Atlantic cod (Gadus morhua) assessment approaches in the North and Baltic Sea: A comparison of environmental DNA analysis versus bottom trawl sampling

Abstract

The assessment of fish stocks is often dependent on scientific trawl fisheries surveys, which are both invasive and costly. The analysis of environmental DNA (eDNA) from water samples is regarded as a non-invasive and cost-effective alternative, but meaningful performance evaluations are required for a wider application. The goal of this study was to comparatively analyze a newly developed, more sensitive real-time PCR based eDNA approach with bottom trawl fisheries catches to locally detect and quantify Atlantic cod (Gadus morhua) in the North and Baltic Seas. With a species-specificity of the qPCR assay of 100%, a minimal limit of 15 Cytochrome b eDNA copies was determined for the detection of cod. In addition, a Gaussian processing regression proved a significant correlation (95%) between eDNA (copies per L of water) and cod biomass (CPUE/Ha) found by bottom trawling. The results presented here prove the potential of eDNA analyses for quantitative assessments of commercial fish stocks in the open ocean, although additional comparative analyses are needed to demonstrate its performance under different oceanographic conditions.

Tide impacts the dispersion of eDNA from nearshore net pens in a dynamic high‐latitude marine environment

“…Similarly, a study of eDNA from four Atlantic salmon farms, raising adult fish, detected eDNA farther than 5 km from the nearest farm—consistent with the substantially larger biomass among the Atlantic salmon farms (Shea et al., 2022). More broadly, the relationship between biomass/abundance and eDNA concentration has been correlated with trawl catches (Kasmi et al., 2023; Maes et al., 2023; Salter et al., 2019), acoustic data (Shelton et al., 2022), beach seines (Shelton et al., 2019), and angling catches (Ogonowski et al., 2023). These studies generally identify a positive relationship between biomass and DNA concentration, presumably due to increased DNA shed by more individuals.…”

State-of-the-art of data analyses in environmental DNA approaches towards its applicability to sustainable fisheries management

“…When designed stringently and after thorough validation, these are highly reliable and often effectively linked to the biomass and abundance of the target organism (e.g. in Takahara et al, 2012;Doi et al, 2015;Lacoursière-Roussel et al, 2016;Yamamoto et al, 2016;Capo et al, 2019;Knudsen et al, 2019;Salter et al, 2019;LeBlanc et al, 2020;Brys et al, 2021;Fukaya et al, 2021;Shelton et al, 2022;Kasmi et al, 2023;Urban et al, 2023). Nowadays, the main technique used in species-specific detection of environmental samples is real-time quantitative PCR (qPCR).…”

“…Studies also considering the different variables that may be having an influence on eDNA concentration (such as temperature or salinity) use linear mixed-effects models (Itakura et al, 2019) or generalized linear models (Thomsen et al, 2016;Tillotson et al, 2018;Knudsen et al, 2019). However, Kasmi et al (2023) found differences in the relationship between eDNA copies and biomass depending on the statistical methods, getting better results when using Gaussian Process Regression (GPR), neural network and non-linear regression model, than with simple regression models.…”

“…High correspondence between abundance or biomass estimated from traditional and eDNA methods have been found (eg. Shelton et al, 2022;Kasmi et al, 2023;Urban et al, 2023). However, natural environmental conditions (e.g.…”

“…Stoeckle et al, 2021, see BOX 1-TASK 3) and it is advisable when monitoring fish communities.Moreover, uncertainties about detection probabilities are decreased when DNA studies are performed in fisheries-related conditions (e.g. Russo et al, 2021;Stoeckle et al, 2021;Maiello et al, 2022;Kasmi et al, 2023, andUrban et al, 2023 presented in BOX 1-TASK 4).…”