Metabarcoding of pond environmental DNA samples towards development of DNA-based metrics for the assessment of pond condition

Metabarcoding of pond environmental DNA samples towards development of DNA-based metrics for the assessment of pond condition. This project processed and sequenced water samples (c. 1 L volume) from 61 freshwater ponds of varying habitat condition surveyed by Natural England as part of their England Ecosystem Survey. Additional, equivalent samples (48) from high quality freshwater pond habitats were provided by the Freshwater Habitats Trust. All samples were collected between May and September 2023, and sequenced in March 2024. All pond water samples were processed to extract environmental DNA (eDNA), which was sequenced using five metabarcoding markers. This produced species lists for each sampled pond for five taxonomic groups: vertebrates, invertebrates, plants and fungi, microbial eukaryotes, and prokaryotes (bacteria and archaea). Alongside water samples, physicochemical and plant observation data were collected for all ponds surveyed, as presented in separate Natural England-commissioned reports. The analysis of pond sequence data alongside these data is subject to ongoing metric development.