A preliminary study into the detection of fish environmental DNA in selected South African estuaries

Environmental DNA (eDNA) is a powerful technique for the non-invasive and comprehensive monitoring of entire ecosystems. Despite its many advantages, the use of eDNA in South Africa as an assessment tool for fish biodiversity is largely underutilised. This study was performed as an initial screening to assess the efficiency of the eDNA method for characterising fish communities in South African waters using the metabarcoding approach. Water samples were collected from eight estuaries and vacuum filtered using 0.45 μm nylon membrane filters. DNA was extracted from the filters, and sample extracts underwent PCR assaying using MiFish primers for the 12S rRNA gene, prior to being sequenced on the Illumina MiSeq platform. The resulting sequence data produced 1 574 092 raw reads, which resulted in 119 operational taxonomic units (OTUs) after filtering and clustering. Taxonomic assignment of the OTUs produced four different taxonomic groups and one group representing unidentified sequences. The group with the highest number of OTUs (54%) was assigned to fish taxa consisting of 12 families and 22 genera identified across all estuaries, with only 16 taxa identified to species level. As this was a preliminary study, few samples were collected, and therefore several recommendations for a more comprehensive study design are provided. Overall, these results support the hypothesis that the eDNA metabarcoding approach can efficiently detect fish species in South African estuarine environments.