experienced in commercial RAS is ongoing.
Exploitation Route Results from this project are directly implemented in commercial production by industry partners.
Sectors Agriculture, Food and Drink,Environment

Description The findings from this project inform the fundamental approach taking by commercial salmon producers in terms of the basic understanding of how smolts are produced through the relatively new RAS freshwater production units. The key findings that highlight the differential performance of RAS-produced smolts may be related to the water chemistry of RAS systems themselves. Key inorganic ion concentrations appear to have a direct impact upon smolt performance. Industrial units can use these analyses to fine tune future production cohorts through the science informing the differences. The ability to undertake climate controlled experiments in a highly controlled manner to investigate the impacts of features of water chemistry and climate on fish growth, health and performance has opened up new research opportunities for us in understanding (for example) how the application of recirculating aquaculture systems may impact on salmon production. Applying this system we are now able to can now investigate how the conditions experienced by salmon in major commercial RAS production systems may impact on their long term health ( data yet to be published). This information will be provisioned - through our collaborative partnerships in this grant -directly to the major salmon producers globally as well as via publication in the open literature
First Year Of Impact 2023
Sector Agriculture, Food and Drink
Impact Types Economic

Description EASTBIO
Amount £100,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2020 
End 09/2024
Description Industry workshop on salmon RAS 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact The purpose of the event was to exchange knowledge and data on RAS in Scotland.
Year(s) Of Engagement Activity 2020