Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes. Issue 1 (2nd October 2020)

• Record Type: Journal Article
• Authors: 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
• Is Part Of: Environmental DNA. Volume 3:Issue 1(2021)
• Page Start: 142
• Page End: 156
• Publication Date: 2020-10-02
• Subjects: biodiversity -- biomonitoring -- Caribbean Sea -- environmental DNA -- reef fishes -- underwater visual census; DNA -- Periodicals; Biology -- Periodicals; Microbial ecology -- Periodicals; Biology; DNA; Microbial ecology; Electronic journals; Periodicals; 572.86
• DOI: 10.1002/edn3.140
• Languages: English
• ISSNs: 2637-4943

Abstract

Abstract: 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. Abstract : We examined the capacity of eDNA to provide accurate biodiversity measures in species‐rich ecosystems with a case study in two Colombian tropical marine reefs. We compared the results of eDNA analyses with historical data of underwater visual census monitoring. We found that eDNA allows a fast and broader detection of biodiversity and that it is applicable to species‐rich ecosystems in the tropic, but requires to increase the coverage of the reference database before replacing traditional census methods.