Species detection using environmental DNA from water samples

Gentile Francesco Ficetola; Claude Miaud; FRANÇOIS POMPANON; PIERRE TABERLET

doi:10.1098/rsbl.2008.0118

journal article Apr 09, 2008

Species detection using environmental DNA from water samples

Gentile Francesco Ficetola

Claude Miaud FRANÇOIS POMPANON PIERRE TABERLET

Biology Letters Vol. 4 No. 4 pp. 423-425 · The Royal Society

View at Publisher Save 10.1098/rsbl.2008.0118

Abstract

The assessment of species distribution is a first critical phase of biodiversity studies and is necessary to many disciplines such as biogeography, conservation biology and ecology. However, several species are difficult to detect, especially during particular time periods or developmental stages, potentially biasing study outcomes. Here we present a novel approach, based on the limited persistence of DNA in the environment, to detect the presence of a species in fresh water. We used specific primers that amplify short mitochondrial DNA sequences to track the presence of a frog (
Rana catesbeiana
) in controlled environments and natural wetlands. A multi-sampling approach allowed for species detection in all environments where it was present, even at low densities. The reliability of the results was demonstrated by the identification of amplified DNA fragments, using traditional sequencing and parallel pyrosequencing techniques. As the environment can retain the molecular imprint of inhabiting species, our approach allows the reliable detection of secretive organisms in wetlands without direct observation. Combined with massive sequencing and the development of DNA barcodes that enable species identification, this approach opens new perspectives for the assessment of current biodiversity from environmental samples.

Topics

No keywords indexed for this article. Browse by subject →

References

23

[1]

10.1016/j.ympev.2004.03.006

[2]

10.1046/j.1461-0248.2002.00352.x

[3]

10.1126/science.289.5482.1139b

[4]

10.1111/j.1472-4642.2007.00377.x

[5]

10.1007/s10530-006-9080-y

[6]

10.1111/j.1365-294x.2007.03622.x

[7]

10.1098/rsbl.2006.0494

[8]

Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness

Nicholas J. Gotelli, Robert K. Colwell

Ecology Letters 10.1046/j.1461-0248.2001.00230.x

[9]

10.1111/j.1471-8286.2006.01470.x

[10]

10.1016/j.cub.2003.08.039

[11]

10.1111/j.1365-2664.2006.01227.x

[12]

10.1046/j.1472-4642.2003.00013.x

[13]

MacKenzie D.I Nichols J.D Royle J.A Pollock K.H Bailey L.A& Hines J.E Occupancy estimation and modeling: inferring patterns and dynamics of species occurrence. 2006 Amsterdam The Netherlands:Elsevier.

[14]

Genome sequencing in microfabricated high-density picolitre reactors

Marcel Margulies, Michael Egholm, William E. Altman et al.

Nature 10.1038/nature03959

[15]

Margurran A.E Measuring biological diversity. 2004 Malden MA:Blackwell Science.

[16]

10.3354/ame026095

[17]

R Development Core Team R: a language and environment for statistical computing. 2006 Vienna Austria:R Foundation for Statistical Computing.

[18]

10.1093/nar/24.16.3189

[19]

Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding

P. Taberlet, E. Coissac, F. Pompanon et al.

Nucleic Acids Research 10.1093/nar/gkl938

[20]

10.1046/j.1365-294x.2000.11142.x

[21]

Environmental Genome Shotgun Sequencing of the Sargasso Sea

J. Craig Venter, Karin Remington, John F. Heidelberg et al.

Science 10.1126/science.1093857

[22]

10.1126/science.1084114

[23]

10.1126/science.1141758

Cited By

1,460

Wild Chinese giant salamander persist in Zhangjiajie, Hunan, China: Evidence from 10 years of monitoring

Zhiqiang Liang, Qianqian Wu · 2026

Global Ecology and Conservation

Environmental DNA metabarcoding: Current applications and future prospects for freshwater fish monitoring

Shuaishuai Liu, Juan Chen · 2025

Journal of Environmental Management

Research Trends and Hotspots in eDNA-Based Surveys of Macroinvertebrates: A Bibliometric Analysis

Xinyu Ge, Junyu Zhang · 2025

Diversity

Environmental DNA and Hydroacoustic Surveys for Monitoring the Spread of the Invasive European Catfish (Silurus glanis Linnaeus, 1758) in the Guadalquivir River Basin, Spain

Ruth Coya, Amadora Rodríguez-Ruiz · 2025

Animals

Environmental RNA ‐Based Metatranscriptomics as a Novel Biomonitoring Tool: A Case Study of Glyphosate‐Based Herbicide Effects on Freshwater Eukaryotic Communities

Xiaoping He, Takahiro Maruki · 2025

Molecular Ecology

From anarchy to clarity, data pre‐processing and statistical choices influence quantitative environmental DNA ( eDNA ) analyses

Jonas Bylemans, Teun Everts · 2025

Methods in Ecology and Evolution

Measuring the state of aquatic environments using eDNA—upscaling spatial resolution of biotic indices

Rosetta C. Blackman, Luca Carraro · 2024

Philosophical Transactions of the R...

Combining environmental DNA and visual surveys can inform conservation planning for coral reefs

Dominic Muenzel, Alessia Bani · 2024

Proceedings of the National Academy...

Assessing the utility of marine filter feeders for environmental DNA ( eDNA ) biodiversity monitoring

Gert‐Jan Jeunen, Jasmine S. Cane · 2023

Molecular Ecology Resources

Unveiling the hidden diversity of marine eukaryotes in the Ross Sea: A comparative analysis of seawater and sponge eDNA surveys

Gert‐Jan Jeunen, Miles Lamare · 2023

Environmental DNA

Genomics for monitoring and understanding species responses to global climate change

Louis Bernatchez, Anne-Laure Ferchaud · 2023

Nature Reviews Genetics

Short‐term temporal variation of coastal marine eDNA

Mads Reinholdt Jensen, Eva Egelyng Sigsgaard · 2022

Environmental DNA

Sea lice (Lepeophtherius salmonis) detection and quantification around aquaculture installations using environmental DNA

Adriana Krolicka, Mari Mæland Nilsen · 2022

PLoS ONE

Detection of Fish Pathogens in Freshwater Aquaculture Using eDNA Methods

Kailash Bohara, Amit K. Yadav · 2022

Diversity

Fine‐tuning the performance of abundance estimation based on environmental DNA (eDNA) focusing on eDNA particle size and marker length

Toshiaki Jo, Hiroki Yamanaka · 2022

Ecology and Evolution

eDNAir: proof of concept that animal DNA can be collected from air sampling

Elizabeth L. Clare, Chloe K. Economou · 2021

PeerJ

Linking the state of environmental DNA to its application for biomonitoring and stock assessment: Targeting mitochondrial/nuclear genes, and different DNA fragment lengths and particle sizes

Toshiaki Jo, Kenta Takao · 2021

Environmental DNA

Advanced molecular-based surveillance of quagga and zebra mussels: A review of environmental DNA/RNA (eDNA/eRNA) studies and considerations for future directions

Sheena M. Feist, Richard F. Lance · 2021

NeoBiota

Screening marker sensitivity: Optimizing eDNA‐based rare species detection

Zhiqiang Xia, Aibin Zhan · 2021

Diversity and Distributions

DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity

Jordan M. Casey, Emma Ransome · 2021

Environmental DNA

Metrics

1,460

Citations

23

References

Details

Published: Apr 09, 2008
Vol/Issue: 4(4)
Pages: 423-425
License: View

Authors

G

Gentile Francesco Ficetola

Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph FourierBP 53, 38041 Grenoble Cedex 09, France; Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université de Savoie73376 Le Bourget du Lac Cedex, France

C

Claude Miaud

Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université de Savoie73376 Le Bourget du Lac Cedex, France

F

FRANÇOIS POMPANON

Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph FourierBP 53, 38041 Grenoble Cedex 09, France

P

PIERRE TABERLET

Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph FourierBP 53, 38041 Grenoble Cedex 09, France

Cite This Article

Gentile Francesco Ficetola, Claude Miaud, FRANÇOIS POMPANON, et al. (2008). Species detection using environmental DNA from water samples. Biology Letters, 4(4), 423-425. https://doi.org/10.1098/rsbl.2008.0118

Species detection using environmental DNA from water samples

You May Also Like