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

Scientific Reports
Isabel CanteraSébastien Brosse

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 su...Continue Reading

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Citations

Oct 9, 2019·Biodiversity Data Journal·Jérôme MurienneSébastien Brosse
Oct 10, 2020·Molecular Ecology·Alessia GuerrieriGentile Francesco Ficetola
Nov 5, 2020·PloS One·Beverly McClenaghanMehrdad Hajibabaei
Oct 16, 2020·The Science of the Total Environment·Shuping WangJianlong Li
Feb 24, 2021·Communications Biology·Cindy BesseyOliver Berry
Apr 1, 2021·Molecular Ecology Resources·Opale CoutantSébastien Brosse
Mar 30, 2021·Ecological Applications : a Publication of the Ecological Society of America·José Luis MenaArnaud Lyet
May 16, 2021·Scientific Reports·Rosetta C BlackmanFlorian Altermatt
Jun 4, 2021·Scientific Reports·Andrew BuxtonRichard A Griffiths
May 19, 2021·Molecular Ecology Resources·Laetitia MathonStéphanie Manel
Sep 2, 2021·The Science of the Total Environment·Holly A BroadhurstAllan D McDevitt
Aug 18, 2021·Molecular Ecology Resources·Christina LynggaardKristine Bohmann
Nov 2, 2021·Molecular Ecology Resources·Isabel CanteraSébastien Brosse

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Methods Mentioned

BETA
PCR

Software Mentioned

VigiDNA
R
ANOSIM
ecotag
vegan
OBITools

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