Species detection using environmental DNA from water samples. Biol Lett 4:423-425

Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, Grenoble Cedex 09, France.
Biology letters (Impact Factor: 3.25). 09/2008; 4(4):423-5. DOI: 10.1098/rsbl.2008.0118
Source: PubMed


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.

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    • "This includes PCR-sequencing, real-time PCR and PCR-cloning (Krcmar and Rencova, 2005; Ong et al., 2007; Martín et al., 2010; Doosti et al., 2011; Ardura et al., 2012). Recently, next generation sequencing (NGS) techniques have produced a real advancement of genomic methods, allowing the establishment of DNA metabarcoding as a reliable and powerful option for animal species identification (Ficetola et al., 2008; Bott et al., 2010; Taberlet et al., 2012; Thomsen et al., 2012; Pawlowski et al., 2014; Rees et al., 2014; Ardura et al., 2015; Zaiko et al., 2015a,b). There are several platforms available for NGS including Ion Torrent's PGM, Roche/454 Life Sciences, Illumina MiSeq and Pacific Biosciences' RS (Quail et al., 2012; Pochon et al., 2013; Frey et al., 2014; Salipante et al., 2014). "
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    • "One of the earliest studies to target detection of vertebrate eDNA collected terrestrial mammal mitochondrial eDNA from aquatic environments, implicating fecal origins of such material (Martellini et al. 2005). Although feces remains a probable source of eDNA from a wide range of taxa targeted in aquatic (Thomsen et al. 2012a) and terrestrial environments (Andersen et al. 2012), high rates of success detecting taxa which produce slimy coatings such as amphibians (Ficetola et al. 2008) and fish (Jerde et al. 2011) suggest that other bodily fluids also act as a source of eDNA. Still other studies have demonstrated that dead carcasses and predator feces may also serve as an eDNA source in some cases (Merkes et al. 2014). "
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    • "In addition, aquatic eDNA is representative of local populations at the sampling sites, thus avoiding the need to sample and analyse individual organisms (Ficetola et al. 2008; Blanchet 2012). "
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