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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Available from: Gentile Francesco Ficetola
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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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    ABSTRACT: Aquaculture is currently the fastest-growing food production system worldwide. It is highly dependent upon marine capture fisheries as its key dietary inputs, what could seriously compromise oceans biodiversity. Here we employed a DNA metabarcoding approach, based on 454 Next generation sequencing (NGS), for fish species detection in seven Egyptian aqua-feed samples. Up to 13 fish species belonging to four orders (Clupeiformes, Perciformes, Aulopiformes and Siluriformes) were uniquely identified. Saurida undosquamis, Sardinella jussieu, Pangasianodon hypophthalmus and Chelidonichthys kumu were detected as major components. DNA metabarcoding revealed slight differences in the compositions among aqua-feeds presented for herbivorous or omnivorous fish. More important, approximately 46% of all fish species detected are either overexploited or suffering strong decline. These results suggest that more endeavors are necessary for precise fisheries management and biodiversity protection. Although further studies are needed, NGS approaches may provide an effective tool that could help in the implementation of traceability systems for the seafood industry.
    Full-text · Article · Feb 2016 · Fisheries Research
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    • "This approach is especially useful for detecting species that are difficult to sample using traditional methods (Taberlet et al., 2012), for non-invasively sampling critically endangered species (Sigsgaard et al., 2015), and for distinguishing cryptic species (Fukumoto et al., 2015). Since it was first used to detect aquatic animals (Ficetola et al., 2008) there has been an explosion of research on eDNA methods, particularly with respect to rare invasive species (e.g., Dejean et al., 2012; Goldberg et al., 2013; Moyer et al., 2014) and threatened native species (Spear et al., 2015; Thomsen et al., 2012). "
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    ABSTRACT: Environmental DNA sampling (eDNA) has emerged as a powerful tool for detecting aquatic animals. Previous research suggests that eDNA methods are substantially more sensitive than traditional sampling. However, the factors influencing eDNA detection and the resulting sampling costs are still not well understood. Here we use multiple experiments to derive independent estimates of eDNA production rates and downstream persistence from brook trout (Salvelinus fontinalis) in streams. We use these estimates to parameterize models comparing the false negative detection rates of eDNA sampling and traditional backpack electrofishing. We find that using the protocols in this study eDNA had reasonable detection probabilities at extremely low animal densities (e.g., probability of detection 0.18 at densities of one fish per stream kilometer) and very high detection probabilities at population-level densities (e.g., probability of detection >0.99 at densities of ≥3 fish per 100m). This is substantially more sensitive than traditional electrofishing for determining the presence of brook trout and may translate into important cost savings when animals are rare. Our findings are consistent with a growing body of literature showing that eDNA sampling is a powerful tool for the detection of aquatic species, particularly those that are rare and difficult to sample using traditional methods.
    Full-text · Article · Feb 2016 · Biological Conservation
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    • "This technique was first described by Ogram et al. (1987) who extracted microbial DNA from the sediment and, today, several papers are available describing the use of eDNA in analyses of soils, waters, and even air (e.g., Taberlet et al. 2012). Andersen et al. (2011) examined the possibility of monitoring large mammals using eDNA soil samples, and eDNA-based monitoring of fish (Minamoto et al. 2012; Thomsen et al. 2012a, b) and amphibians (Ficetola et al. 2008; Goldberg et al. 2011) has been successful. An alarm system for control of biological invasion of Asian carp has been developed by the U.S. Army Corps of Engineers using water eDNA (Darling and Mahon 2011). "
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    ABSTRACT: Ecological monitoring contributes to the understanding of complex ecosystem functions. The diets of fish reflect the surrounding environment and habitats and may, therefore, act as useful integrating indicators of environmental status. It is, however, often difficult to visually identify items in gut contents to species level due to digestion of soft-bodied prey beyond visual recognition, but new tools rendering this possible are now becoming available. We used a molecular approach to determine the species identities of consumed diet items of an introduced generalist feeder, brown trout (Salmo trutta), in 10 Tasmanian lakes and compared the results with those obtained from visual quantification of stomach contents. We obtained 44 unique taxa (OTUs) belonging to five phyla, including seven classes, using the barcode of life approach from cytochrome oxidase I (COI). Compared with visual quantification, DNA analysis showed greater accuracy, yielding a 1.4-fold higher number of OTUs. Rarefaction curve analysis showed saturation of visually inspected taxa, while the curves from the DNA barcode did not saturate. The OTUs with the highest proportions of haplotypes were the families of terrestrial insects Formicidae, Chrysomelidae, and Torbidae and the freshwater Chironomidae. Haplotype occurrence per lake was negatively correlated with lake depth and transparency. Nearly all haplotypes were only found in one fish gut from a single lake. Our results indicate that DNA barcoding of fish diets is a useful and complementary method for discovering hidden biodiversity.
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