Using eDNA to estimate biomass of bycatch in pelagic fisheries

Abstract

In recent years, the analysis of environmental DNA (eDNA) has significantly improved, allowing for high‐resolution species identification and possible biomass quantification from water samples. Fisheries management typically requires monitoring of catches, including precise information about bycatch quantities to make sound assessments of exploitation rates. Bycatch assessment is particularly challenging in large catches (>500 T), and the current practice of visual assessment of subsampled catches is time‐consuming, requires extensive labor, and often has low precision. We explored the feasibility for applying eDNA‐based methods for studying catch composition using the pelagic North Sea herring fishery with bycatch of mackerel as a case. First, we experimentally simulate a series of catches using a range of herring and mackerel weight proportions to establish relationships under real fisheries scenarios. The relationship is subsequently used to estimate the biomass of mackerel bycatch from eDNA from three herring catches, by sampling and comparing processing water both onboard ships and at the processing factory. All samples are analyzed using species‐specific quantitative PCR (qPCR). The experiments reveled a strong correlation between DNA and weight fractions characterized by a constant overrepresentation of mackerel DNA compared to expected mackerel weight. We found that eDNA‐based and visual methods applied to the same landing reflect the within catch variability in species composition alike, however, the methods can show disparity in total estimates of mackerel biomass. Accounting for haul mixing within total landed catches increases the precision of the factory and ship eDNA‐based estimates for the same catch. We show that eDNA‐based bycatch estimates provide coherent quantitative data, and likely improve quality and reduce costs of collecting fisheries‐dependent data and thereby contribute to securing sustainable fisheries.

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

“…eDNA targeted approach is better suited for quantification of the abundance of target species (e.g. in Takahara et al, 2012;Lacoursière-Roussel et al, 2016;Yamamoto et al, 2016;Knudsen et al, 2019;Salter et al, 2019;Brys et al, 2021;Fukaya et al, 2021;Shelton et al, 2022;Urban et al, 2023), and therefore it could be applied in monitoring fish stocks and vulnerable species.…”

“…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).…”

“…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.…”

“…However, natural environmental conditions (e.g. Lacoursière-Roussel et al, 2016) and species-specific characteristics such as eDNA shed and decay (Urban et al, 2023), are source of uncertainty and need to be considered in results interpretation. Nevertheless, occupancy and process-based modelling can help to better interpret eDNA quantification results obtained from natural environments (See Section 5).…”

“…structure of the stocks. Moreover, fisheries-dependent data are also collected to monitor in situ fisheries accordingly to the authority's regulation (Bradley et al, 2019;Urban et al, 2023). Altogether, these methods give essential information to assess the status of fisheries resources and to provide scientific advice on the best management strategies to achieve a sustainable exploitation.…”