eDNA biomonitoring in aquaculture: planktonic threats

Farmed salmon is the UK’s second largest food export. Despite its commercial success, salmon farming is subject to up to 20% losses per annum due to harmful agents including viral and bacterial disease, parasites, jellyfish and harmful algal blooms. In many cases, these planktonic threats to salmon cause debilitating and irreversible damage to the gills. Salmon farmers monitor the plankton daily to anticipate such threats and mitigate their impacts, however traditional counts data generated are not actionable and lack the specificity or sensitivity required to predict a bloom. To this end, we aim to combine both  an environmental DNA (eDNA) approach with microscopy methods to biomonitor salmon farms and provide useful and actionable information to our aquaculture partners.

Biomonitoring by using eDNA techniques is a novel approach which provides a potentially powerful toolkit by using genetic material obtained from small volumes of seawater from in and around cultivation areas. Such material includes free DNA sloughed off metazoans or cellular material from entire organisms in the case of unicellular species. Our project team has previously provided proof-of-principle that DNA sequence-based environmental DNA metabarcoding can simultaneously identify and quantify multiple planktonic threats around salmon farms.

pilot data 2019.jpg

Pilot data on eDNA metabarcoding-based detection of multiple planktonic threats, Summer 2019 in Loch Sian, Mull. The y axis indicates the normalised proportion of reads based on the 18s rDNA locus.

In this project we will translate this proof-of-concept by: 1) Identifying key planktonic drivers of poor gill health using eDNA metabarcoding and 2) Developing and deploying a proven, customer-operated, low cost, paper-based PCR device for the detection of multiple planktonic agents on farms.

This project is funded by BBSRC and EPSRC.