Detecting aquatic and terrestrial biodiversity in a tropical estuary using environmental DNA
2021
Polanco Fernández, Andrea | Mutis Martinezguerra, Maria | Marques, Virginie | Villa‐navarro, Francisco | Borrero Pérez, Giomar Helena | Cheutin, Marie-Charlotte | Dejean, Tony | Hocdé, Régis | Juhel, Jean-Baptiste | Maire, Eva | Manel, Stéphanie | Spescha, Manuel | Valentini, Alice | Mouillot, David | Albouy, Camille | Pellissier, Loïc | MARine Biodiversity Exploitation and Conservation (UMR MARBEC) ; Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS) | Auteur indépendant | Centre d’Ecologie Fonctionnelle et Evolutive (CEFE) ; Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE) ; Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [Occitanie])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro ; Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro) | Universidad del Tolima | SPYGEN [Le Bourget-du-Lac] | Lancaster Environment Centre ; Lancaster University | Institute of Terrestrial Ecosystems (ITES) ; Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich) | Unité Écologie et Modèles pour l'Halieutique (EMH) ; Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER) | Swiss Federal Institute for Forest, Snow and Landscape Research WSL
International audience
Show more [+] Less [-]English. Estuaries are characterized by a tidal regime and are strongly influenced by hydrodynamics and host diverse and highly dynamic habitats, from fresh, brackish, or saltwater to terrestrial, whose biodiversity is especially difficult to monitor. Here, we investigated the potential of environmental DNA (eDNA) metabarcoding, with three primer sets targeting different regions of the mitochondrial DNA 12S ribosomal RNA gene, to detect vertebrate diversity in the estuary of the Don Diego River in Colombia. With eDNA, we detected not only aquatic organisms, including fishes, amphibians, and reptiles, but also a large diversity of terrestrial, arboreal, and flying vertebrates, including mammals and birds, living in the estuary surroundings. Further, the eDNA signal remained relatively localized along the watercourse. A transect from the deep outer section of the estuary, across the river mouth toward the inner section of the river, showed marked taxonomic turnover from typical marine to freshwater fishes, while eDNA of terrestrial and arboreal species was mainly found in the inner section of the estuary. Our results indicate that eDNA enables the detection of a large diversity of vertebrates and could become an important tool for biodiversity monitoring in estuaries, where water integrates information across the ecosystem.
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