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 Citationer (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 into the environment. In this study, we tested if 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) versus 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. This article is protected by copyright. All rights reserved.

Originalsprog	Engelsk
Tidsskrift	Molecular Ecology
Vol/bind	25
Udgave nummer	4
Sider (fra-til)	929-942
Antal sider	14
ISSN	0962-1083
DOI	https://doi.org/10.1111/mec.13428
Status	Udgivet - 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, bind 25, nr. 4, s. 929-942. https://doi.org/10.1111/mec.13428

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title = "Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding",

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.",

author = "Alice Valentini and Pierre Taberlet and Claude Miaud and Rapha{\"e}l Civade and Jelger Herder and Thomsen, {Philip Francis} and Eva Bellemain and Aur{\'e}lien Besnard and Eric Coissac and Fr{\'e}d{\'e}ric Boyer and Coline Gaboriaud and Pauline Jean and Nicolas Poulet and Nicolas Roset and Copp, {Gordon H} and Philippe Geniez and Didier Pont and Christine Argillier and Jean-Marc Baudoin and Tiphaine Peroux and Crivelli, {Alain Jean} and Anthony Olivier and Manon Acqueberge and {Le Brun}, Matthieu and M{\o}ller, {Peter Rask} and Eske Willerslev and Tony Dejean",

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doi = "10.1111/mec.13428",

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AU - Valentini, Alice

AU - Taberlet, Pierre

AU - Miaud, Claude

AU - Civade, Raphaël

AU - Herder, Jelger

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

PY - 2016/2/1

Y1 - 2016/2/1

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.

U2 - 10.1111/mec.13428

DO - 10.1111/mec.13428

M3 - Journal article

C2 - 26479867

SN - 0962-1083

VL - 25

SP - 929

EP - 942

JO - Molecular Ecology

JF - Molecular Ecology

IS - 4

ER -

Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

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