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. As such, it has high
potential utility for routine environmental assessments of benthic
impacts of marine finfish farming. In this study, 126 sediment grab
samples from 42 stations were collected along an organic enrichment
gradient at six salmon farms in British Columbia, Canada, and benthic
biotic community changes were assessed by both eDNA metabarcoding of
metazoans and macrofaunal polychaete surveys. The latter was done by
analyzing 11,466 individuals using a combination of morpho-taxonomy and
DNA barcoding. Study objectives were to: (1) compare biotic signals
associated with benthic impacts of salmon farming in the two data types;
and (2) identify potential eDNA indicators to facilitate eDNA-based
monitoring in Canada. Across both data types, alpha diversity parameters
were reduced in sediments near fish cage edge and were negatively
correlated with pore-water sulphide concentration. Presence/absence of
known indicator taxon Capitella generally agreed well between the two
methods despite that they differed in both the volume of sediment
sampled and the molecular marker used. In eDNA data, there was a strong
negative correlation between Nematoda OTU richness and pore-water
sulphide concentration, and 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 a local biotic index.