--- title: Seabed Compliance image: https://appliedgenomics.co.uk/hubfs/DJI_0245-1.jpg --- [Skip to content](https://appliedgenomics.co.uk/seabed-compliance#main-content) [![Applied Genomics, eDNA, Biodiversity. Applied Genomics logo.](https://appliedgenomics.co.uk/hs-fs/hubfs/AGL%20logo-white.png?width=391&height=111&name=AGL%20logo-white.png "Applied Genomics, eDNA, Biodiversity. Applied Genomics logo.")](https://appliedgenomics.co.uk?hsLang=en) - [Home](https://appliedgenomics.co.uk) - Services - [Services](https://appliedgenomics.co.uk/services) - [Sample](https://appliedgenomics.co.uk/sample) - [Analyse](https://appliedgenomics.co.uk/analyse) - [Insights](https://appliedgenomics.co.uk/insights) - [Haplotype Analysis](https://appliedgenomics.co.uk/haplotype-analysis) - About - [Who We Are](https://appliedgenomics.co.uk/about-us) - [Case Studies](https://appliedgenomics.co.uk/case-studies-0) - [FAQs](https://appliedgenomics.co.uk/frequently-asked-questions) - [Contact Us](https://appliedgenomics.co.uk/contact) ## A Decade of Progress in eDNA-based Seabed Monitoring for Aquaculture   ## From Research Concept to Regulatory Confidence Over the past decade, environmental DNA (eDNA) has moved from research concept to operational tool, changing how aquaculture understands and manages seabed condition. Our collaboration with [Mowi](https://mowi.com/uk/), which began in 2015, has been central to that shift, taking eDNA from early trials to routine farm-scale practice. ### Building the evidence base Our early work with Mowi focused on developing eDNA-based indicators of the Infaunal Quality Index (IQI), the core metric the [Scottish Environment Protection Agency](https://www.sepa.org.uk/) (SEPA) uses to assess seabed health. We combined DNA data from three biological communities: - the bacterial microbiome - the eukaryotic microbiome - benthic meiofauna and invertebrates The results showed that DNA-derived biodiversity patterns could reliably predict traditional macrofaunal IQI values, demonstrating that eDNA could deliver faster, more scalable and more forward-looking seabed assessments. SEPA then supported the MeioMetBar (MMB) project, led by the [Scottish Association for Marine Science](https://www.sams.ac.uk/) (SAMS), which independently validated the use of the bacterial microbiome to estimate IQI through machine learning. Our datasets contributed to that evidence base, and the project was an important step towards regulatory confidence. ## Engineered for Commercial Aquaculture Producers need environmental tools that are stable, predictable and easy to run within day-to-day operations. Working within the collaborative framework and intellectual property provisions of the MMB partnership, we developed our own implementation of the same modelling approach, built for commercial reliability and straightforward integration with farm workflows. ### Applied Genomics now provides two complimentary eDNA assessment tools: - **Bacterial microbiome model:** mirrors SEPA's IQI predictions, helping farm managers anticipate likely compliance outcomes - **Whole community model:** combines the bacterial microbiome, the eukaryotic microbiome, and benthic invertebrates and meiofauna, giving a fuller ecological picture that aligns closely with traditional macrofaunal data. Together, they give producers an early, well-evidenced view of seabed condition that supports proactive management and reduces uncertainty in regulatory engagement. ## Proven Performance and the Future of eDNA Monitoring SEPA's BactMetBar project has since produced the eDNA2IQI data analysis package (Wyness et al., 2025), which is being adopted by SEPA for DNA-based seabed compliance monitoring.  Applied Genomics is currently the only company delivering operational eDNA-based benthic assessments at scale in the UK. Our workflows continue to demonstrate strong performance in real farming environments, and feedback from clients and regulators consistently highlights their reliability and clarity. Producers consistently point to the same benefits: rapid turnaround, reproducibility, and straightforward integration into existing compliance frameworks.  Looking ahead, eDNA monitoring is set to become even more integral to sustainable aquaculture. As automation and real-time analytics advance, the ability to continuously track environmental change using DNA will enable more responsive, lower-impact operations. At Applied Genomics, our focus is on making that future a reality through delivering proven, dependable, and industry-ready eDNA solutions that support both environmental stewardship and commercial success.    ### Applied Genomics are proud of what has been achieved since 2015, and we look forward to supporting industry, regulators and researchers as eDNA becomes a standard part of aquaculture monitoring ## Case Study: Tracking Post-closure Recovery with MOWI at Loch Ewe Guided by its vision of "Leading the Blue Revolution", Mowi is committed to farming in harmony with nature, a commitment reinforced by its recent biodiversity strategy. When Mowi closed its Loch Ewe farm in Wester Ross in late 2020, it launched a three-year study of seabed recovery, the first of its kind in Scotland. The project also supported a UKRI-funded PhD through the University of the Highlands and Islands. ### Our Role ### Applied Genomics provided eDNA analysis which was interpreted alongside traditional benthic surveys and habitat mapping by [Benthic Solutions](https://benthicsolutions.com/). Because eDNA captures a much broader spectrum of biodiversity than conventional sampling, it gave a more complete picture of how seabed communities changed over time. Because the site was surveyed while still operating, the study could identify where communities shifted from impacted to unimpacted, establishing a clear baseline for measuring recovery. ### Results exceeded expectations - **Within six months** of closure the distance over which the seabed was affected had halved - **Within a year** all sampling stations had almost completely recovered Salmon farming has operated in Scotland for around 50 years, yet data on post-closure recovery has been very limited. At Loch Ewe, the study provides robust evidence that seabed impacts were temporary and that recovery happened far faster than previously assumed. ### Watch the video below to learn more about the project and its findings!   Video player - scottish-salmon-farm-aerial-view-credit-saic.jpg-1 - Click to play video Basic Content ### Want to know more about our monitoring services? 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