Optimizing environmental DNA sampling effort for fish inventories in tropical streams and rivers

Kévin Cilleros,Isabel Cantera,Axel Cerdan,Régis Vigouroux,Alice Valentini,Pierre Taberlet,Tony Dejean,Amaia Iribar,Sébastien Brosse

doi:10.1038/s41598-019-39399-5

Abstract

Environmental DNA (eDNA) metabarcoding is a promising tool to estimate aquatic biodiversity. It is based on the capture of DNA from a water sample. The sampled water volume, a crucial aspect for efficient species detection, has been empirically variable (ranging from few centiliters to tens of liters). This results in a high variability of sampling effort across studies, making comparisons difficult and raising uncertainties about the completeness of eDNA inventories. Our aim was to determine the sampling effort (filtered water volume) needed to get optimal inventories of fish assemblages in species-rich tropical streams and rivers using eDNA. Ten DNA replicates were collected in six Guianese sites (3 streams and 3 rivers), resulting in sampling efforts ranging from 17 to 340 liters of water. We show that sampling 34 liters of water detected more than 64% of the expected fish fauna and permitted to distinguish the fauna between sites and between ecosystem types (stream versus rivers). Above 68 liters, the number of detected species per site increased slightly, with a detection rate higher than 71%. Increasing sampling effort up to 340 liters provided little additional information, testifying that filtering 34 to 68 liters is sufficient to inventory most of the fauna in highly diverse tropical aquatic ecosystems.

Highlights

In recent years, environmental DNA metabarcoding has been claimed as a promising tool to estimate biodiversity and its change through time[1,2]
A proportion of the undetected species using Environmental DNA (eDNA) are not informed in the molecular reference database, but some species were not detected referenced in our reference database
The eDNA metabarcoding approach has been claimed as an efficient tool to obtain inventories of aquatic organisms[10], but the optimal sampling effort to get those inventories has never been investigated in running waters

Summary

Introduction

Environmental DNA (eDNA) metabarcoding has been claimed as a promising tool to estimate biodiversity and its change through time[1,2]. The use of eDNA has been widely developed during the last years and has turned from the detection of specific species of amphibians, fish, mammals, insects and crustaceans[4] to the detection of whole communities[5,6,7,8,9,10] The latter studies besides reconstructing entire aquatic communities of fishes and amphibians, compared the detection performance between eDNA metabarcoding and capture-based sampling methods used to collect specimens in streams and rivers. Nascimento et al.[18] found that the volume of sampled sediments strongly impacted diversity assessments of benthic eukaryotic communities The stakes of this understanding will be higher in tropical ecosystems, where large sampling efforts are often needed[19]. Describing tropical communities can be challenging given the wide range of species diversity they host[20], and the strong contribution of rare species to tropical biodiversity and ecosystem functioning[21,22]

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