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

Li, Jianlong

Biological sciences
May 2019

Thesis or dissertation


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

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.

Publisher
School of Biological, Biomedical and Environmental Sciences, The University of Hull
Supervisor
Hänfling, B. (Bernd); Lawson Handley, Lori
Sponsor (Organisation)
University of Hull; China Scholarship Council
Qualification level
Doctoral
Qualification name
PhD
Language
English
Extent
11 MB
Identifier
hull:17293
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