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

• Published in: Environmental DNA (Hoboken, N.J.) Vol. 6; no. 3
• Main Authors: Maggini, Sara, Jacobsen, Magnus Wulff, Urban, Paulina, Hansen, Brian Klitgaard, Kielgast, Jos, Bekkevold, Dorte, Jardim, Ernesto, Martinsohn, Jann T., Carvalho, Gary R., Nielsen, Einar E., Papadopulos, Alexander S. T.
• Format: Journal Article
• Language: English
• Published: Hoboken John Wiley & Sons, Inc 01-05-2024; Wiley
• Subjects: Biodiversity; bottom trawling; Bycatch; bycatch and discards; Commercial fishing; Composition; Conserved sequence; Crustaceans; Data collection; DNA sequencing; eDNA; Effectiveness; Endangered & extinct species; Endangered species; Environmental DNA; Fish; Fisheries; Fisheries management; Fishing; Fishing vessels; Gene sequencing; Genetic diversity; landing obligation; Legislation; marine fish species; metabarcoding; monitoring; Nanopore sequencing; Seawater; Species composition; Sustainable fisheries; Sustainable practices; Threatened species; Wildlife conservation; Norway
• ISSN: 2637-4943; 2637-4943
• DOI: 10.1002/edn3.555

Bycatch and discards, representing unwanted catches, undermine sustainable fisheries and hinder the conservation of vulnerable and endangered species. To effectively monitor bycatch and enhance the effectiveness of management measures while promoting sustainable fishing practices, reliable data is essential. Here, we explore the use of Nanopore metabarcoding to analyze the catch composition in demersal bottom fisheries. We collected eDNA samples directly from an onboard catch holding tank (catch water) for 10 fishing hauls from a fishing vessel operating in the Skagerrak (North‐East Atlantic). The approach involved sequencing a combination of long (~2 kb) and short (~170–313 bp) mitochondrial amplicons and was validated by analyzing a fishery‐related mock community sample and fishing haul replicates. Overall, the detection rate accuracy was 95% for landed species, and replicates obtained from the same fishing haul showed consistent results, validating the robustness of this approach. The detection rate accuracy for all caught species observed on board (including the non‐landed fraction) was 81%. Undetected species were always limited to species in low abundance, but may also be attributed to problems with identifying closely related species due to the impact of sequencing errors and limited diagnostic variation in the genetic regions used. In the future, such biases may be reduced by using additional markers to increase species discrimination power and applying newly available technological advantages in flow cell chemistry to improve sequencing accuracy. In conclusion, this study demonstrates the effectiveness of Nanopore eDNA sequencing of catch water for estimating species composition in demersal bottom trawl fisheries, including catches of non‐commercial and threatened and vulnerable species, without disrupting fishing activities. Incorporating eDNA analysis of catch water may therefore help facilitate effective monitoring, leading to better‐informed fisheries management, biodiversity conservation efforts, and the implementation of relevant legislation such as the EU landing obligation.
Reliable data on bycatch and discards are essential for effective management and sustainable fisheries. We collected samples from a tank (catch water) on board a fishing vessel targeting demersal species to evaluate the effectiveness of Nanopore eDNA sequencing for estimating species composition. Our results indicate that eDNA analysis of catch water for estimating catch and bycatch composition is possible, showcasing its potential for non‐invasive, cost‐effective, and comprehensive species monitoring.