Comparing eDNA metabarcoding and morphology-based surveys for environmental monitoring of aquaculture enriched soft sediments.

Mr Alex Coutts¹, Dr Beth Strain¹, Professor John  Bowman², Dr David  Moreno¹, Professor Jeff Ross¹

¹Institute for Marine and Antarctic Science, Taroona, Australia, ²Tasmanian Institute for Agriculture, Sandy Bay, Australia

Abstract:

Environmental DNA (eDNA) metabarcoding of bacterial and eukaryote communities has been proposed as a cost-effective alternative to morphology-based faunal surveys for soft-sediment environments around salmon farms. However, studies comparing morphology and eDNA techniques for measuring the impact of organic enrichment on soft-sediment communities, in different directions from salmon farms, and their cost and time efficiency are lacking. Here, we performed 16S metabarcoding, 18S metabarcoding and morphology-based surveys of macrofauna on soft sediment samples (n = 36) collected at six distances, on three transects radiating in different directions from an Atlantic Salmon (Salmo salar) farm in Tasmania, Australia. The transects were subjected to high (north), medium (west) and low (east) organic enrichment based on current and sulphide concentrations. We also conducted a detailed cost-benefit analysis comparing the cost and time efficiency of morphology-based surveys against a combined 16S and 18S metabarcoding approach. Results from all methods indicated a higher impact of salmon farming on the north transect compared to the east and west transects, in terms of the Shannon diversity, species richness and relative abundances of indicator taxa. The combined metabarcoding approach was cheaper than the morphology method for 100 or more samples and more time efficient for 13 or more samples. Thus, monitoring programs involving large numbers of samples could benefit most from implementing eDNA metabarcoding approaches. Furthermore, we recommend that eDNA based salmon farm environmental monitoring programs should implement sampling designs which explicitly account for spatial variation in farm impact.

Biography:

Alex is a research assistant in the aquaculture environment interactions team at the Institute for Marine and Antarctic Science in Tasmania. Alex completed his masters research on single species eDNA detection of sea urchins and oysters in Port Phillip Bay. Alex joined IMAS in 2021 to work on the implementation of eDNA metabarcoding for salmon aquaculture environmental monitoring in Tasmania.