Doctoral Degree. University of KwaZulu-Natal, Pietermaritzburg.Zooplankton are abundant and diverse marine organisms that form ecologically important
communities in marine pelagic ecosystems. They are well-suited for biomonitoring of ecosystem
health and changes in biodiversity because their community structure and biomass respond rapidly
to environmental variation. Biomonitoring of zooplankton communities using traditional
morphology-based species identification methods is labor-intensive due to their cryptic
morphology, high diversity and small body size. Fast-developing molecular techniques such as
DNA metabarcoding (large-scale, high-throughput DNA sequencing of targeted gene regions to
simultaneously identify multiple species present in samples) may provide higher resolution,
accurate, faster and more cost-effective biomonitoring tools. The primary objectives of this
dissertation were to develop and test a novel DNA metabarcoding approach for biomonitoring of
marine zooplankton over the continental shelf of eastern South Africa. Novel taxon-specific DNA
mini-barcode primers were designed to increase species identification rates of selected taxa.
Artificially assembled mock communities with known composition and relative abundances were
then used in an experimental setup to test detection rates and the accuracy of designed and
published primers. The DNA metabarcoding protocol was then used to assess connectivity among
zooplankton communities over the narrow KwaZulu-Natal continental shelf. Plankton tow nets
were used to sample cross-shelf transects at three sites (uThukela, Durban and Aliwal), which are
strongly influenced by the Agulhas Current but differ in shelf width, seafloor substrate and benthic
habitat structures. Connectivity network analysis detected distinct clustering of zooplankton
communities associated with each transect. The hypothesis that a dynamic ocean current regime
associated with the offshore Agulhas Current (nearby and flowing parallel to the shelf-edge) would
result in similar well-mixed alongshore zooplankton communities was rejected. A strong benthicpelagic
coupling effect was inferred based on the species composition of planktonic larvae and
benthic adults occurring at the respective transects. This dissertation provides a refined and novel
method for biomonitoring of marine pelagic environments in coastal waters, based on taxonspecific
DNA metabarcoding of zooplankton communities. The approach is well-suited to
measuring the long-term effects of climate change on marine pelagic ecosystems and ocean
productivity
