DNA metabarcoding reveals distinct bacterial and phytoplankton assemblages in the Agulhas Current and the adjacent coastal shelf

Abstract The Agulhas Current is a globally important western boundary current that influences numerous processes (e.g., upwelling, biogeochemical fluxes and distribution of marine taxa) in the southwestern Indian Ocean. The oceanographic processes of the Agulhas Current are well understood, but precisely how they influence coastal ecosystem productivity remains to be elucidated. In the present foundational study, we characterized the bacterial (16S rRNA gene) and phytoplankton (chloroplast 16S rRNA, rbcL , and eukaryotic 18S rRNA genes) community structures of the Agulhas Current system using a metabarcoding approach. All four markers provided consistent data on the bacterial and phytoplankton communities in the Agulhas Current and coastal sites. The study revealed distinct, conserved communities and similar patterns of dominance by taxa adapted to oligotrophic conditions within the Agulhas Current, sampled 2 yr apart. By contrast, there was significant variability in taxonomic diversity and abundance of phytoplankton communities in the adjacent coastal waters that could be linked to localized upwelling. While the Agulhas Current bacterial and phytoplankton communities were diverse and represented many functional groups, the coastal sites were more diatom‐dominated and included genera typically associated with upwelling, for example, Thalassiosira spp. Based on their relative abundance profiles, phytoplankton communities were more responsive to environmental variability than bacteria and may therefore prove more useful in linking ecosystem dynamics to environmental variability in marine systems.