Abstract
Current research targeting filtered macrobial environmental DNA (eDNA) often relies upon cold ambient temperatures at various stages, including the transport of water samples from the field to the laboratory and the storage of water and/or filtered samples in the laboratory. This poses practical limitations for field collections in locations where refrigeration and frozen storage is difficult or where samples must be transported long distances for further processing and screening. This study demonstrates the successful preservation of eDNA at room temperature (20 °C) in two lysis buffers, CTAB and Longmire's, over a 2-week period of time. Moreover, the preserved eDNA samples were seamlessly integrated into a phenol–chloroform–isoamyl alcohol (PCI) DNA extraction protocol. The successful application of the eDNA extraction to multiple filter membrane types suggests the methods evaluated here may be broadly applied in future eDNA research. Our results also suggest that for many kinds of studies recently reported on macrobial eDNA, detection probabilities could have been increased, and at a lower cost, by utilizing the Longmire's preservation buffer with a PCI DNA extraction.
Highlights
IntroductionThe detection of macrobial DNA in environmental water samples, hereafter referred to as ‘environmental DNA (eDNA)’, is a burgeoning field of research often involving the detection of rare species, including invasive species (Dejean et al 2012; Goldberg et al 2013; Jerde et al 2013; Takahara et al 2013; Piaggio et al 2014) and endangered species (Olson et al 2012; Thomsen et al 2012a)
These choices can impact the efficiency of the environmental DNA (eDNA) capture (Liang & Keeley 2013), but are currently difficult to quantify between studies as other aspects are not held constant (Turner et al 2014)
For studies utilizing filtration of water samples, the preservation of eDNA is often reliant on cold ambient temperatures (Mahon et al 2010; Takahara et al 2012, 2013; Jerde et al 2013; Wilcox et al 2013)
Summary
The detection of macrobial DNA in environmental water samples, hereafter referred to as ‘eDNA’, is a burgeoning field of research often involving the detection of rare species, including invasive species (Dejean et al 2012; Goldberg et al 2013; Jerde et al 2013; Takahara et al 2013; Piaggio et al 2014) and endangered species (Olson et al 2012; Thomsen et al 2012a). This is the case at multiple points of the sample collection process, including the use of ice in the transport of water samples from collection sites to laboratories, storage of water samples in freezers for filtering at later time points and freezing of filters following the processing of water samples (Mahon et al 2010; Thomsen et al 2012b; Pilliod et al 2013; Takahara et al 2013; Wilcox et al 2013; Piaggio et al 2014) This reliance on cold ambient temperatures poses practical limitations for field collections in locations where refrigeration and frozen storage is difficult (i.e. backcountry locations accessible only by foot) or where samples must be transported long distances for further processing and screening (i.e. international travel). While in situ field filtration can be overcome with portable pumps (Pilliod et al 2013; Wilcox et al 2013), having a method that preserves filtered eDNA and prevents further degradation would benefit field scientists tasked with collecting samples under transport or temperature limitations
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