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      Environmental DNA reveals quantitative patterns of fish biodiversity in large rivers despite its downstream transportation

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          Abstract

          Despite the ecological and societal importance of large rivers, fish sampling remains costly and limited to specific habitats (e.g., river banks). Using an eDNA metabarcoding approach, we regularly sampled 500 km of a large river (Rhône River). Comparisons with long-term electrofishing surveys demonstrated the ability of eDNA metabarcoding to qualitatively and quantitatively reveal fish assemblage structures (relative species abundance) but eDNA integrated a larger space than the classical sampling location. Combination of a literature review and field data showed that eDNA behaves in the water column like fine particulate organic matter. Its detection distance varied from a few km in a small stream to more than 100 km in a large river. To our knowledge, our results are the first demonstration of the capacity of eDNA metabarcoding to describe longitudinal fish assemblage patterns in a large river, and metabarcoding appears to be a reliable, cost-effective method for future monitoring.

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          Most cited references37

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          Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

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            Environmental DNA for wildlife biology and biodiversity monitoring.

            Extraction and identification of DNA from an environmental sample has proven noteworthy recently in detecting and monitoring not only common species, but also those that are endangered, invasive, or elusive. Particular attributes of so-called environmental DNA (eDNA) analysis render it a potent tool for elucidating mechanistic insights in ecological and evolutionary processes. Foremost among these is an improved ability to explore ecosystem-level processes, the generation of quantitative indices for analyses of species, community diversity, and dynamics, and novel opportunities through the use of time-serial samples and unprecedented sensitivity for detecting rare or difficult-to-sample taxa. Although technical challenges remain, here we examine the current frontiers of eDNA, outline key aspects requiring improvement, and suggest future developments and innovations for research. Copyright © 2014 Elsevier Ltd. All rights reserved.
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              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 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.
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                Author and article information

                Contributors
                didier.pont@boku.ac.at
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                10 July 2018
                10 July 2018
                2018
                : 8
                : 10361
                Affiliations
                [1 ]SPYGEN, 17 rue du Lac Saint-André, Savoie Technolac, 73370 Le Bourget du Lac, France
                [2 ]VIGILIFE, 17 rue du Lac Saint-André, Savoie Technolac, 73370 Le Bourget du Lac, France
                [3 ]ISNI 0000 0001 2298 5320, GRID grid.5173.0, Institute of Hydrobiology and Aquatic Ecosystem Management (IHG), , University of Natural Resources and Life Sciences, ; Gregor-Mendel-Strasse 33, 1180 Vienna, Austria
                [4 ]Compagnie Nationale du Rhône, Direction de l’Ingénierie, 2 rue André Bonin, 69004 Lyon, France
                [5 ]EDF R&D, LNHE (Laboratoire National d’Hydraulique et Environnement), 6 quai Watier, 78401 Chatou Cedex, France
                [6 ]French National Agency for Biodiversity, Auvergne-Rhone-Alpes Regional Directorate, Parc de Parilly, Chemin des Chasseurs, 69500 Bron, France
                [7 ]PRO FISCH OG Ecological Consultants, Hörlgasse 6, A-1090 Vienna, Austria
                Author information
                http://orcid.org/0000-0001-5829-5479
                http://orcid.org/0000-0003-0920-773X
                Article
                28424
                10.1038/s41598-018-28424-8
                6039509
                29991759
                afafaa25-3770-49aa-91d9-9698f8c3171f
                © The Author(s) 2018

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 19 March 2018
                : 18 June 2018
                Funding
                Funded by: Compagnie Nationale du Rhône Association Beauval Nature ANR Aqua-DNA
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