Over the past ten years, environmental DNA (eDNA) has shifted from a research concept to an operational tool that is changing how aquaculture understands and manages seabed condition. At Applied Genomics, our long-standing collaboration with Mowi, which began in 2015, has been instrumental in bringing eDNA from concept to routine farm‑scale practice.
Our early work with Mowi focused on developing eDNA-based indicators of the Infaunal Quality Index (IQI), the core metric used by SEPA to assess seabed health. By combining data from three target communities: the bacterial microbiome, the eukaryotic microbiome, benthic meiofauna and invertebrates, we showed that DNA-derived biodiversity patterns could reliably predict macrofaunal IQI values. This demonstrated that eDNA could deliver faster, scalable and more forward-looking environmental assessments for the sector.
SEPA’s subsequent support for the MeioMetBar project, led by the Scottish Association for Marine Science (SAMS), provided wider academic validation for using the bacterial microbiome to estimate IQI through machine learning. Our datasets contributed to that evidence base, and the project played an important role in achieving regulatory confidence.
However, aquaculture producers need environmental tools that are stable, predictable and easy to operationalise. Working within the collaborative framework and IP provisions of the MMB partnership, we developed an internal implementation of the same modelling approach, engineered specifically for commercial reliability and seamless integration with farm operations.
We now provide two complementary eDNA assessment tools used across aquaculture:
- A bacterial microbiome model that mirrors SEPA’s IQI predictions, helping farm managers anticipate likely compliance outcomes.
- A whole-community model combining the bacterial microbiome, benthic invertebrates and meiofauna, and the eukaryotic microbiome, offering a more complete ecological view that aligns closely with traditional macrofaunal data.
Together, these tools give producers high-confidence seabed insights that support proactive management and reduce uncertainty during regulatory engagement.
The BactMetBar project has since produced the eDNA2IQI package (Wyness et al., 2025), representing further academic advances. While the package is not yet publicly released, it highlights the growing momentum behind DNA-based assessment.
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 and regulators emphasise the same benefits: rapid turnaround, reproducibility and straightforward integration into existing compliance frameworks. eDNA allows farms to understand seabed condition earlier in the production cycle, adapt operations proactively and reduce the likelihood of late-stage compliance surprises.
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, delivering proven, dependable, and industry-ready eDNA solutions that support both environmental stewardship and commercial success.
We’re proud of the progress made since 2015 and look forward to supporting industry, regulators and researchers as eDNA monitoring becomes a standard component of sustainable aquaculture.