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

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.

How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs?

“…Our results reveal that, without adequate replication, sampling variability undermines biodiversity estimates in highly diverse tropical ecosystems, such as coral reefs (Cilleros et al ., 2019; Bessey et al ., 2020; Juhel et al ., 2020; Polanco Fernández et al ., 2020). The variability of eDNA biodiversity estimates showed high compositional dissimilarity between filtration replicates so, for some locations, even extensive sampling with 6-20x 30L replicates could reach an asymptotic number of detected MOTUs.…”

“…A strict contamination protocol in field and laboratory stages was followed using disposable gloves and single-use filtration equipment. More details can be found in Polanco Fernández et al . (2020).…”

“…eDNA extraction, PCR amplification, and purification prior to library preparation were performed in separate, dedicated rooms following the protocols described in Polanco Fernández et al . (2020) and Valentini et al .…”

“…The most common approach for concentrating marine eDNA is water filtration along transects (Kumar, Eble and Gaither, 2020) but the appropriate amount of water to filter to overcome sampling variability remains underdetermined (e.g., 1L in Nguyen et al ., 2020 and 30L in Polanco Fernández et al ., 2020). An increased volume of water should lead to increased compositional similarly among replicates, but even at 2L 30-50% of the total species pool were missing in any given sample (Bessey et al ., 2020).…”

The future of biodiversity monitoring and conservation utilizing environmental DNA

“…Polanco Fernández et al. (2021) conducted an underwater visual census for fish in two bays near Santa Marta, Colombia, and found that eDNA metabarcoding detected a wider range of taxonomic groups than the visual surveys with higher efficiency of eDNA metabarcoding in detecting species with smaller body sizes and those inhabiting deeper water. Overall, it was found that eDNA metabarcoding can provide monitoring results that are comparable to, or more sensitive than, a variety of conventional monitoring methods.…”