Cunnington, A (2024) Enhancing environmental monitoring in anthropogenically modified coastal habitats using eDNA and nsDNA metabarcoding. Doctoral thesis, Liverpool John Moores University.

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Abstract

Understanding the dynamic relationships that exist between species in urban coastal habitats is of critical importance as scientists, policymakers and the public work to address a range of environmental challenges. Developing robust and versatile environmental monitoring methods, refined and optimised for use in such coastal habitats, will be a necessary part of this. This thesis focuses for the most part on one technique - eDNA metabarcoding, where fragments of DNA shed by organisms are analysed - and explores its effectiveness and flexibility across a variety of coastal habitats. This thesis explores firstly fish assemblages in post-industrial Merseyside, using eDNA metabarcoding to produce a comprehensive list of teleost species, including species of ecological and conservation importance. Significant changes in fish community composition between habitats and across different seasons over a year-long period were revealed, demonstrating the method's potential for monitoring environmental impacts on fish communities. A multi-marker approach was then employed (COI and rbcL) to investigate eukaryotic communities in heavily urbanised waterways within Merseyside. It was found that both markers could discern distinct, localised communities while also identifying indicator species, including diatom species and potentially harmful algae. Exploring the use of both markers concurrently provides a comprehensive insight into ecosystem health and capitalises on the strengths, with implications for environmental monitoring. Expanding the scope of this research beyond eDNA metabarcoding, the role of beadlet anemones as natural environmental DNA samplers (nsDNA) for vertebrate biodiversity was also investigated. It was shown that using anemone nsDNA alongside water eDNA expanded the range of taxa detected, thereby enhancing the study's scope and revealing unique potential future applications for vertebrate monitoring. The role of a working mussel farm in supporting environmental monitoring through eDNA metabarcoding was explored. Using the mussel farm’s boat increased accessibility to detect fish communities, and our results highlighted extensive "molecular bycatch" as well as the interaction between land and sea in deep fjordic inlets. Although DNA extracted from the tissue of blue mussels were also analysed, this part of the study yielded no fish sequencing reads, revealing there are limitations to the use of natural sampler DNA in this context. Overall, this thesis emphasises the value of novel biodiversity-screening techniques when applied to coastal habitats particularly impacted by current and historical anthropogenic modifications. It highlights in particular the role that eDNA and nsDNA metabarcoding, when used both in combination with other techniques or as standalone methods, have to play in expanding and enhancing toolkits for future environmental monitoring.

Item Type:	Thesis (Doctoral)
Additional Information:	This article is reproduced within this thesis under license from the copyright holder, Inter-Research. The complete article may not be further reproduced or distributed from this source separately from the reproduction and distribution of the thesis. This restriction ends August 22, 2029.
Uncontrolled Keywords:	eDNA; nsDNA; metabarcoding; biodiversity; Coastal fishes; Diatoms
Subjects:	Q Science > QH Natural history > QH301 Biology Q Science > QL Zoology
Divisions:	Biological and Environmental Sciences (from Sep 19)
SWORD Depositor:	A Symplectic
Date Deposited:	19 Mar 2025 10:04
Last Modified:	19 Mar 2025 10:05
DOI or ID number:	10.24377/LJMU.t.00025156
Supervisors:	Mariani, S, Wilding, C and Scott, K
URI:	https://researchonline.ljmu.ac.uk/id/eprint/25156

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