Drivers of short-term variability in phytoplankton production in an embayment of the southern Benguela upwelling system

St Helena Bay (SHB), a retention zone in the southern Benguela upwelling system, supports 40–50% of the region's primary productivity. It also experiences harmful algal blooms (HABs) and hypoxic conditions that are difficult to predict given the high sub-seasonal variability. To better understand this variability, net primary production (NPP), nitrate and ammonium uptake, and phytoplankton community composition were monitored for ten days in SHB during summer, the season of enhanced upwelling. A period of active upwelling (days 1–5) was followed by one of relaxation (days 6–10). During upwelling, the mixed layer was deeper than the euphotic zone and phytoplankton were light-limited, evidenced by high ambient nitrate concentrations and low rates of NPP and nitrate uptake. During relaxation, stratification increased, restricting phytoplankton production to a shallow euphotic zone in which nitrate was exhausted after three days; the subsequent decline in NPP and nitrate uptake rates confirm that nutrient availability rapidly succeeded light as the dominant control on productivity. Nanophytoplankton (mainly the small diatoms, Chaetoceros spp. and Skeletonema costatum) dominated the biomass, NPP, and nitrate uptake throughout the experiment. We attribute this to their ability to respond quickly to newly-upwelled nitrate and to sustain elevated nitrate uptake rates for longer than pico- and microphytoplankton. They may also engage in luxury nitrate uptake, storing nitrate intracellularly under high-nutrient conditions and assimilating it later when nutrients are depleted. Additionally, Chaetoceros spp. and S. costatum are chain-formers, benefitting from the advantages of being small (i.e., as individual cells) and large (i.e., when aggregated into chains). A weakening of surface stratification late in the experiment may have prevented dinoflagellates, some of which are HAB species, from succeeding the diatoms. One implication of this is that understanding the rapid cycling between light and nutrient limitation of SHB phytoplankton, induced by an actively-upwelling versus stratified water column, may improve our capacity to anticipate HABs and the associated hypoxic events.