1. Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding
- Author
-
Philippe Geniez, Nicolas Poulet, Tiphaine Peroux, Anthony Olivier, Christine Argillier, Gordon H. Copp, Jean-Marc Baudoin, Manon Acqueberge, Alain J. Crivelli, Didier Pont, Tony Dejean, Pauline Jean, Pierre Taberlet, Eske Willerslev, Raphaël Civade, Philip Francis Thomsen, Jelger Herder, Eric Coissac, Frédéric Boyer, Nicolas Roset, Aurélien Besnard, Matthieu Le Brun, Coline Gaboriaud, Claude Miaud, Eva Bellemain, Alice Valentini, Peter Rask Møller, Centre National de la Recherche Scientifique - CNRS (FRANCE), EDF (FRANCE), Institut National de la Recherche Agronomique - INRA (FRANCE), Institut national de Recherche en Sciences et Technologies pour l'Environnement et l'Agriculture - IRSTEA (FRANCE), Institut de Recherche pour le Développement - IRD (FRANCE), Montpellier SupAgro (FRANCE), Université Grenoble Alpes - UGA (FRANCE), Centre for Environment, Fisheries & Aquaculture Science - CEFAS (UNITED KINGDOM), Ecole Pratique des Hautes Etudes - EPHE (FRANCE), Ecosphère (FRANCE), Office national de l'eau et des milieux aquatiques - ONEMA (FRANCE), RAVON (PAYS-BAS), Savoie Technolac (FRANCE), Tour du Valat - Centre de recherche pour la conservation des zones humides méditerranéennes (FRANCE), Trent University (USA), Université de Montpellier 3 (FRANCE), Université de Montpellier (FRANCE), Université de Savoie Mont Blanc - USMB (FRANCE), University of Copenhagen - UCPH (DENMARK), and Laboratoire d'écologie alpine - LECA (Grenoble, France)
- Subjects
0106 biological sciences ,0301 basic medicine ,Monitoring ,Ecology (disciplines) ,Oceans and Seas ,Biodiversité et Ecologie ,Biodiversity ,Fresh Water ,Environmental DNA ,Biology ,010603 evolutionary biology ,01 natural sciences ,DNA, Mitochondrial ,Amphibians ,03 medical and health sciences ,Environmental monitoring ,Genetics ,Animals ,DNA Barcoding, Taxonomic ,Wildlife management ,Ecosystem ,14. Life underwater ,Ecology, Evolution, Behavior and Systematics ,DNA Primers ,Ecology ,Aquatic ecosystem ,Fishes ,15. Life on land ,Amphibian ,030104 developmental biology ,Fish ,13. Climate action ,Detection probability ,Global biodiversity ,Environmental Monitoring - 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.
- Published
- 2015