Comparing environmental metabarcoding and trawling survey of demersal fish communities in the Gulf of St. Lawrence, Canada

Abstract Biodiversity assessment is an important part of conservation management that ideally can be accomplished with noninvasive methods without influencing the structure and functioning of ecosystems. Environmental DNA (eDNA) metabarcoding has provided a promising tool to enable fast and comprehensive monitoring of entire ecosystems, but widespread adoption of this technique requires performance evaluations that compare it with conventional surveys. We compared eDNA metabarcoding and trawling data to evaluate their efficiency to characterize demersal fish communities in the Estuary and Gulf of Saint‐Lawrence, Canada. Seawater and bottom trawling samples were collected in parallel at 84 stations. For a subset of 30 of these stations, water was also collected at three different depths (15, 50, and 250 m) across the water column. An eDNA metabarcoding assay based on the 12S mitochondrial gene using the MiFish‐U primers was applied to detect fish eDNA. We detected a total of 88 fish species with both methods combined, with 72 species being detected by eDNA, 64 species detected by trawl, and 47 species (53%) overlapped between both methods. eDNA was more efficient for quantifying species richness, mainly because it detected species known to be less vulnerable to trawling gear. Our results indicated that the relative abundance estimated by eDNA and trawl is significantly correlated for species detected by both methods, while the relationship was also influenced by environmental variables (temperature, depth, salinity, and oxygen). Integrating eDNA metabarcoding to bottom trawling surveys could provide additional information on vertical fish distribution in the water column. Environmental DNA metabarcoding thus appears to be a reliable and complementary approach to trawling surveys for documenting fish biodiversity, including for obtaining relative quantitative estimates in the marine environment.