Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

Alice Valentini; Pierre Taberlet; Claude Miaud; Raphaël Civade; Jelger Herder; Philip Francis Thomsen; Eva Bellemain; Aurélien Besnard; Eric Coissac; Frédéric  Boyer; Coline Gaboriaud; Pauline Jean; Nicolas Poulet; Nicolas Roset; Gordon H Copp; Philippe Geniez; Didier Pont; Christine Argillier; Jean-Marc Baudoin; Tiphaine Peroux; Alain Jean Crivelli; Anthony Olivier; Manon Acqueberge; Matthieu Le Brun; Peter Rask Møller; Eske Willerslev; Tony Dejean

doi:10.1111/mec.13428

Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

Alice Valentini, Pierre Taberlet, Claude Miaud, Raphaël Civade, Jelger Herder, Philip Francis Thomsen, Eva Bellemain, Aurélien Besnard, Eric Coissac, Frédéric Boyer, Coline Gaboriaud, Pauline Jean, Nicolas Poulet, Nicolas Roset, Gordon H Copp, Philippe Geniez, Didier Pont, Christine Argillier, Jean-Marc Baudoin, Tiphaine PerouxAlain Jean Crivelli, Anthony Olivier, Manon Acqueberge, Matthieu Le Brun, Peter Rask Møller, Eske Willerslev, Tony Dejean

399 Citations (Scopus)

Abstract

Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for assessing and monitoring aquatic biodiversity, especially for rare and secretive species, are important for efficient and timely management. Recent advances in DNA sequencing have provided a new tool for species detection from DNA present in the environment. In this study, we tested whether an environmental DNA (eDNA) metabarcoding approach, using water samples, can be used for addressing significant questions in ecology and conservation. Two key aquatic vertebrate groups were targeted: amphibians and bony fish. The reliability of this method was cautiously validated in silico, in vitro and in situ. When compared with traditional surveys or historical data, eDNA metabarcoding showed a much better detection probability overall. For amphibians, the detection probability with eDNA metabarcoding was 0.97 (CI = 0.90-0.99) vs. 0.58 (CI = 0.50-0.63) for traditional surveys. For fish, in 89% of the studied sites, the number of taxa detected using the eDNA metabarcoding approach was higher or identical to the number detected using traditional methods. We argue that the proposed DNA-based approach has the potential to become the next-generation tool for ecological studies and standardized biodiversity monitoring in a wide range of aquatic ecosystems.

Original language	English
Journal	Molecular Ecology
Volume	25
Issue number	4
Pages (from-to)	929-942
Number of pages	14
ISSN	0962-1083
DOIs	https://doi.org/10.1111/mec.13428
Publication status	Published - 1 Feb 2016

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Valentini, A., Taberlet, P., Miaud, C., Civade, R., Herder, J., Thomsen, P. F., Bellemain, E., Besnard, A., Coissac, E., Boyer, F., Gaboriaud, C., Jean, P., Poulet, N., Roset, N., Copp, G. H., Geniez, P., Pont, D., Argillier, C., Baudoin, J-M., ... Dejean, T. (2016). Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology, 25(4), 929-942. https://doi.org/10.1111/mec.13428

Valentini, A, Taberlet, P, Miaud, C, Civade, R, Herder, J, Thomsen, PF, Bellemain, E, Besnard, A, Coissac, E, Boyer, F, Gaboriaud, C, Jean, P, Poulet, N, Roset, N, Copp, GH, Geniez, P, Pont, D, Argillier, C, Baudoin, J-M, Peroux, T, Crivelli, AJ, Olivier, A, Acqueberge, M, Le Brun, M, Møller, PR , Willerslev, E & Dejean, T 2016, 'Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding', Molecular Ecology, vol. 25, no. 4, pp. 929-942. https://doi.org/10.1111/mec.13428

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abstract = "Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for assessing and monitoring aquatic biodiversity, especially for rare and secretive species, are important for efficient and timely management. Recent advances in DNA sequencing have provided a new tool for species detection from DNA present in the environment. In this study, we tested whether an environmental DNA (eDNA) metabarcoding approach, using water samples, can be used for addressing significant questions in ecology and conservation. Two key aquatic vertebrate groups were targeted: amphibians and bony fish. The reliability of this method was cautiously validated in silico, in vitro and in situ. When compared with traditional surveys or historical data, eDNA metabarcoding showed a much better detection probability overall. For amphibians, the detection probability with eDNA metabarcoding was 0.97 (CI = 0.90-0.99) vs. 0.58 (CI = 0.50-0.63) for traditional surveys. For fish, in 89% of the studied sites, the number of taxa detected using the eDNA metabarcoding approach was higher or identical to the number detected using traditional methods. We argue that the proposed DNA-based approach has the potential to become the next-generation tool for ecological studies and standardized biodiversity monitoring in a wide range of aquatic ecosystems.",

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AU - Thomsen, Philip Francis

AU - Bellemain, Eva

AU - Besnard, Aurélien

AU - Coissac, Eric

AU - Boyer, Frédéric

AU - Gaboriaud, Coline

AU - Jean, Pauline

AU - Poulet, Nicolas

AU - Roset, Nicolas

AU - Copp, Gordon H

AU - Geniez, Philippe

AU - Pont, Didier

AU - Argillier, Christine

AU - Baudoin, Jean-Marc

AU - Peroux, Tiphaine

AU - Crivelli, Alain Jean

AU - Olivier, Anthony

AU - Acqueberge, Manon

AU - Le Brun, Matthieu

AU - Møller, Peter Rask

AU - Willerslev, Eske

AU - Dejean, Tony

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N2 - Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for assessing and monitoring aquatic biodiversity, especially for rare and secretive species, are important for efficient and timely management. Recent advances in DNA sequencing have provided a new tool for species detection from DNA present in the environment. In this study, we tested whether an environmental DNA (eDNA) metabarcoding approach, using water samples, can be used for addressing significant questions in ecology and conservation. Two key aquatic vertebrate groups were targeted: amphibians and bony fish. The reliability of this method was cautiously validated in silico, in vitro and in situ. When compared with traditional surveys or historical data, eDNA metabarcoding showed a much better detection probability overall. For amphibians, the detection probability with eDNA metabarcoding was 0.97 (CI = 0.90-0.99) vs. 0.58 (CI = 0.50-0.63) for traditional surveys. For fish, in 89% of the studied sites, the number of taxa detected using the eDNA metabarcoding approach was higher or identical to the number detected using traditional methods. We argue that the proposed DNA-based approach has the potential to become the next-generation tool for ecological studies and standardized biodiversity monitoring in a wide range of aquatic ecosystems.

AB - Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for assessing and monitoring aquatic biodiversity, especially for rare and secretive species, are important for efficient and timely management. Recent advances in DNA sequencing have provided a new tool for species detection from DNA present in the environment. In this study, we tested whether an environmental DNA (eDNA) metabarcoding approach, using water samples, can be used for addressing significant questions in ecology and conservation. Two key aquatic vertebrate groups were targeted: amphibians and bony fish. The reliability of this method was cautiously validated in silico, in vitro and in situ. When compared with traditional surveys or historical data, eDNA metabarcoding showed a much better detection probability overall. For amphibians, the detection probability with eDNA metabarcoding was 0.97 (CI = 0.90-0.99) vs. 0.58 (CI = 0.50-0.63) for traditional surveys. For fish, in 89% of the studied sites, the number of taxa detected using the eDNA metabarcoding approach was higher or identical to the number detected using traditional methods. We argue that the proposed DNA-based approach has the potential to become the next-generation tool for ecological studies and standardized biodiversity monitoring in a wide range of aquatic ecosystems.

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SP - 929

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JO - Molecular Ecology

JF - Molecular Ecology

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ER -

Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

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