Trawl and eDNA assessment of marine fish diversity, seasonality, and relative abundance in coastal New Jersey, USA 

Abstract

Environmental DNA (eDNA) technology potentially improves the monitoring of marine fish populations. Realizing this promise awaits better understanding of how eDNA relates to fish presence and abundance. Here, we evaluate performance by comparing bottom trawl catches to eDNA from concurrent water samples. In conjunction with New Jersey Ocean Trawl Survey, 1-l water samples were collected at surface and depth prior to tows at about one-fourth of Survey sites in January, June, August, and November 2019. eDNA fish diversity from 1 l was same as or higher than trawl fish diversity from 66 M litres swept by one tow. Most (70–87%) species detected by trawl in a given month were also detected by eDNA, and vice versa, including nearly all (92–100%) abundant species. Trawl and eDNA peak seasonal abundance agreed for ∼70% of fish species. In log-scale comparisons by month, eDNA species reads correlated with species biomass, and more strongly with an allometric index calculated from biomass. In this 1-year study, eDNA reporting largely concorded with monthly trawl estimates of marine fish species richness, composition, seasonality, and relative abundance. Piggybacking eDNA onto an existing survey provided a relatively low-cost approach to better understand eDNA for marine fish stock assessment.

Fieldable Environmental DNA Sequencing to Assess Jellyfish Biodiversity in Nearshore Waters of the Florida Keys, United States

“…Accordingly, eDNA-based investigations have proven to be as valuable as traditional survey methods that require capture and subsampling of target organisms. Importantly, eDNA methods are a less-intrusive approach to studying invasive or declining species (Zhou et al, 2013;Bucklin et al, 2016;Holman et al, 2019;Nelson-Chorney et al, 2019), documenting the distribution of difficult to sample taxa (Parsons et al, 2018), and estimating relative seasonal biomass of target species (Takasu et al, 2019;Stoeckle et al, 2020). Marine-derived eDNA has also been likened to a "barometer of disturbance" with respect to its potential to assess anthropogenic effects on ecosystems (Dibattista et al, 2020).…”

Characterizing Industrial and Artisanal Fishing Vessel Catch Composition Using Environmental DNA and Satellite-Based Tracking Data

“…Here, we have demonstrated that eDNA barcoding can be employed to characterize the species composition of captured fish from the meltwater leftover in industrial and artisanal fishing operations. eDNA is gaining popularity and utility in fisheries and seafood research and has the potential to be a potent and complementary tool to the growing number of approaches to improving traceability throughout the seafood supply chain [ 38 , 40 , 54 , 55 ]. Built upon nearly two decades of studies applying the well-vetted concept of DNA barcoding to identify fish to species level [ 16 , 56 ], the eDNA approach is positioned to be both a familiar and a transformative tool in improving seafood monitoring.…”

“…Lastly, we were unable to identify species relative abundance or biomass from a catch. The ability to use eDNA metabarcoding for abundance or biomass estimation remains equivocal [ 65 ], although recent applications appear promising [ 40 , 66 ]. Importantly, theoretical advancement in our understanding of PCR bias suggests that the application of mock communities can be strategically used to allow for the correction and estimation of abundance [ 67 , 68 ].…”

“…To date, there have been successful applications of eDNA to identify unique haplotypes associated with specific stock structures and geographic location [ 72 , 73 , 74 , 75 ]. As these methods improve, such applications could provide critical information for not only identifying species from fishing holds, but also stocks and likely geographic origin [ 40 , 76 ], aiding in the management and traceability of fishing fleets. To meet the objectives of national and multinational fisheries policies to improve seafood traceability and combat IUU fishing, transformative action should aim to (a) apply the most appropriate technologies that are also portable and accessible [ 77 ] and (b) build a monitoring and enforcement capacity that spans from fisher to consumer [ 5 ].…”

“…While eDNA methods are a relatively new approach and efforts are underway to reduce uncertainty and improve accuracy in validating species presence, the realized benefits for fisheries include non-lethal assessments, early detection of invasive species, and cost effectiveness [ 27 , 32 , 38 ]. eDNA also holds promise for aiding in assessing fish biomass [ 39 , 40 ], screening for threatened species unintentionally corralled as fisheries by-catch [ 41 ], conducting gut content analysis [ 42 ], investigating holobiont/microbiome biodiversity [ 43 ], and tracking the frequency and impact of species that escape from aquaculture farms into open-water systems [ 44 ]. With growing national and international support to improve the MCS of fisheries, eDNA is an emerging tool that could be leveraged early in the seafood supply chain at points where monitoring has been previously limited or inaccessible.…”