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Limited dispersion and quick degradation of environmental DNA in fish ponds inferred by metabarcoding

Li, Jianlong; Lawson Handley, Lori J.; Harper, Lynsey R.; Brys, Rein; Watson, Hayley V.; Di Muri, Cristina; Zhang, Xiang; Hänfling, Bernd


Jianlong Li

Lynsey R. Harper

Rein Brys

Hayley V. Watson

Cristina Di Muri

Xiang Zhang

Bernd Hänfling


Background: Environmental DNA (eDNA) metabarcoding is a promising tool for rapid, non-invasive biodiversity monitoring. Aims: In this study, eDNA metabarcoding is applied to explore the spatial and temporal distribution of fish communities in two aquaculture ponds and to evaluate the detection sensitivity of this tool for low-density species alongside highly abundant species. Materials & Methods: This study was carried out at two artificially stocked ponds with a high fish density following the introduction and removal of two rare fish species. Results & Discussion: When two rare species were introduced and kept at a fixed location in the ponds, eDNA concentration (i.e., proportional read counts abundance) of the introduced species typically peaked after two days. The increase in eDNA concentration of the introduced fish after 43 hrs may have been caused by increased eDNA shedding rates as a result of fish being stressed by handling, as observed in other studies. Thereafter, it gradually declined and stabilised after six days. These findings are supported by the highest community dissimilarity of different sampling positions being observed on the second day after introduction, which then gradually decreased over time. On the sixth day, there was no longer a significant difference in community dissimilarity between sampling days. The introduced species were no longer detected at any sampling positions on 48 hrs after removal from the ponds. eDNA is found to decay faster in the field than in controlled conditions, which can be attributed to the complex effects of environmental conditions on eDNA persistence or resulting in the vertical transport of intracellular DNA and the extracellular DNA absorbed by particles in the sediment. The eDNA signal and detection probability of the introduced species were strongest near the keepnets, resulting in the highest community variance of different sampling events at this position. Thereafter, the eDNA signal significantly decreased with increasing distance, although the signal increased slightly again at 85 m position away from the keepnets. Conclusions: Collectively, these findings reveal that eDNA distribution in lentic ecosystems is highly localised in space and time, which adds to the growing weight of evidence that eDNA signal provides a good approximation of the presence and distribution of species in ponds. Moreover, eDNA metabarcoding is a powerful tool for detection of rare species alongside more abundant species due to the use of generic PCR primers, and can enable monitoring of spatial and temporal community variance.


Li, J., Lawson Handley, L. J., Harper, L. R., Brys, R., Watson, H. V., Di Muri, C., …Hänfling, B. (2019). Limited dispersion and quick degradation of environmental DNA in fish ponds inferred by metabarcoding. Environmental DNA, 1(3), 238-250.

Journal Article Type Article
Acceptance Date May 31, 2019
Online Publication Date Jun 25, 2019
Publication Date Sep 1, 2019
Deposit Date Oct 17, 2019
Publicly Available Date Oct 18, 2019
Journal Environmental DNA
Print ISSN 2637-4943
Electronic ISSN 2637-4943
Publisher Wiley Open Access
Peer Reviewed Peer Reviewed
Volume 1
Issue 3
Pages 238-250
Keywords Community variances; eDNA dynamics; eDNA ecology; Fish monitoring; Ponds
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Copyright Statement
This is an open access article under the terms of the Creative Commons Attribution‚ÄźNonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes. © 2019 The Authors. Environmental DNA published by John Wiley & Sons Ltd

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