Biotic signals associated with benthic impacts of salmon farms from eDNA metabarcoding of sediments

Abstract Environmental DNA (eDNA) metabarcoding can rapidly characterize the composition and diversity of benthic communities, thus it has high potential utility for routine assessments of benthic impacts of marine finfish farming. In this study, 126 sediment grab samples from 42 stations were collected at six salmon farms in British Columbia, Canada. Benthic community changes were assessed by both eDNA metabarcoding of metazoans and macrofaunal polychaete surveys. The latter was done by analysing 11,466 individuals using a combination of morphology‐based taxonomy and DNA barcoding. Study objectives were to: (i) compare biotic signals associated with benthic impacts of salmon farming in the two data sources, and (ii) identify potential eDNA indicators to facilitate monitoring in Canada. Alpha diversity parameters were consistently reduced near fish cage edge and negatively correlated with pore‐water sulphide concentration, with coefficients ranging from −0.62 to −0.48. Although Polychaeta are a common indicator group, the negative correlation with pore‐water sulphide concentration was much stronger for Nematoda OTU richness (correlation coefficient: −0.86) than for Polychaeta (correlation coefficient: −0.38). Presence/absence of Capitella generally agreed well between the two methods despite that they differed in the volume of sediments sampled and the molecular marker used. Multiple approaches were used to identify OTUs related to organic enrichment statuses. We demonstrate that eDNA metabarcoding generates biotic signals that could be leveraged for environmental assessment of benthic impacts of fish farms in multiple ways: both alpha diversity and Nematoda OTU richness could be used to assess the spatial extent of impact, and OTUs related to organic enrichment could be used to develop local biotic indices.