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 Edinburgh
Department Name: The Roslin Institute


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

See Lead Institution Form
Description BBSRC Responsive Mode
Amount £1,640,000 (GBP)
Funding ID BB/V009818/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 08/2021 
End 08/2025
Description Genome editing for resistance to viral disease in rainbow trout
Amount £161,786 (GBP)
Organisation Hendrix Genetics 
Sector Private
Country Netherlands
Start 11/2020 
End 02/2022
Description Strategic research partnership with WorldFish 
Organisation Worldfish
Country Malaysia 
Sector Charity/Non Profit 
PI Contribution Roslin and Worldfish have a strategic research partnership since 2018 which focuses on selective breeding of Nile tilapia, one of the world's most important farmed fish species. Roslin scientists are developing genomic tools, and investigating how those genomic tools can be used to improve disease resistance of tilapia via breeding.
Collaborator Contribution The partners WorldFish run a tilapia breeding programme which provides samples and data to support the research undertaken at Roslin. This breeding programme also provides the route to impact by which the improved strains can be disseminated to benefit low and middle income country fish farmers.
Impact This has led to a peer reviewed publication describing genetic resistance to tilapia lake virus, which is one of the most problematic pathogens for global aquaculture. The story was presented in news form via the University of Edinburgh and also Science magazine
Start Year 2017
Description New Scientist Future of Food Webinar 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Ross Houston took part in the New Scientist Future of Food and Agriculture workshop by taking part in a panel discussion on genome editing.
Year(s) Of Engagement Activity 2020