Next‐generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

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...

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Vydáno v:	Molecular ecology Ročník 25; číslo 4; s. 929 - 942
Hlavní autoři:	Valentini, Alice, Taberlet, Pierre, Miaud, Claude, Civade, Raphaël, Herder, Jelger, Thomsen, Philip Francis, Bellemain, Eva, Besnard, Aurélien, Coissac, Eric, Boyer, Frédéric, Gaboriaud, Coline, Jean, Pauline, Poulet, Nicolas, Roset, Nicolas, Copp, Gordon H, Geniez, Philippe, Pont, Didier, Argillier, Christine, Baudoin, Jean‐Marc, Peroux, Tiphaine, Crivelli, Alain J, Olivier, Anthony, Acqueberge, Manon, Le Brun, Matthieu, Møller, Peter R, Willerslev, Eske, Dejean, Tony
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	England Blackwell Scientific Publications 01.02.2016 Blackwell Publishing Ltd Wiley
Témata:	amphibian Amphibians Amphibians - classification Amphibians - genetics Animals Aquatic ecosystems Biodiversity Biodiversity and Ecology Conservation biology Deoxyribonucleic acid detection probability DNA DNA Barcoding, Taxonomic - methods DNA Primers DNA, Mitochondrial - genetics Ecological studies Ecosystem Environmental DNA Environmental Monitoring Environmental Sciences fish Fishes - classification Fishes - genetics Fresh Water freshwater monitoring Oceans Oceans and Seas probability Rare species sequence analysis surveys Water analysis Water sampling wildlife management wildlife management detection probability environmental DNA amphibian monitoring fish Environmental DNA FAUNE AQUATIQUE aquatic fauna ADN LAC INVENTAIRE FAUNISTIQUE dna ichthyology animal population Fish ICHTYOLOGIE lakes Wildlife management Amphibian Detection probability Monitoring
ISSN:	0962-1083, 1365-294X, 1365-294X
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Popis
Shrnutí:	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.
Bibliografie:	http://dx.doi.org/10.1111/mec.13428 STOWA ark:/67375/WNG-2M5B4DXD-1 Waterboard de Dommel Waterboard Brabantse Delta EDF SPYGEN ONEMA Table S1 Amphibian tissue samples used for the reference database construction. Table S2 Fish tissue samples used for the reference database construction. Table S3 Geographical coordinates, sampling date and results of traditional and eDNA metabarcoding surveys for amphibians. Table S4 Location, site characteristics and sampling methods used for eDNA metabarcoding and traditional surveys for the fish comparative study. Table S5 In silico assessment of different primer pairs targeting Batrachia and Teleostei. Table S6 Number of reads obtained from the NGS runs per sample before and after bioinformatic filtering. Table S7 Number of detection events of amphibian species using eDNA metabarcoding and traditional surveys; species detection probability with confidence intervals between brackets for eDNA metabarcoding, traditional surveys and historical data and number of visits required to achieve a 95% chance of species detection. Table S8 Results from the eDNA metabarcoding survey and historical data for fish in control sites (sites 1-4). Table S9 Results from eDNA metabarcoding and traditional surveys for fish in pond ecosystems (sites 5-8). Table S10 Results from eDNA metabarcoding and traditional surveys for fish in ditch ecosystems (sites 9-12). Table S11 Results from eDNA metabarcoding and traditional surveys for fish in lake ecosystems (site 13). Table S12 Results from eDNA metabarcoding and traditional surveys for fish in stream ecosystems in the Netherlands (sites 14-17). Table S13 Results from eDNA metabarcoding and traditional surveys for fish in stream ecosystems in France (sites 18-19). Table S14 Results from eDNA metabarcoding and traditional surveys for fish in river ecosystems (sites 20-23). Table S15 Results from eDNA metabarcoding for fish in the marine ecosystem (site 23). istex:4D7493F68E343E2BAB7D9DE51124DF4CBF78D950 Parc National du Mercantour Waterboard Rijn en Ijssel Network Ecological Monitoring (NEM) ArticleID:MEC13428 Waterboard Vallei en Veluwe ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23
ISSN:	0962-1083 1365-294X 1365-294X
DOI:	10.1111/mec.13428