TY - JOUR

T1 - Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

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

Y1 - 2016

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 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.

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 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.

U2 - 10.1111/mec.13428

DO - 10.1111/mec.13428

M3 - Journal article

C2 - 26479867

VL - 25

SP - 929

EP - 942

JO - Molecular Ecology

JF - Molecular Ecology

SN - 0962-1083

IS - 4

ER -