Beyond the surface: Enhancing freshwater pond ecosystem assessment through eDNA metabarcoding

Robertson, Claire 2024. Beyond the surface: Enhancing freshwater pond ecosystem assessment through eDNA metabarcoding. PhD Thesis, Cardiff University. Item availability restricted.

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Abstract

Freshwater ponds are small, lentic freshwater habitats. Composing an estimated 30 % of global standing water area, they are important reservoirs of freshwater biodiversity providing key ecosystem services. Environmental DNA (eDNA) metabarcoding is a novel method of sampling biodiversity, where an organism’s presence is inferred by sampling and identifying their DNA present in the environment. This method has advantages in terms of efficiency, scalability and identifying small and cryptic species. This PhD examines the use of eDNA metabarcoding to monitor freshwater ponds. Firstly, I developed new techniques, including using genetic markers never previously used in ponds or other freshwater environments (Chapter 2). This increased the taxonomic breadth of pond monitoring by targeting prokaryotic and eukaryotic microbes, fungi, microfauna and algae alongside the traditionally used macrophytes and macroinvertebrates. I examined seasonal dynamics of communities in pond water and sediment via eDNA metabarcoding (Chapter 3). I also used eDNA metabarcoding to test ecological hypotheses at the landscape level (Chapter 4), investigating environmental and spatial drivers of pond community composition. I compared community metrics derived from metabarcoding data with a traditional pond ecosystem assessment tool (the Habitat Suitability Index for Great Crested Newts). Pond communities in water and sediment were significantly dissimilar, and this difference was bigger for microbes than for larger organisms. Communities in pond water displayed significant seasonal turnover, but this was less pronounced in sediment communities. Higher plant eDNA sequence reads from water samples were over 70 % terrestrial in origin. Prokaryotic communities were structured by pond water chemistry and surrounding land use, and their composition differed in ponds of different HSI levels. Green plant and algal communities were spatially structured, and other eukaryotes showed no clear structuring pattern. These findings encourage a shift in eDNA surveying of ponds, demonstrating that bacteria communities in sediments are good bioindicators of overall pond ecosystem health.

Item Type:	Thesis (PhD)
Date Type:	Completion
Status:	Unpublished
Schools:	Biosciences
Subjects:	Q Science > Q Science (General)
Date of First Compliant Deposit:	3 October 2024
Last Modified:	11 Nov 2024 15:00
URI:	https://orca.cardiff.ac.uk/id/eprint/172588

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