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Development of an environmental DNA method for monitoring freshwater fish communities using metabarcoding

Li, Jianlong


Jianlong Li


B. (Bernd) Hänfling


Monitoring current global biodiversity decline is essential to maintain ecosystem functioning, especially freshwater ecosystems. However, the conventional physical, acoustic and visual-based methods for monitoring biodiversity have some limitations such as morphological identification bias, recording small-bodied, rare and/or elusive species, and destructive impacts on the environment. The significant ―game-changer‖ in biodiversity monitoring is environmental DNA (eDNA) metabarcoding, which refers to the simultaneous identification of a multitude of species from environmental samples. However, developing, validating and improving eDNA-based metabarcoding monitoring methods is not trivial. Firstly, for further eDNA metabarcoding studies focusing on freshwater fish communities, two marker-specific reference databases were compiled and two metabarcoding primer pairs were rigorously tested. Subsequently, a PCR-based metabarcoding approach is applied to investigate (1) the effect of filtration method on the efficiency of eDNA capture and quantification, (2) the spatial and temporal distribution of eDNA in fish ponds, and (3) the potential of eDNA as a tool for biodiversity monitoring in diverse lakes with characterised fish faunas. The results show that the 0.8 μm filters are advocated for turbid and eutrophic water such as ponds to reduce the filtration time, the 0.45 μm filters are appropriate for clear water sampling to obtain consistent results, and the 0.45 μm Sterivex enclosed filters are suitable in situations where on-site filtration is required. Furthermore, eDNA distribution in ponds was highly localised in space and time, and 10 shore samples distributed along the full perimeter of lakes is adequate for capturing the majority of species. Lastly, this thesis provides further evidence that eDNA metabarcoding could be a powerful monitoring tool for freshwater fish communities, considerably outperforming other established survey techniques whether in species detection, relative abundance estimate or characterisation ecological fish communities. These outcomes constitute a significant advance towards a standardised and efficient assessment procedure for the ecological monitoring of aquatic ecosystems.


Li, J. (2019). Development of an environmental DNA method for monitoring freshwater fish communities using metabarcoding. (Thesis). University of Hull. Retrieved from

Thesis Type Thesis
Deposit Date May 13, 2019
Publicly Available Date Feb 23, 2023
Keywords Biological sciences
Public URL
Additional Information School of Biological, Biomedical and Environmental Sciences, The University of Hull
Award Date May 1, 2019


Thesis (11.9 Mb)

Copyright Statement
© 2019 Li, Jianlong. All rights reserved. No part of this publication may be reproduced without the written permission of the copyright holder.

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