Metabarcoding of ichthyoplankton communities associated with a highly dynamic shelf region of the southwest Indian Ocean

Drifting fish eggs and larvae (ichthyoplankton) can be identified to species using DNA metabarcoding, allowing for community analyses at a high taxonomic resolution. We undertook a regional-scale study of ichthyoplankton distribution along the east coast of South Africa, focused on narrow shelf and sheltered bight habitats in the contrasting environments of the tropical Delagoa and subtropical Natal ecoregions. Zooplankton samples were collected with tow nets at discrete stations along cross-shelf transects (20–200 m depth) spaced along a latitudinal gradient that incorporates a known biogeographical boundary. Metabarcoding detected 67 fish species, of which 64 matched prior distribution records of fishes from South Africa, with the remaining three known from the western Indian Ocean. Detections included fish species classified as coastal, neritic, and oceanic, with adult habitats ranging from epi- and mesopelagic to benthopelagic and benthic. By family, Myctophidae (10 species), Carangidae, Clupeidae, Labridae (each with 4 species) and Haemulidae (3 species) were most speciose. Ichthyoplankton community composition varied significantly with latitude, distance to coast, distance to the shelf edge and transect. Small pelagic fishes had the highest frequency of occurrence: Engraulis capensis, Emmelichthys nitidus and Benthosema pterotum increased in frequency towards the north, whereas Etrumeus whiteheadi increased towards the south. Chub mackerel Scomber japonicus accounted for most variability related to distance from the coast, whilst African scad Trachurus delagoa showed relatively strong correlation with distance to the shelf edge. Dissimilarity between communities in the Delagoa and Natal ecoregions was 98-100%, whereas neighbouring transects located within the sheltered KwaZulu-Natal Bight had lower dissimilarity (56-86%). Onshore transport of ichthyoplankton by intrusions of south-flowing Agulhas Current water may explain the large proportion of oceanic species collected over the shelf. The value of metabarcoding as a tool to facilitate marine ecological studies at a high taxonomic resolution is discussed.