A comparison of visual and molecular methods for inferring biological communities in aquaculture enriched sediments - Impact assessment and cost-benefit analysis

Abstract

Nutrients introduced to the environment by finfish aquaculture pose environmental risks, which can be mitigated by robust environmental monitoring. Biological communities in soft sediments are good indicators of aquaculture derived environmental changes. Traditionally, monitoring programs have visually surveyed macrofauna communities. However, DNA metabarcoding is a potentially more efficient alternative. We compared alpha diversity, multivariate dispersion and taxonomic composition of macrofauna communities with metabarcoding derived bacterial and eukaryote communities along an organic enrichment gradient at a salmon farm in Tasmania, Australia. Additionally, we conducted a cost-benefit analysis comparing the approaches. All methods identified indicator taxa that changed in abundance over the enrichment gradient. Macrofauna analysis was the most sensitive method for detecting changes in alpha diversity, while metabarcoding was most sensitive for multivariate dispersion. Taxonomic composition of animal communities derived from the two methods differed drastically. Metabarcoding was cheaper than macrofauna for ≥93 samples and quicker for ≥14 samples.

Keywords: Aquaculture; Environmental monitoring; Macrofauna; Soft sediment; eDNA metabarcoding.