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.
authors.affiliation: SPYGEN, Savoie Technolac-Bât. Koala, 17, Rue du Lac Saint-André-BP 274, Le Bourget-du-Lac Cedex, 73375, France.
authors.forename: Alice
authors.initials: A
authors.lastname: Valentini
authors.affiliation: Laboratoire d'Ecologie Alpine (LECA), CNRS, Grenoble, 38000, France.|Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Grenoble, 38000, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Taberlet
authors.affiliation: Laboratoire Biogéographie et Ecologie des Vertébrés, CEFE UMR 5175, Montpellier, 34293, France.
authors.forename: Claude
authors.initials: C
authors.lastname: Miaud
authors.affiliation: Hydrosystems and Bioprocesses Research Unit, IRSTEA, Antony Cedex, 92761, France.
authors.forename: Raphaël
authors.initials: R
authors.lastname: Civade
authors.affiliation: RAVON, Postbus 1413, Nijmegen, 6501 BK, The Netherlands.
authors.forename: Jelger
authors.initials: J
authors.lastname: Herder
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark.
authors.forename: Philip Francis
authors.initials: PF
authors.lastname: Thomsen
authors.affiliation: SPYGEN, Savoie Technolac-Bât. Koala, 17, Rue du Lac Saint-André-BP 274, Le Bourget-du-Lac Cedex, 73375, France.
authors.forename: Eva
authors.initials: E
authors.lastname: Bellemain
authors.affiliation: Laboratoire Biogéographie et Ecologie des Vertébrés, CEFE UMR 5175, Montpellier, 34293, France.
authors.forename: Aurélien
authors.initials: A
authors.lastname: Besnard
authors.affiliation: Laboratoire d'Ecologie Alpine (LECA), CNRS, Grenoble, 38000, France.|Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Grenoble, 38000, France.
authors.forename: Eric
authors.initials: E
authors.lastname: Coissac
authors.affiliation: Laboratoire d'Ecologie Alpine (LECA), CNRS, Grenoble, 38000, France.|Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Grenoble, 38000, France.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Boyer
authors.affiliation: SPYGEN, Savoie Technolac-Bât. Koala, 17, Rue du Lac Saint-André-BP 274, Le Bourget-du-Lac Cedex, 73375, France.
authors.forename: Coline
authors.initials: C
authors.lastname: Gaboriaud
authors.affiliation: SPYGEN, Savoie Technolac-Bât. Koala, 17, Rue du Lac Saint-André-BP 274, Le Bourget-du-Lac Cedex, 73375, France.
authors.forename: Pauline
authors.initials: P
authors.lastname: Jean
authors.affiliation: Direction de l'Action Scientifique et Technique, ONEMA, Vincennes, 94300, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Poulet
authors.affiliation: Rhône-Alpes Regional Direction, ONEMA, Bron, 69500, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Roset
authors.affiliation: Centre for Environment, Fisheries and Aquaculture Science, Pakefield Road, Lowestoft, Suffolk, NR33 0HT, UK.|Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, K9J 7B8, Canada.
authors.forename: Gordon H
authors.initials: GH
authors.lastname: Copp
authors.affiliation: Laboratoire Biogéographie et Ecologie des Vertébrés, CEFE UMR 5175, Montpellier, 34293, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Geniez
authors.affiliation: Hydrosystems and Bioprocesses Research Unit, IRSTEA, Antony Cedex, 92761, France.
authors.forename: Didier
authors.initials: D
authors.lastname: Pont
authors.affiliation: Pole ONEMA/IRSTEA Hydroécologie des plans d'eau, Centre d'Aix-en-Provence, IRSTEA UR HYAX, Aix-en-Provence, 13182, France.
authors.forename: Christine
authors.initials: C
authors.lastname: Argillier
authors.affiliation: Pole ONEMA/IRSTEA Hydroécologie des plans d'eau, Centre d'Aix-en-Provence, IRSTEA UR HYAX, Aix-en-Provence, 13182, France.
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Baudoin
authors.affiliation: Pole ONEMA/IRSTEA Hydroécologie des plans d'eau, Centre d'Aix-en-Provence, IRSTEA UR HYAX, Aix-en-Provence, 13182, France.
authors.forename: Tiphaine
authors.initials: T
authors.lastname: Peroux
authors.affiliation: Le Sambuc, Tour du Valat, Arles, 13200, France.
authors.forename: Alain J
authors.initials: AJ
authors.lastname: Crivelli
authors.affiliation: Le Sambuc, Tour du Valat, Arles, 13200, France.
authors.forename: Anthony
authors.initials: A
authors.lastname: Olivier
authors.affiliation: Agence Centre-Ouest, Ecosphère, Orléans, 45000, France.
authors.forename: Manon
authors.initials: M
authors.lastname: Acqueberge
authors.affiliation: LNHE Department, EDF R&D, Chatou Cedex, 78401, France.
authors.forename: Matthieu
authors.initials: M
authors.lastname: Le Brun
authors.affiliation: Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, Copenhagen, 2100, Denmark.
authors.forename: Peter R
authors.initials: PR
authors.lastname: Møller
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark.
authors.forename: Eske
authors.initials: E
authors.lastname: Willerslev
authors.affiliation: SPYGEN, Savoie Technolac-Bât. Koala, 17, Rue du Lac Saint-André-BP 274, Le Bourget-du-Lac Cedex, 73375, France.
authors.forename: Tony
authors.initials: T
authors.lastname: Dejean
mesh_terms: D000663:Amphibians / Q000145:classification* / Q000235:genetics; D000818:Animals; D044822:Biodiversity; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D017931:DNA Primers; D004272:DNA, Mitochondrial / Q000235:genetics; D017753:Ecosystem; D004784:Environmental Monitoring; D005399:Fishes / Q000145:classification* / Q000235:genetics; D005618:Fresh Water; D009792:Oceans and Seas
chemical_list: D017931:DNA Primers; D004272:DNA, Mitochondrial
keywords: amphibian; detection probability; environmental DNA; fish; monitoring; wildlife management