A comparison of mangrove and estuarine fish diversity using eDNA metabarcoding and baited remote underwater visual surveys in South Africa and Mozambique

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Stellenbosch : Stellenbosch University
ENGLISH ABSTRACT: Within estuaries, mangroves and seagrass beds are critical habitats that act as nurseries and refuge areas for fishes and provide food for coastal communities. However, in southern Africa, there are knowledge gaps regarding fish diversity in 1) mangrove ecosystems and 2) under-studied estuarine bays such as Inhambane Bay, Mozambique. Environmental DNA (eDNA) metabarcoding and baited remote underwater video systems (BRUVs) are used as complementary tools for biomonitoring as they provide a better insight into the presence of species and their interactions with the environment. This project investigates OTU (operational taxonomic unit) and genera richness in South Africa and Inhambane Bay using eDNA metabarcoding and BRUVs. The aims were to 1) identify whether mangrove fish diversity varies over a latitudinal gradient, 2) compare genera richness inside and outside the locally managed marine areas (LMMAs) in Inhambane Bay, and 3) compare the use of complementary tools BRUVs and eDNA in both sites. At all study sites, estuarine water was sampled and BRUVs were deployed for an hour. In South Africa, eDNA recovered 110 OTUs with 58 genera and BRUVs recovered 28 genera with only 12 common taxa detected using both methods. Fish diversity did not follow a latitudinal gradient in the mangroves as hypothesized. In Inhambane Bay, eDNA recovered 176 OTUs between the three locations. For the comparison between methods, 76 genera were recovered by metabarcoding and BRUVs only recovered 10 genera. There was no significant difference in fish diversity inside and outside the LMMAs. In both studies, the dual use of BRUVs and eDNA was valuable by detecting species unique to those methods. The results indicated a need to improve the study design, conduct more research on estuarine and mangrove fish diversity, and to improve reference databases and fish guides for southern Africa.
AFRIKAANSE OPSOMMING: Geen opsomming beskikbaar.
Thesis (MSc)--Stellenbosch University, 2023.