Species-specific detection and quantification of environmental DNA from marine fishes in the Baltic Sea

Steen Wilhelm Knudsen*, Rasmus Bach Ebert, Martin Hesselsøe, Franziska Kuntke, Jakob Hassingboe, Peter Bondgaard Mortensen, Philip Francis Thomsen, Eva Egelyng Sigsgaard, Brian Klitgaard Hansen, Einar Eg Nielsen, Peter Rask Møller

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

Biomass assesment of fish stocks is a difficult task that often involves costly fisheries trawl surveys. Trawl surveys rarely return replicate samples, as trawling attempts are expensive and difficult to reproduce. Furthermore, traditional benthic trawling is often detrimental to habitats and the organisms associated with the sea bottom. The rapidly developing field of environmental DNA (eDNA) analysis offers a new approach to non-invasive monitoring of fish. In the present study, we develop and test species-specific primers and probes for qPCR detection of eDNA from Atlantic herring (Clupea harengus), Atlantic cod (Gadus morhua), European flounder (Platichthys flesus), European plaice (Pleuronectes platessa), and Atlantic mackerel (Scomber scombrus) in the Baltic Sea. A recently published qPCR system was applied for European eel (Anguilla anguilla). Filtered water samples were collected during a stratified benthic trawl survey, enabling parallel comparisons of eDNA concentrations with biomass caught by trawling. No significant correlation was found between eDNA concentrations and the biomass of fish caught by the trawl, although an association was observed between the measured concentrations of eDNA and the known distributions and main abundances of cod, herring, plaice and flounder. This indicates that while eDNA concentrations may not be directly comparable to results from existing methods – likely because aquatic eDNA concentrations are not controlled by the same combinations of factors as e.g. trawl biomass catch – eDNA analysis could prove a useful supplement for monitoring fish stocks in the future
Original languageEnglish
JournalJournal of Experimental Marine Biology and Ecology
Volume510
Pages (from-to)31-45
ISSN0022-0981
DOIs
Publication statusPublished - 2019

Keywords

  • eDNA
  • Fish stock monitoring
  • North Eastern Atlantic Ocean
  • qPCR

Cite this

Knudsen, S. W., Ebert, R. B., Hesselsøe, M., Kuntke, F., Hassingboe, J., Mortensen, P. B., ... Møller, P. R. (2019). Species-specific detection and quantification of environmental DNA from marine fishes in the Baltic Sea. Journal of Experimental Marine Biology and Ecology, 510, 31-45. https://doi.org/10.1016/j.jembe.2018.09.004
Knudsen, Steen Wilhelm ; Ebert, Rasmus Bach ; Hesselsøe, Martin ; Kuntke, Franziska ; Hassingboe, Jakob ; Mortensen, Peter Bondgaard ; Thomsen, Philip Francis ; Sigsgaard, Eva Egelyng ; Hansen, Brian Klitgaard ; Eg Nielsen, Einar ; Møller, Peter Rask. / Species-specific detection and quantification of environmental DNA from marine fishes in the Baltic Sea. In: Journal of Experimental Marine Biology and Ecology. 2019 ; Vol. 510. pp. 31-45.
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title = "Species-specific detection and quantification of environmental DNA from marine fishes in the Baltic Sea",
abstract = "Biomass assesment of fish stocks is a difficult task that often involves costly fisheries trawl surveys. Trawl surveys rarely return replicate samples, as trawling attempts are expensive and difficult to reproduce. Furthermore, traditional benthic trawling is often detrimental to habitats and the organisms associated with the sea bottom. The rapidly developing field of environmental DNA (eDNA) analysis offers a new approach to non-invasive monitoring of fish. In the present study, we develop and test species-specific primers and probes for qPCR detection of eDNA from Atlantic herring (Clupea harengus), Atlantic cod (Gadus morhua), European flounder (Platichthys flesus), European plaice (Pleuronectes platessa), and Atlantic mackerel (Scomber scombrus) in the Baltic Sea. A recently published qPCR system was applied for European eel (Anguilla anguilla). Filtered water samples were collected during a stratified benthic trawl survey, enabling parallel comparisons of eDNA concentrations with biomass caught by trawling. No significant correlation was found between eDNA concentrations and the biomass of fish caught by the trawl, although an association was observed between the measured concentrations of eDNA and the known distributions and main abundances of cod, herring, plaice and flounder. This indicates that while eDNA concentrations may not be directly comparable to results from existing methods – likely because aquatic eDNA concentrations are not controlled by the same combinations of factors as e.g. trawl biomass catch – eDNA analysis could prove a useful supplement for monitoring fish stocks in the future",
keywords = "eDNA, Fish stock monitoring, North Eastern Atlantic Ocean, qPCR",
author = "Knudsen, {Steen Wilhelm} and Ebert, {Rasmus Bach} and Martin Hessels{\o}e and Franziska Kuntke and Jakob Hassingboe and Mortensen, {Peter Bondgaard} and Thomsen, {Philip Francis} and Sigsgaard, {Eva Egelyng} and Hansen, {Brian Klitgaard} and {Eg Nielsen}, Einar and M{\o}ller, {Peter Rask}",
year = "2019",
doi = "10.1016/j.jembe.2018.09.004",
language = "English",
volume = "510",
pages = "31--45",
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Knudsen, SW, Ebert, RB, Hesselsøe, M, Kuntke, F, Hassingboe, J, Mortensen, PB, Thomsen, PF, Sigsgaard, EE, Hansen, BK, Eg Nielsen, E & Møller, PR 2019, 'Species-specific detection and quantification of environmental DNA from marine fishes in the Baltic Sea', Journal of Experimental Marine Biology and Ecology, vol. 510, pp. 31-45. https://doi.org/10.1016/j.jembe.2018.09.004

Species-specific detection and quantification of environmental DNA from marine fishes in the Baltic Sea. / Knudsen, Steen Wilhelm; Ebert, Rasmus Bach; Hesselsøe, Martin; Kuntke, Franziska; Hassingboe, Jakob; Mortensen, Peter Bondgaard; Thomsen, Philip Francis; Sigsgaard, Eva Egelyng; Hansen, Brian Klitgaard; Eg Nielsen, Einar; Møller, Peter Rask.

In: Journal of Experimental Marine Biology and Ecology, Vol. 510, 2019, p. 31-45.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

T1 - Species-specific detection and quantification of environmental DNA from marine fishes in the Baltic Sea

AU - Knudsen, Steen Wilhelm

AU - Ebert, Rasmus Bach

AU - Hesselsøe, Martin

AU - Kuntke, Franziska

AU - Hassingboe, Jakob

AU - Mortensen, Peter Bondgaard

AU - Thomsen, Philip Francis

AU - Sigsgaard, Eva Egelyng

AU - Hansen, Brian Klitgaard

AU - Eg Nielsen, Einar

AU - Møller, Peter Rask

PY - 2019

Y1 - 2019

N2 - Biomass assesment of fish stocks is a difficult task that often involves costly fisheries trawl surveys. Trawl surveys rarely return replicate samples, as trawling attempts are expensive and difficult to reproduce. Furthermore, traditional benthic trawling is often detrimental to habitats and the organisms associated with the sea bottom. The rapidly developing field of environmental DNA (eDNA) analysis offers a new approach to non-invasive monitoring of fish. In the present study, we develop and test species-specific primers and probes for qPCR detection of eDNA from Atlantic herring (Clupea harengus), Atlantic cod (Gadus morhua), European flounder (Platichthys flesus), European plaice (Pleuronectes platessa), and Atlantic mackerel (Scomber scombrus) in the Baltic Sea. A recently published qPCR system was applied for European eel (Anguilla anguilla). Filtered water samples were collected during a stratified benthic trawl survey, enabling parallel comparisons of eDNA concentrations with biomass caught by trawling. No significant correlation was found between eDNA concentrations and the biomass of fish caught by the trawl, although an association was observed between the measured concentrations of eDNA and the known distributions and main abundances of cod, herring, plaice and flounder. This indicates that while eDNA concentrations may not be directly comparable to results from existing methods – likely because aquatic eDNA concentrations are not controlled by the same combinations of factors as e.g. trawl biomass catch – eDNA analysis could prove a useful supplement for monitoring fish stocks in the future

AB - Biomass assesment of fish stocks is a difficult task that often involves costly fisheries trawl surveys. Trawl surveys rarely return replicate samples, as trawling attempts are expensive and difficult to reproduce. Furthermore, traditional benthic trawling is often detrimental to habitats and the organisms associated with the sea bottom. The rapidly developing field of environmental DNA (eDNA) analysis offers a new approach to non-invasive monitoring of fish. In the present study, we develop and test species-specific primers and probes for qPCR detection of eDNA from Atlantic herring (Clupea harengus), Atlantic cod (Gadus morhua), European flounder (Platichthys flesus), European plaice (Pleuronectes platessa), and Atlantic mackerel (Scomber scombrus) in the Baltic Sea. A recently published qPCR system was applied for European eel (Anguilla anguilla). Filtered water samples were collected during a stratified benthic trawl survey, enabling parallel comparisons of eDNA concentrations with biomass caught by trawling. No significant correlation was found between eDNA concentrations and the biomass of fish caught by the trawl, although an association was observed between the measured concentrations of eDNA and the known distributions and main abundances of cod, herring, plaice and flounder. This indicates that while eDNA concentrations may not be directly comparable to results from existing methods – likely because aquatic eDNA concentrations are not controlled by the same combinations of factors as e.g. trawl biomass catch – eDNA analysis could prove a useful supplement for monitoring fish stocks in the future

KW - eDNA

KW - Fish stock monitoring

KW - North Eastern Atlantic Ocean

KW - qPCR

U2 - 10.1016/j.jembe.2018.09.004

DO - 10.1016/j.jembe.2018.09.004

M3 - Journal article

VL - 510

SP - 31

EP - 45

JO - Journal of Experimental Marine Biology and Ecology

JF - Journal of Experimental Marine Biology and Ecology

SN - 0022-0981

ER -