Abstract
Freshwater ecosystems support the environment, society, and the economy by providing ecosystem services. The rapid expansion of urbanization and increase in human activities in the past decade resulted in a deterioration of the ecological conditions of freshwater bodies. Freshwater biota is the most impacted, with biodiversity facing declines of 3.9% annually. With the projected increase of 60% of people living in urban areas by 2030, knowledge of species communities contained within the city is vital in establishing and implementing conservation and management strategies for biodiversity. Traditional approaches use historical data, knowledge of species’ ecology, and time-consuming survey methods to detect and survey species, whereas eDNA metabarcoding provides a rapid tool to survey plant communities. Numerous studies have focussed on assessing microbial and animal biodiversity from different water sources; however, eDNA metabarcoding assessments of plant communities are less common. In this study, environmental DNA metabarcoding was used to detect plant biodiversity from cell deposits present in water samples from the Westdene dam, Johannesburg. Water samples (in total, 24 samples) were collected from six sites around the dam's perimeter. The collected water samples were filtered, genomic DNA was extracted using CTAB, and PCR targeted the rbcL and trnH-psbA regions. Sequencing was done using Ion Torrent S5 next-generation 600 bp chemistry and 520 chip. A total of 3,683,168 single-end (SE) sequences were obtained for both markers. Quality control was conducted using FASTQC. Clustering and demultiplexing yielded 490 OTUs for rbcL and 83 OTUs for trnH-psbA. The obtained OTUs were assigned to 35 families for rbcL and three families for trnH-psbA. Also, the presence
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of Morus alba, an alien invasive species on the Category 3 NEM:BA list, was detected, highlighting the potential application of eDNA metabarcoding in the early detection of alien invasive species. Overall, the observed taxonomic coverage was limited due to the demand for South African plant specimens in genetic reference databases. This study thus advocates for increased barcoding efforts to expand the plant reference database, a critical step in the successful use of eDNA metabarcoding for biodiversity research in South Africa.