eDNA capture challenges
@Zerina Rahic
Pond as an environment
eDNA capture
Two broad methods are used in the capture of eDNA: filtration or ethanol precipitation. Comparative studies have generally shown that filtration approaches have higher sample throughput and can process greater water volumes, thereby increasing potential to recover greater amounts of DNA (Spens et al., 2016; Hinlo et al., 2017; Klymus et al., 2017b).
- Filtration: Since ponds can contain high levels of suspended solids and algae as well as organic debris from dtached, degrading aquatic and terrestrial vegetation, filters tend to become blocked when sampling comparatively small water volumes (Klymus et al., 2017b; Raemy & Ursenbacher, 2018). Where water is turbid, centrifugation, increased pore size, or pre-filtering will be necessary (Fig. 1) (Takahara et al., 2012; Robson et al., 2016; Klymus et al., 2017b). However, prefilters increase cost and larger pore sizes trade capture of smaller particle sizes for greater proportions of target DNA, reducing total eDNA yield (Turner et al., 2014).
- Ethanol precipitation: In contrast to filtration, water volumes are consistent with ethanol precipitation and species recovery may be the same or higher (Klymus et al., 2017b; Raemy & Ursenbacher, 2018). However, water volume is usually limited to * 90 ml per sample due to logistical and financial constraints on the number of tubes of ethanol that can be taken into the field (Biggs et al., 2015). Moreover, ethanol is not always easy to obtain and is subject to dangerous goods regulations for transportation. Where possible, we advise filtration is performed on site using enclosed capsule or syringe filters (Spens et al., 2016) to minimise risk of contamination (see Online Resource 2). If on-site filtration is unfeasible, samples should be processed in the laboratory within 24 h (Hinlo et al., 2017), or preservative solution (e.g. Longmire’s, benzalkonium chloride) added if this time frame cannot be met (Williams et al., 2016; Yamanaka et al., 2016), to maximise DNA recovery. Filters should be placed in preservative solution or frozen to prevent eDNA degradation prior to extraction (Hinlo et al., 2017).e
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