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The effect of filtration method on the efficiency of environmental DNA capture and quantification via metabarcoding

Li, Jianlong; Lawson Handley, Lori Jayne; Read, Daniel S.; Hänfling, Bernd

Authors

Jianlong Li

Lori Jayne Lawson Handley

Daniel S. Read

Dr Bernd Haenfling B.Haenfling@hull.ac.uk
Senior Lecturer/ Chair of the Evolutionary Biology Group (EvoHull)



Abstract

© 2018 John Wiley & Sons Ltd. 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 in situations 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.

Journal Article Type Article
Publication Date 2018-09
Journal Molecular Ecology Resources
Print ISSN 1755-098X
Electronic ISSN 1755-0998
Publisher Wiley
Peer Reviewed Peer Reviewed
Volume 18
Issue 5
Pages 1102-1114
APA6 Citation Li, J., Lawson Handley, L. J., Read, D. S., & Hänfling, B. (2018). The effect of filtration method on the efficiency of environmental DNA capture and quantification via metabarcoding. Molecular Ecology Resources, 18(5), 1102-1114. https://doi.org/10.1111/1755-0998.12899
DOI https://doi.org/10.1111/1755-0998.12899
Keywords eDNA method development; Fish monitoring; Lentic systems; Prefiltration
Publisher URL https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.12899
Copyright Statement ©2018 University of Hull

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