Abstract
Environmental DNA (eDNA) is a promising tool for rapid and noninvasive biodiversity monitoring. eDNA density is low in environmental samples, and a capture method, such as filtration, is often required to concentrate eDNA for downstream analyses. In this study, six treatments, with differing filter types and pore sizes for eDNA capture, were compared for their efficiency and accuracy to assess fish community structure with known fish abundance and biomass via eDNA metabarcoding. Our results showed that different filters (with the exception of 20-μm large-pore filters) were broadly consistent in their DNA capture ability. The 0.45-μm filters performed the best in terms of total DNA yield, probability of species detection, repeatability within pond and consistency between ponds. However performance of 0.45-μm filters was only marginally better than for 0.8-μm filters, while filtration time was significantly longer. Given this trade-off, the 0.8-μm filter is the optimal pore size of membrane filter for turbid, eutrophic and high fish density ponds analysed here. The 0.45-μm Sterivex enclosed filters performed reasonably well and are suitable insituations where on-site filtration is required. Finally, prefilters are applied only if absolutely essential for reducing the filtration time or increasing the throughput volume of the capture filters. In summary, we found encouraging similarity in the results obtained from different filtration methods, but the optimal pore size of filter or filter type might strongly depend on the water type under study.
Highlights
The analysis of environmental DNA is a non-invasive genetic method to detect the presence of organisms, including cryptic taxa, that takes advantage of intracellular or extra-organismal DNA in the environment (Lawson Handley 2015; Thomsen & Willerslev 2015; Goldberg et al 2016)
We found encouraging similarity in the results obtained from different filtration methods, but the optimal pore size of filter or filter type might strongly depend on the water type under study
Filtration time decreased on average by 27.00±13.87 min (Mean±SD) when comparing the 0.45 μm filters after pre-filtration (“PF_0.45MCE”) to those without pre-filtration (“0.45MCE”); and this significant trend was observed in ponds E1 and E3 (Fig. 3A, C)
Summary
The analysis of environmental DNA (eDNA) is a non-invasive genetic method to detect the presence of organisms, including cryptic taxa, that takes advantage of intracellular or extra-organismal DNA in the environment (Lawson Handley 2015; Thomsen & Willerslev 2015; Goldberg et al 2016). Previous studies have used a wide range of filter types (e.g. different membrane materials and pore sizes) and approaches (e.g. on-site or in laboratory) to filtration. On-site filtration followed by immediate preservation theoretically enhances DNA integrity and is critical for some remote field surveys where access to laboratory facilities is not available. Enclosed filters such Sterivex units (Millipore) or Nalgene analytical test filter funnels (Thermo Fisher Scientific), in combination with a portable peristaltic or hand-driven pump are popular protocols for the capture of eDNA in the field (Keskin 2014; Bergman et al 2016; Wilcox et al 2016; Spens et al 2017). Four main types of membrane filter (so-called “open filters”) are commonly used in the laboratory set-ups of freshwater studies: (1) 0.45 μm cellulose nitrate (CN) filters (e.g. Goldberg et al 2011; Pilliod et al 2013), (2) 0.45 μm nylon filters (e.g. Thomsen et al 2012), (3) 0.7 or 1.5 μm glass fibre (GF) filters (e.g. Wilcox et al 2013; Miya et al 2015) and (4) 1.2 μm polycarbonate (PC) filters (e.g. Egan et al 2015)
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
