Metabarcoding of zooplankton confirms southwards dispersal of decapod crustacean species in the western Indian Ocean

Abstract

Metabarcoding to determine marine zooplankton species composition is a fast-developing method, yet to be fully standardised. DNA barcode reference libraries that link species to barcode sequences remain incomplete, taxonomically imprecise, and biased towards well-studied regions. We used metabarcoding to determine the decapod crustacean species present in the marine zooplankton off eastern South Africa, a region for which reference libraries are comparatively poor. Zooplankton communities were sampled with tow nets at stations on the shelf (20- and 50-m isobaths) and at the shelf edge (100- and 200-m isobaths), and the samples were processed using high-throughput sequencing technology. The cytochrome c oxidase subunit I (COI) gene region was used for taxonomic assignment of amplicon sequence variants to species level at 95% and 99% similarity to barcode records. Detected species were cross-referenced against occurrence records from the region. Eightyone decapod species were detected at 95% sequence similarity, but this declined to 60 species at the stricter 99% threshold. False-positive identifications were reduced by 60%. True crabs (Brachyura) were proportionally over-represented; the ratios of prawns (Dendrobranchiata), lobsters (Achelata) and burrowing shrimp (Axiidea) were consistent with occurrence records; and true shrimps (Caridea) and hermit crabs (Anomura) were under-represented. Metabarcoding identified 19 tropical western Indian Ocean (WIO) species in the samples from eastern Africa, confirming a southwards dispersal of drifting phases through the Mozambique Channel. Congruence of WIO species with the Agulhas Bioregion (shelf-edge detections) and Delagoa Biozone (shallow detections) was consistent with the dispersal of tropical species in warmer water masses. Metabarcoding of marine zooplankton communities to obtain species-level information advances high-resolution ecological research in pelagic ecosystems.