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.