Abstract
In South Africa, mangrove forests and seagrass meadows often co‐occur in estuarine systems and in combination host rich, often endemic biodiversity. There is an urgent need to explore community diversity in coastal vegetated ecosystems, given the degrading effects of climate change and anthropogenic pressures. Environmental DNA metabarcoding is a promising biomonitoring tool in South African coastal ecosystems, although studies highlight the need to optimise and standardise sampling protocols. This study aimed to contribute to developing sampling protocols by understanding the applicability of environmental DNA (eDNA) metabarcoding within coastal vegetated habitats and by investigating diversity using two different sample types. Aquatic and sedimentary environmental DNA samples from three estuaries along the east coast of South Africa, in combination with MiFish metabarcoding, detected 148 operational taxonomic units (OTUs) representing 67 fish genera from 50 families, although only 16% were resolved to species. We observed that aquatic eDNA samples detected 97% of the total fish diversity, suggesting that this is an efficient tool to comprehensively detect ichthyofaunal diversity. We did not detect different fish communities between mangroves and seagrasses and our findings underscore the importance of taking hydrological connectivity into consideration for sampling design. Overall, our work reinforces key considerations for future eDNA metabarcoding studies focused on fish fauna in estuaries, and therefore contributes to optimising sampling protocols to support the biomonitoring of coastal biodiversity.