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

doi:10.1016/j.jembe.2018.09.004

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

28 Citations (Scopus)

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 language	English
Journal	Journal of Experimental Marine Biology and Ecology
Volume	510
Pages (from-to)	31-45
ISSN	0022-0981
DOIs	https://doi.org/10.1016/j.jembe.2018.09.004
Publication status	Published - 1 Jan 2019

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Knudsen, S. W., Ebert, R. B., Hesselsøe, M., Kuntke, F., Hassingboe, J., Mortensen, P. B., Thomsen, P. F., Sigsgaard, E. E., Hansen, B. K., Nielsen, E. E., & 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, SW, Ebert, RB, Hesselsøe, M, Kuntke, F, Hassingboe, J, Mortensen, PB, Thomsen, PF, Sigsgaard, EE, Hansen, BK, Nielsen, EE & 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

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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.",

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AU - Hassingboe, Jakob

AU - Mortensen, Peter Bondgaard

AU - Thomsen, Philip Francis

AU - Sigsgaard, Eva Egelyng

AU - Hansen, Brian Klitgaard

AU - Nielsen, Einar Eg

AU - Møller, Peter Rask

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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.

U2 - 10.1016/j.jembe.2018.09.004

DO - 10.1016/j.jembe.2018.09.004

M3 - Journal article

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EP - 45

JO - Journal of Experimental Marine Biology and Ecology

JF - Journal of Experimental Marine Biology and Ecology

ER -

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

Abstract

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