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Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

Valentini, Alice and Taberlet, Pierre and Miaud, Claude and Civade, Raphael and Herder, Jelger and Thomsen, Philip Francis and Bellemain, Eva and Besnard, Aurelien and Coissac, Eric and Boyer, Frederic and Gaboriaud, Coline and Jean, Pauline and Poulet, Nicolas and Roset, Nicolas and Copp, Gordon H. and Geniez, Philippe and Pont, Didier and Argillier, Christine and Baudoin, Jean-Marc and Peroux, Tiphaine and Crivelli, Alain J. and Olivier, Anthony and Acqueberge, Manon and Le Brun, Matthieu and Moller, Peter R. and Willerslev, Eske and Dejean, Tony Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. (2015) Molecular Ecology, 25 (4). 929-942. ISSN 0962-1083

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Official URL: https://doi.org/10.1111/mec.13428

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, invitro and insitu. 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. see also the Perspective by Hoffmann, Schubert and Calvignac-Spencer.

Item Type:Article
HAL Id:hal-01419572
Audience (journal):International peer-reviewed journal
Uncontrolled Keywords:
Institution:French research institutions > Centre National de la Recherche Scientifique - CNRS (FRANCE)
Other partners > EDF (FRANCE)
French research institutions > Institut National de la Recherche Agronomique - INRA (FRANCE)
French research institutions > Institut national de Recherche en Sciences et Technologies pour l'Environnement et l'Agriculture - IRSTEA (FRANCE)
French research institutions > Institut de Recherche pour le Développement - IRD (FRANCE)
Other partners > Montpellier SupAgro (FRANCE)
Other partners > Université Grenoble Alpes - UGA (FRANCE)
Other partners > Centre for Environment, Fisheries & Aquaculture Science - CEFAS (UNITED KINGDOM)
Other partners > Ecole Pratique des Hautes Etudes - EPHE (FRANCE)
Other partners > Ecosphère (FRANCE)
Other partners > Office national de l'eau et des milieux aquatiques - ONEMA (FRANCE)
Other partners > RAVON (PAYS-BAS)
Other partners > Savoie Technolac (FRANCE)
Other partners > Tour du Valat - Centre de recherche pour la conservation des zones humides méditerranéennes (FRANCE)
Other partners > Trent University (USA)
Other partners > Université de Montpellier 3 (FRANCE)
Other partners > Université de Montpellier (FRANCE)
Other partners > Université de Savoie Mont Blanc - USMB (FRANCE)
Other partners > University of Copenhagen - UCPH (DENMARK)
Laboratory name:
Funders:
SPYGEN - ONEMA - EDF - Parc National du Mercantour - STOWA - Waterboard Brabantse Delta - Waterboard Rijn en Ijssel - Waterboard Vallei en Veluwe - Waterboard de Dommel - Network Ecological Monitoring (NEM)
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Deposited By: Nicolas POULET
Deposited On:03 Apr 2019 12:22

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