Persistence of Environmental DNA in Freshwater Ecosystems

By Tony Dejean, A. Valentini, A. Duparc, Stéphanie Pellier-Cuit, F. Pompanon, P. Taberlet, C. Miaud. PLoS ONE, 2011

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The precise knowledge of species distribution is a key step in conservation biology. However, species detection can be extremely difficult in many environments, specific life stages and in populations at very low density. The aim of this study was to improve the knowledge on DNA persistence in water in order to confirm the presence of the focus species in freshwater ecosystems. Aquatic vertebrates (fish: Siberian sturgeon and amphibian: Bullfrog tadpoles) were used as target species. In control conditions (tanks) and in the field (ponds), the DNA detectability decreases with time after the removal of the species source of DNA. DNA was detectable for less than one month in both conditions. The density of individuals also influences the dynamics of DNA detectability in water samples. The dynamics of detectability reflects the persistence of DNA fragments in freshwater ecosystems. The short time persistence of detectable amounts of DNA opens perspectives in conservation biology, by allowing access to the presence or absence of species e.g. rare, secretive, potentially invasive, or at low density. This knowledge of DNA persistence will greatly influence planning of biodiversity inventories and biosecurity surveys.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f3d6029b2bddb220172fffe58c01867031c95904

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Citations in the corpus

Quantifying relative fish abundance with eDNA: a promising tool for fisheries management (2016, background): “Overall, DNA fragments have been shown to persist for only a few weeks in freshwater ecosystem (Dejean et al. 2011; Thomsen et al. 2012b; Goldberg et al. 2013; Pilliod et al. 2013b; Piaggio et al. 2014; Strickler, Fremier & Goldberg 2015).”
Detection of a Diverse Marine Fish Fauna Using Environmental DNA from Seawater Samples (2012, positive): “In freshwater, the decay of eDNA beyond the threshold of detectability has been demonstrated to happen at a scale of days or weeks [32,46].”
Sedimentary eDNA provides different information on timescale and fish species composition compared with aqueous eDNA (2020, background): “…after removing carp fish (Turner et al., 2015), whereas the detectable time of aqueous eDNA was reported to be several days to several weeks (Barnes et al., 2014; Dejean et al., 2011; Goldberg et al., 2013; Pilliod, Goldberg, Arkle, & Waits, 2014; Thomsen, Kielgast, Iversen, Møller, et al., 2012).”
Environmental DNA particle size distribution from Brook Trout (Salvelinus fontinalis) (2015, background): “A key example is the particle size of eDNA, which has not been determined empirically for most species, but has been attributed in the literature to everything from extracellular DNA to sloughed tissues (e.g., Dejean et al. 2011).”
Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes (2020, methodology): “…(Cilleros et al., 2019; Gomes et al., 2017). eDNA is a noninvasive method demonstrating higher detection capabilities and cost-effectiveness compared to traditional methods, especially when deployed in remote locations (Dejean et al., 2011; Kelly et al., 2014; Thomsen & Willerslev, 2015).”
REVIEW: The detection of aquatic animal species using environmental DNA – a review of eDNA as a survey tool in ecology (2014, methodology): “It is known that eDNA can survive from hours in freshwater to thousands of years in fossil ice and permafrost (Willerslev, Hansen & Poinar 2004), but species-specific DNA persistence has only recently been investigated in freshwater and seawater samples (Dejean et al. 2011; Thomsen et al. 2012a,b; G”
Improved detection of an alien invasive species through environmental DNA barcoding: the example of the American bullfrog Lithobates catesbeianus (2012, background): “In addition, the persistence of eDNA in water has been tested (Dejean et al. 2011) and bullfrog eDNA was detected only for a maximum of 2 weeks after the removal of the source animal.”
Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples (2013, background): “to be investigated (Dejean et al. 2011; Takahara et al. 2012).”
Critical considerations for the application of environmental DNA methods to detect aquatic species (2016, background): “Degradation has been shown to limit the detectability of eDNA in water to between 1 day and 8 weeks (Dejean et al. 2011; Thomsen et al. 2012a,b; Pilliod et al. 2014) and can thus result in fine-scale temporal inference about the species’ presence.”
Monitoring the near-extinct European weather loach in Denmark based on environmental DNA from water samples (2015, methodology): “The decay of eDNA beyond the threshold of detectability in controlled experiments has been shown to occur on a scale of days or weeks (Dejean et al., 2011; Thomsen et al., 2012a,b; Barnes et al., 2014; Pilliod et al., 2014), indicating that the method provides an almost contemporary picture of…”
Downstream transport and seasonal variation in freshwater pearl mussel ( Margaritifera margaritifera ) eDNA concentration (2019, background): “While eDNA degradation and deposition may be rapid (Barnes et al., 2014; Dejean et al., 2011; Jerde et al., 2016; Pilliod, Goldberg, Arkle, & Waits, 2014; Tillotson et al., 2018), downstream transport can be highly efficient (Deiner & Altermatt, 2014; Jane et al., 2015; Sansom & Sassoubre, 2017;…”