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

• Published in: Marine pollution bulletin Vol. 209; no. Pt A; p. 117172
• Main Authors: Coutts, Alexander, Zimmermann, Danielle, Davey, Adam, Bowman, John P., Ross, Donald J., Strain, Elisabeth M.A.
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01-12-2024
• Subjects: Aquaculture; eDNA metabarcoding; Environmental monitoring; Macrofauna; Soft sediment; Soft sediment; eDNA metabarcoding; Environmental monitoring; Macrofauna; Aquaculture
• ISSN: 0025-326X; 1879-3363; 1879-3363
• DOI: 10.1016/j.marpolbul.2024.117172

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.
•16S and 18S rRNA metabarcoding both detect aquaculture derived organic enrichment.•Sediment metazoan communities derived from metabarcoding and visual methods differ.•Metabarcoding was faster than visual identification for 14 or more samples.•Metabarcoding was cheaper than visual identification for 96 or more samples.