SEPA ushers in a new era for seabed sample testing

The Scottish Environment Protection Agency (SEPA) today said that the use of environmental DNA (eDNA) to monitor the condition of the seabed around salmon farms has been incorporated into its regulatory process.

It means that farm operators can use eDNA results as evidence of seabed condition rather than traditional analysis being required in every case.

Traditionally, assessing seabed condition requires specialist analysis to identify and count the organisms living within sediment samples, which can take around 16 weeks. Results from eDNA analysis are potentially available in around six weeks.

If eDNA results show that the required environmental standards are being met, the seabed assessment can be completed without further traditional analysis.

Where results indicate potential non-compliance, a full sample of the seabed collected for eDNA analysis remains available for further traditional analysis where required.

A quicker response

SEPA said the use of eDNA significantly reduces the time between monitoring taking place and understanding what the evidence is showing, helping fish farmers respond more quickly and supporting earlier regulatory action where necessary.

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

Standards remain the same

Mike Montague, lead specialist for qquaculture at SEPA, said: “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.”

The use of eDNA has been made possible through a partnership project, called BactMetBar, bringing together scientific, regulatory, and industry expertise 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 the University of the Highland and Islands, as well as the Technical University of Kaiserslautern (TUK). Other partners in BactMetBar included salmon farmers Mowi Scotland and Scottish Sea Farms, trade body Salmon Scotland, and the Institute for Biodiversity and Freshwater Conservation (UHI).

Record of innovation

Dr Iain Berrill, technical director at Salmon Scotland, said fish farmers had 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,” said Berrill.

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

SAMS associate professor Tom Wilding said the eDNA analysis uses a combination of machine learning and metabarcoding to show 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,” explained Wilding.

“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.”

The development of eDNA was informed by the following research paper - eDNA2IQI: an eDNA/random forest-based prediction tool that accurately predicts ecological status for regulatory-compliance assessment - ScienceDirect