eDNA based bycatch assessment in pelagic fish catches

Abstract

Pelagic fish like herring, sardines, and mackerel constitute an essential and nutritious human food source globally. Their sustainable harvest is promoted by the application of precise, accurate, and cost-effective methods for estimating bycatch. Here, we experimentally test the new concept of using eDNA for quantitative bycatch assessment on the illustrative example of the Baltic Sea sprat fisheries with herring bycatch. We investigate the full pipeline from sampling of production water on vessels and in processing factories to the estimation of species weight fractions. Using a series of controlled mixture experiments, we demonstrate that the eDNA signal from production water shows a strong, seasonally consistent linear relationship with herring weight fractions, however, the relationship is influenced by the molecular method used (qPCR or metabarcoding). In four large sprat landings analyzed, despite examples of remarkable consistency between eDNA and visual reporting, estimates of herring bycatch biomass varied between the methods applied, with the eDNA-based estimates having the highest precision for all landings analyzed. The eDNA-based bycatch assessment method has the potential to improve the quality and cost effectiveness of bycatch assessment in large pelagic fisheries catches and in the long run lead to more sustainable management of pelagic fish as a precious marine resource.

Nanopore environmental DNA sequencing of catch water for estimating species composition in demersal bottom trawl fisheries

“…The development of a quantitative eDNA assay tailored to the complexities of fisheries catches represents a promising area for future research. This holds true for both demersal (Afzali et al, 2021;Kirtane et al, 2021;Maiello et al, 2023;Russo et al, 2021;Stoeckle et al, 2021) and pelagic fisheries (Urban et al, 2022(Urban et al, , 2023(Urban et al, , 2024, offering more precise insights into catch composition and enhancing the utility of eDNA analysis in fisheries management.…”

“…Furthermore, eDNA has recently emerged as a promising tool for assessing the abundance of Atlantic mackerel bycatch in Atlantic herring pelagic fisheries (Urban et al, 2022), as well as analyzing catch mixtures of European sprat and Atlantic herring (Urban et al, 2023(Urban et al, , 2024. Finally, comparisons between eDNA in seawater and bottom trawl catches revealed significant correlations, demonstrating the overlap in species detection in different environments, including subarctic deep-sea habitats (Thomsen et al, 2016), coastal areas (Stoeckle et al, 2021), demersal fish communities (Afzali et al, 2021), and oceanic waters (Salter et al, 2019).…”