Nanopore environmental DNA sequencing of catch water for estimating species composition in demersal bottom trawl fisheries
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 e...
Published in: | Environmental DNA |
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Format: | Article in Journal/Newspaper |
Language: | English |
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2024
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Online Access: | https://orbit.dtu.dk/en/publications/94a1d96a-a37e-4139-b42e-663865f5cde6 https://doi.org/10.1002/edn3.555 https://backend.orbit.dtu.dk/ws/files/360803657/Environmental_DNA_-_2024_-_Maggini_-_Nanopore_environmental_DNA_sequencing_of_catch_water_for_estimating_species.pdf |
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ftdtupubl:oai:pure.atira.dk:publications/94a1d96a-a37e-4139-b42e-663865f5cde6 2024-06-23T07:55:23+00:00 Nanopore environmental DNA sequencing of catch water for estimating species composition in demersal bottom trawl fisheries 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. 2024 application/pdf https://orbit.dtu.dk/en/publications/94a1d96a-a37e-4139-b42e-663865f5cde6 https://doi.org/10.1002/edn3.555 https://backend.orbit.dtu.dk/ws/files/360803657/Environmental_DNA_-_2024_-_Maggini_-_Nanopore_environmental_DNA_sequencing_of_catch_water_for_estimating_species.pdf eng eng https://orbit.dtu.dk/en/publications/94a1d96a-a37e-4139-b42e-663865f5cde6 info:eu-repo/semantics/openAccess Maggini , S , Jacobsen , M W , Urban , P , Hansen , B K , Kielgast , J , Bekkevold , D , Jardim , E , Martinsohn , J T , Carvalho , G R , Nielsen , E E & Papadopulos , A S T 2024 , ' Nanopore environmental DNA sequencing of catch water for estimating species composition in demersal bottom trawl fisheries ' , Environmental DNA , vol. 6 , no. 3 , e555 . https://doi.org/10.1002/edn3.555 Bottom trawling Bycatch and discards eDNA Landing obligation Marine fish species Metabarcoding Monitoring Nanopore sequncing /dk/atira/pure/sustainabledevelopmentgoals/life_below_water name=SDG 14 - Life Below Water article 2024 ftdtupubl https://doi.org/10.1002/edn3.555 2024-06-04T15:49:48Z 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, ... Article in Journal/Newspaper North East Atlantic Technical University of Denmark: DTU Orbit Environmental DNA 6 3 |
institution |
Open Polar |
collection |
Technical University of Denmark: DTU Orbit |
op_collection_id |
ftdtupubl |
language |
English |
topic |
Bottom trawling Bycatch and discards eDNA Landing obligation Marine fish species Metabarcoding Monitoring Nanopore sequncing /dk/atira/pure/sustainabledevelopmentgoals/life_below_water name=SDG 14 - Life Below Water |
spellingShingle |
Bottom trawling Bycatch and discards eDNA Landing obligation Marine fish species Metabarcoding Monitoring Nanopore sequncing /dk/atira/pure/sustainabledevelopmentgoals/life_below_water name=SDG 14 - Life Below Water 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. Nanopore environmental DNA sequencing of catch water for estimating species composition in demersal bottom trawl fisheries |
topic_facet |
Bottom trawling Bycatch and discards eDNA Landing obligation Marine fish species Metabarcoding Monitoring Nanopore sequncing /dk/atira/pure/sustainabledevelopmentgoals/life_below_water name=SDG 14 - Life Below Water |
description |
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, ... |
format |
Article in Journal/Newspaper |
author |
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. |
author_facet |
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. |
author_sort |
Maggini, Sara |
title |
Nanopore environmental DNA sequencing of catch water for estimating species composition in demersal bottom trawl fisheries |
title_short |
Nanopore environmental DNA sequencing of catch water for estimating species composition in demersal bottom trawl fisheries |
title_full |
Nanopore environmental DNA sequencing of catch water for estimating species composition in demersal bottom trawl fisheries |
title_fullStr |
Nanopore environmental DNA sequencing of catch water for estimating species composition in demersal bottom trawl fisheries |
title_full_unstemmed |
Nanopore environmental DNA sequencing of catch water for estimating species composition in demersal bottom trawl fisheries |
title_sort |
nanopore environmental dna sequencing of catch water for estimating species composition in demersal bottom trawl fisheries |
publishDate |
2024 |
url |
https://orbit.dtu.dk/en/publications/94a1d96a-a37e-4139-b42e-663865f5cde6 https://doi.org/10.1002/edn3.555 https://backend.orbit.dtu.dk/ws/files/360803657/Environmental_DNA_-_2024_-_Maggini_-_Nanopore_environmental_DNA_sequencing_of_catch_water_for_estimating_species.pdf |
genre |
North East Atlantic |
genre_facet |
North East Atlantic |
op_source |
Maggini , S , Jacobsen , M W , Urban , P , Hansen , B K , Kielgast , J , Bekkevold , D , Jardim , E , Martinsohn , J T , Carvalho , G R , Nielsen , E E & Papadopulos , A S T 2024 , ' Nanopore environmental DNA sequencing of catch water for estimating species composition in demersal bottom trawl fisheries ' , Environmental DNA , vol. 6 , no. 3 , e555 . https://doi.org/10.1002/edn3.555 |
op_relation |
https://orbit.dtu.dk/en/publications/94a1d96a-a37e-4139-b42e-663865f5cde6 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1002/edn3.555 |
container_title |
Environmental DNA |
container_volume |
6 |
container_issue |
3 |
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1802647972974952448 |