Environmental DNA : from detection of priority invasive species to monitoring entire macroinvertebrate communities in freshwater ecosystems

Blackman, Rosetta Charlotte

Environmental sciences
November 2017

Thesis or dissertation

© 2017 Rosetta Charlotte Blackman. All rights reserved. No part of this publication may be reproduced without the written permission of the copyright holder.

Freshwater ecosystems are among the most threatened habitats on Earth, facing challenges from a range of anthropogenic pressures. Accurate biodiversity assessment is essential to identify these pressures prior to irreversible damage. Current monitoring techniques for freshwater systems rely heavily on capture methods to infer the status of an ecosystem. However, these methods are often inefficient at detecting and identifying all species at a site and often miss those in low abundance. Emerging molecular methods such as environmental DNA (eDNA) could be a “game changer” for freshwater biodiversity monitoring. This thesis focuses on the application of eDNA for detection of invasive non-native species (INNS) and whole macroinvertebrate community assessment. Firstly, targeted eDNA PCR assays were developed for four priority freshwater INNS, and validated in mesocosm experiments and field trials. Targeted (PCR and qPCR) and passive (metabarcoding) eDNA approaches were then compared to traditional methods for detecting quagga mussels, Dreissena rostriformis bugensis. The targeted approaches were the most sensitive for detection of quagga mussels at low densities and both qPCR and metabarcoding showed correlations with mussel density. The power and utility of eDNA metabarcoding for detecting rare or unexpected taxa was then demonstrated by passive detection of a new INNS, Gammarus fossarum, in UK rivers. Finally, metabarcoding of both bulk DNA and eDNA from water and sediment was compared to the traditional method of macroinvertebrate sampling, to evaluate the potential of emerging molecular methods for ecological assessment. The results show metabarcoding approaches are not suitable to retrofit or replace existing methods of assessment, but provide an exciting opportunity for greater taxonomic identification and have the ability to detect a combination of taxa across groups, some of which are not utilised in current ecological assessment methods. This work has demonstrated a huge potential for eDNA methods to be applied to INNS monitoring and further our ability to carry out complete biodiversity assessment of waterbodies.

School of Environmental Sciences, The University of Hull
Sponsor (Organisation)
University of Hull; Great Britain. Environment Agency; Freshwater Biological Association
Qualification level
Qualification name
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