Urine collected in the field as a source of DNA for species and individual identification

Valière, Nathaniel; Taberlet, Pierre

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

Cited by 77 publications

(46 citation statements)

References 11 publications

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“…To recover the precipitated DNA and/or the cellular remains, we centrifuged the mixture (5500g, 35 min, 68C) and discarded the supernatant ( Valiere & Taberlet 2000). The pellet was then subjected to a classical DNA extraction using QIAamp Tissue Extraction Kit (Qiagen).…”

Section: Methodsmentioning

confidence: 99%

Species detection using environmental DNA from water samples

et al. 2008

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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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Section: Methodsmentioning

confidence: 99%

Species detection using environmental DNA from water samples

et al. 2008

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“…To reduce the total number of combinations to be tested, we first used a concentration technique (sodium acetate and ethanol precipitation) that was effective in other studies [2, 18, 33] along with 5 extraction methods (detailed below, Fig 2); we selected the top two best-performing techniques. We evaluated these two techniques (detailed below) in combination with two additional capture methods (three total) to identify the overall best combination for the capture and extraction.…”

Section: Methodsmentioning

confidence: 99%

“…Each 50 mL subsample was aliquoted into three replicates of 15 mL each. Aliquots were concentrated by sodium acetate/ethanol precipitation (addition of 1.5 mL of sodium acetate and 33 mL of absolute ethanol to 15 mL sample) [33] with a centrifugation modification (3220 g for 45 minutes) [18]. Sodium acetate and ethanol were added to each of the aliquots and stored overnight at -20°C and then centrifuged [39].…”

Section: Methodsmentioning

confidence: 99%

“…Concentration of DNA using precipitation with sodium acetate and ethanol [2, 33], centrifugation [15, 34], and filtration [5, 6, 35] have all been shown to successfully capture eDNA from bodies of water. Precipitation and centrifugation constrain the water sample volume but filtration methods often clog, hindering the capture of eDNA, particularly in turbid waters [18].…”

Section: Introductionmentioning

confidence: 99%

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Clearing muddied waters: Capture of environmental DNA from turbid waters

2017

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Understanding the differences in efficiencies of various methods to concentrate, extract, and amplify environmental DNA (eDNA) is vital for best performance of eDNA detection. Aquatic systems vary in characteristics such as turbidity, eDNA concentration, and inhibitor load, thus affecting eDNA capture efficiency. Application of eDNA techniques to the detection of terrestrial invasive or endangered species may require sampling at intermittent water sources that are used for drinking and cooling; these water bodies may often be stagnant and turbid. We present our best practices technique for the detection of wild pig eDNA in water samples, a protocol that will have wide applicability to the detection of elusive vertebrate species. We determined the best practice for eDNA capture in a turbid water system was to concentrate DNA from a 15 mL water sample via centrifugation, purify DNA with the DNeasy mericon Food kit, and remove inhibitors with Zymo Inhibitor Removal Technology columns. Further, we compared the sensitivity of conventional PCR to quantitative PCR and found that quantitative PCR was more sensitive in detecting lower concentrations of eDNA. We show significant differences in efficiencies among methods in each step of eDNA capture, emphasizing the importance of optimizing best practices for the system of interest.

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“…For higher organisms, this DNA may come from excreted cells or tissue such as urine (e.g. Valiere and Taberlet, 2000), faeces (e.g. Poinar et al, 1998), hairs and skin (e.g.…”

Section: Introductionmentioning

confidence: 99%