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New DNA approach speeds up assessment of fish farm seabed impacts

Marine finfish operators are required to monitor the condition of the seabed around their farms and provide environmental evidence to the Scottish Environment Protection Agency (SEPA) as part of their regulatory requirements. 

Fish waste and uneaten feed can settle on the seabed and affect the organisms living there. Understanding those changes helps SEPA assess whether operators are meeting the environmental standards required by their permits and whether further investigation or intervention is needed. 

Traditionally, assessing seabed condition requires specialist analysis to identify and count the organisms living within sediment samples. The types and abundance of those organisms provide evidence about the ecological condition of the seabed, but this detailed analysis can take around 16 weeks. 

A different approach, known as eDNA, analyses bacterial environmental DNA from a small amount of sediment to assess seabed condition, with results potentially available in around six weeks. Comparison of the eDNA to the traditional method demonstrate it can be used to show the ecological condition of the seabed, giving confidence in the technique and the results.  

eDNA has now been incorporated into SEPA's regulatory process, meaning operators can use its results as evidence of seabed condition rather than traditional analysis being required in every case. 

Where eDNA results show that the required environmental standards are being met, the assessment can be completed without further traditional analysis. Where results indicate potential non-compliance, the full seabed grab has already been collected and remains available for further traditional analysis where required.  

This significantly reduces the time between monitoring taking place and understanding what the evidence is showing, helping operators respond more quickly and supporting earlier regulatory action where necessary. 

Environmental standards and permit requirements have not changed. 

eDNA is not a new technology. It has been developed and tested over a number of years through collaboration involving SEPA and partners across industry, science and academia. 

The latest milestone sees that collaborative science move from research and development into practical regulatory use, with SEPA publishing guidance setting out how the approach can be used. 

Mike Montague, Lead Specialist for Aquaculture at SEPA, said: 

“Our role as Scotland's environmental regulator is to make sure operators understand and meet the standards required to protect the environment. 

“Monitoring gives us important evidence about what is happening on the seabed around marine fish farms. eDNA gives us the potential to understand what that evidence is telling us much sooner. 

“That matters because where there is evidence of a potential problem, operators can respond and we can investigate and intervene sooner where required. 

“The environmental standards haven't changed and neither has our regulatory role. What has changed is the science available to support that regulation. 

“This shows what can be achieved when scientific, regulatory and industry expertise come together to solve a practical problem. We are taking innovative science and putting it to work, helping make environmental regulation more efficient and responsive while maintaining the protections Scotland's environment depends on.” 

From research to regulatory use

The new approach has been made possible through a partnership project, called BactMetBar, bringing together scientific, regulatory and industry expertise from across the aquaculture industry to develop and test a faster way of assessing seabed condition. 

It builds on previous eDNA projects and has been supported through funding from the Sustainable Aquaculture Innovation Cluster (SAIC). 

The research effort behind the new sampling method was led by the Scottish Association for Marine Science (SAMS), a partner of UHI, as well as the University of Kaiserslautern. 

The approach looks at the bacterial community within seabed sediment. Changes in that community can provide evidence about changes in environmental condition, providing a faster route to assessment than identifying and counting the organisms traditionally used to assess seabed condition. 

The BactMetBar collaboration project has already received national recognition this year after winning two prestigious industry awards - the Collaboration Award at the UK Aquaculture Awards in June and the Laboratory Excellence in Environmental Measurement award at the Environment Monitoring & Measurement Achievement Awards held on Wednesday 16^th September.  

The recognition reflects the collaborative scientific and regulatory work that has taken eDNA from research and development into practical environmental regulation. 

Dr Iain Berrill, technical director at Salmon Scotland, said: 

“Scotland’s salmon farmers have a strong track record of supporting research and innovation that delivers practical improvements on farms and in the marine environment. 

“This new approach is a great example of that, bringing together salmon farmers, scientists and regulators to develop new science and turn it into a practical tool for environmental monitoring. 

“We are constantly looking at how new technology and better science can improve our understanding of the environment around our farms and inform how we operate. 

“It is really encouraging to see this work now moving from research into practical use.” 

SAMS Associate Professor, Tom Wilding, said:  

“This will revolutionise the way that fish farms are sampled and monitored, updating a practice that has been standard for half a century. 

“The method uses a combination of machine learning and metabarcoding to tell us which bacteria are present in the sediment. A bit like a barcode on a supermarket item, we can scan the DNA sequence to see what’s there. 

“Using a random forest, which is a form of artificial intelligence, we have trained the model on 950 samples, so it knows which bacteria are most useful in predicting the health status of sediment. 

“This is far quicker than the traditional method of sampling and removes a lot of the time pressure on taxonomists delivering more manual analysis.” 

Looking ahead

Incorporating eDNA into the regulatory process also creates the potential for further benefits as experience of using the approach develops. 

Faster access to environmental information could in future support more timely monitoring and environmental management, giving operators greater opportunity to understand how the seabed is responding and make changes where appropriate. 

These remain potential future benefits. Operators will continue to be required to meet the environmental standards and monitoring requirements set through their permits. 

Notes to Editors

Further support and useful links

The development of the new seabed monitoring approach was informed by this eDNA research paper.

Further information including SEPA's regulatory guidance on eDNA seabed monitoring is available on the SEPA website. 

Partners involved in the project

• Salmon Scotland 

• Scottish Environment Protection Agency (SEPA) 

• The Technical University of Kaiserslautern (TUK) 

• Mowi Scotland Limited (Mowi) 

• Scottish Sea Farms Limited (SSF) 

• Scottish Association for Marine Science (University of the Highlands and Islands) 

• Institute for Biodiversity and Freshwater Conservation (University of the Highlands and Islands)