New case study: using eDNA to modernise seabed monitoring in Scottish salmon farming
Monitoring the health of the seabed around salmon farms is essential for protecting Scotland’s marine environment. Traditionally, this involves collecting sediment samples and identifying the tiny animals living within them - a process that is accurate but slow, labour‑intensive, and dependent on specialists. As regulatory requirements increase, the sector needs faster and more scalable tools to assess environmental quality.
Valued at over two million pounds, the BactMetBar project brought together Salmon Scotland, SAMS, UHI, SEPA, Mowi, Scottish Sea Farms and international research partners to develop a new approach based on environmental DNA (eDNA). Instead of identifying animals under a microscope, eDNA metabarcoding analyses fragments of DNA found in seabed sediments to reveal the biological community present.
Earlier SAIC‑funded work showed that bacterial DNA patterns could reliably predict the Infaunal Quality Index (IQI) - the metric used in Scotland to determine seabed compliance. BactMetBar expanded this into a fully operational tool, creating standard methods for sampling and processing, generating large new datasets and developing the eDNA2IQI software package. This tool uses machine‑learning models to convert bacterial DNA data into IQI predictions automatically.
Testing across multiple sites showed that the eDNA‑based approach provides predictions consistent with the natural variability of traditional assessments, while delivering results far more quickly. Additional work explored whether eDNA could also help assess conditions right at pen edges, an area where extreme enrichment can make traditional measures less reliable.
SEPA is now considering eDNA2IQI as part of future regulatory practice, supporting faster, more consistent and more cost‑effective compliance assessments for Scotland’s salmon farming sector.
The full title of this project is ‘Developing an eDNA-based tool for regulatory benthic compliance in Scottish salmon aquaculture (BactMetBar)’.
Read the case studyShare this