Marine zooplankton community analysis confirms the ecological role of a sheltered bight along a narrow shelf exposed to the Agulhas Current.

Zooplankton play an essential role in marine ecosystems as the linkage between primary producers (phytoplankton) and higher trophic levels in food webs, and by forming a dynamic pool of recruits for multiple invertebrate and fish species. Zooplankton have high taxonomic diversity and abundance, and are distributed patchily in oceans, facilitated by a combination of physical processes and biological interactions. At larger spatial scales, ocean currents are key determinants of zooplankton species composition and abundance. The Agulhas Current is one of the strongest western boundary currents in the world, flowing southwestwards along the edge of a narrow, exposed shelf off eastern South Africa. A single sizable bight (KwaZulu-Natal Bight) along the coastline provides a shallow productive enclave, sheltered against strong directional flow. We used metabarcoding and community analysis of plankton collected near the surface of four cross-shelf transects in sheltered (KZN Bight) and exposed shelf habitats to test hypotheses that: species richness and relative abundance differ between sheltered- and exposed shelf areas; sub-mesoscale processes (eddies, counter-currents) retain zooplankton in the sheltered bight; and that the bight acts as a spawning and nursery area. Metabarcoding recovered much higher species richness and diversity at a finer species-level resolution than could previously be achieved with microscopy. Of the 271 species clusters recovered through metabarcoding, 63% could be attributed to species based on barcode reference databases. Species richness was dominated by crustaceans from the Malacostraca class (161 spp.), ray-finned fishes (45 spp.) and copepods (28 spp.). Connectivity analyses confirmed the retention of zooplankton in the sheltered bight by semi-permanent current circulation patterns. Ray-finned fishes had the highest relative abundance in the sheltered bight, comprising mainly of pelagic fish (<i>Scomber japonicus</i>) eggs, thus confirming the importance of the bight as a spawning area along a narrow continental shelf exposed to strong directional currents. The intersection of metabarcoding, community analysis and physical oceanography is a promising new direction for marine ecological research in the Western Indian Ocean and beyond.