TY - JOUR
T1 - The effect of filtration method on the efficiency of environmental DNA capture and quantification via metabarcoding
AU - Li, Jianlong
AU - Lawson Handley, Lori Jayne
AU - Read, Daniel S.
AU - Hänfling, Bernd
N1 - Funding Information:
This work is part of PhD project of J.L., who is supported by University of Hull and China Scholarship Council. We are particularly grateful to Mr Alan Henshaw and other staff of the National Coarse Fish Rearing Unit of UK Environment Agency for sampling and providing fish stock information, and Drs Christoph Hahn and Amir Szitenberg for helping on the bioinformatics analysis. Furthermore, Dr James Kitson provided excellent advice on library preparation. We would like to thank three anonymous reviewers for constructive criticism on the initial submission which helped to strengthen the manuscript, and Lynsey Harper and Cristina Di Muri for helping proofreading and discussion on DNA quantification.
Publisher Copyright:
© 2018 John Wiley & Sons Ltd
PY - 2018/5/16
Y1 - 2018/5/16
N2 - 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.
AB - 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.
KW - eDNA method development
KW - fish monitoring
KW - lentic systems
KW - prefiltration
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U2 - 10.1111/1755-0998.12899
DO - 10.1111/1755-0998.12899
M3 - Article
AN - SCOPUS:85047724440
SN - 1755-098X
VL - 18
SP - 1102
EP - 1114
JO - Molecular Ecology Resources
JF - Molecular Ecology Resources
IS - 5
ER -