Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes

Type Article
Date 2021-01
Language English
Author(s) Polanco Fernández Andrea1, Marques Virginie2, 3, Fopp Fabian4, 5, Juhel Jean‐baptiste2, Borrero‐pérez Giomar Helena1, Cheutin Marie‐charlotte2, Dejean Tony6, González Corredor Juan David1, Acosta‐chaparro Andrés1, Hocdé Régis2, Eme David7, Maire Eva2, 8, Spescha Manuel4, 5, Valentini Alice6, Manel Stéphanie3, Mouillot David2, Albouy CamilleORCID7, Pellissier Loïc4, 5
Affiliation(s) 1 : Programa de Biodiversidad y Ecosistemas Marinos Museo de Historia Natural Marina de Colombia (MHNMC) Instituto de Investigaciones Marinas y Costeras‐INVEMAR Santa Marta, Colombia
2 : MARBEC CNRS Ifremer IRD University of Montpellier Montpellier, France
3 : EPHE CNRS UM, UM3 IRD UMR5175 CEFE PSL Research University Montpellier, France
4 : Landscape Ecology Institute of Terrestrial Ecosystems Department of Environmental Systems Science ETH Zürich Zürich ,Switzerland
5 : Unit of Land Change Science Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf ,Switzerland
6 : SPYGEN Le Bourget‐du‐Lac, France
7 : Unité Ecologie et Modèles pour l'Halieutique EMH IFREMER Nantes ,France
8 : Lancaster Environment Centre Lancaster University Lancaster, UK
Source Environmental DNA (2637-4943) (Wiley), 2021-01 , Vol. 3 , N. 1 , P. 142-156
DOI 10.1002/edn3.140
Note Special Issue: The future of biodiversity monitoring and conservation utilizing environmental DNA
Keyword(s) biodiversity, biomonitoring, Caribbean Sea, environmental DNA, reef fishes, underwater visual census

Environmental DNA (eDNA) analysis is a revolutionary method to monitor marine biodiversity from animal DNA traces. Examining the capacity of eDNA to provide accurate biodiversity measures in species‐rich ecosystems such as coral reefs is a prerequisite for their application in long‐term monitoring. Here, we surveyed two Colombian tropical marine reefs, the island of Providencia and Gayraca Bay near Santa Marta, using eDNA and underwater visual census (UVC) methods. We collected a large quantity of surface water (30 L per filter) above the reefs and applied a metabarcoding protocol using three different primer sets targeting the 12S mitochondrial DNA, which are specific to the vertebrates Actinopterygii and Elasmobranchii. By assigning eDNA sequences to species using a public reference database, we detected the presence of 107 and 85 fish species, 106 and 92 genera, and 73 and 57 families in Providencia and Gayraca Bay, respectively. Of the species identified using eDNA, 32.7% (Providencia) and 18.8% (Gayraca) were also found in the UVCs. We further found congruence in genus and species richness and abundance between eDNA and UVC approaches in Providencia but not in Gayraca Bay. Mismatches between eDNA and UVC had a phylogenetic and ecological signal, with eDNA detecting a broader phylogenetic diversity and more effectively detecting smaller species, pelagic species and those in deeper habitats. Altogether, eDNA can be used for fast and broad biodiversity surveys and is applicable to species‐rich ecosystems in the tropics, but improved coverage of the reference database is required before this new method could serve as an effective complement to traditional census methods.

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Polanco Fernández Andrea, Marques Virginie, Fopp Fabian, Juhel Jean‐baptiste, Borrero‐pérez Giomar Helena, Cheutin Marie‐charlotte, Dejean Tony, González Corredor Juan David, Acosta‐chaparro Andrés, Hocdé Régis, Eme David, Maire Eva, Spescha Manuel, Valentini Alice, Manel Stéphanie, Mouillot David, Albouy Camille, Pellissier Loïc (2021). Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes. Environmental DNA, 3(1), 142-156. Publisher's official version : , Open Access version :