Abstract
Ecosystems within cities can play a crucial role in conserving local biodiversity amid rapidly expanding urban sprawl, but they face significant threats from anthropogenic activities and the introduction of alien invasive species (AIS). A comprehensive management plan is required to effectively preserve the biodiversity supported by urban ecosystems. However, the ecological information needed to establish, implement and monitor such plans is often incomplete. In this study, we assessed the application of eDNA metabarcoding in surveying plant biodiversity in an aquatic habitat by collecting water samples at five sites in an urban dam in the City of Johannesburg. Out of 1001 reconstructed Amplicon Sample Variants (ASVs), plant taxa were assigned to 47 unique taxonomic ranks at the family level, 42 unique ranks at the generic level and only 13 unique ranks at the species level (including three AIS). The remaining ASVs could only be identified at higher taxonomic ranks, indicating that no DNA barcodes have yet been generated for the putative species in question. Although this study provides a good overview of plant community structure, it also highlights a gap in the taxonomic coverage of South African plants on public DNA databases. To address this shortcoming, increased national DNA barcoding efforts are needed to expand current reference databases. This will be indispensable for the effective application of eDNA metabarcoding in studying South Africa's unique biodiversity.