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The Benguela upwelling system (BUS) is one of the world's most productive ecosystems, supporting globally relevant fisheries. The BUS marine community is modulated by the availability of nutrients and omega‐3 long chain polyunsaturated fatty acid (hereafter, LC omega‐3). Phytoplankton growth in the BUS can be supported by upwelled nitrate, a new nitrogen (N) source to the surface, or by recycled N such as ammonium. Preferential assimilation of one N source over another may yield differences in LC omega‐3 production between high and low food‐quality species. To evaluate how upwelling and the N source(s) consumed by phytoplankton influence LC omega‐3 production, we sampled a BUS anchor station daily for 10 days. Upwelling on days 5–7 supplied high concentrations of nutrients to the surface, while pre‐ and post‐upwelling, surface waters were stratified and nutrient concentrations were low. LC omega‐3 and phytoplankton concentrations were near‐zero during upwelling, and elevated pre‐ and post‐upwelling. Throughout our sampling, nanoplankton (2.7–10 µm) dominated primary production (30–95%), relying mainly on nitrate to support their growth. Surface LC omega‐3 concentrations reached peaks of 215 and 175 µg L−1 pre‐ and post‐upwelling, up to 10 times higher than previous measurements from the BUS (<5 µg L−1). Pre‐upwelling, non‐diatom trophic markers (18:1n − 9, 18:4n − 3, 18:5n − 3) were dominant, with a switch over just two days to diatom trophic markers post‐upwelling (16:1n − 7, 16:2n − 4, 16:2n − 7, 16:3n − 4, 16:4n − 1). This study reveals the key role of upwelling in promoting phytoplankton LC omega‐3 production, which is tightly coupled to the supply of new nitrate. Additionally, the high observed LC omega‐3 concentrations suggest that global LC omega‐3 production is underestimated. Plain Language Summary: Omega‐3 are lipids found in foods such as fish that are extremely important for human health. However, humans and most animals cannot produce omega‐3 in sufficient quantities to satisfy their health requirements and must thus acquire them through their diet. In the ocean, the main source of omega‐3 is phytoplankton, with different species producing different quantities and kinds of omega‐3. Phytoplankton growth also depends on the availability of nutrients, including nitrogen (N). Dominant assimilation of a new N source such as upwelled nitrate versus a recycled N source such as ammonium typically leads to the proliferation of different phytoplankton communities, which may also produce different amounts of omega‐3. This study evaluates how upwelling, and the N source(s) used by phytoplankton, influence omega‐3 production. During a 10‐day investigation conducted off the west coast of South Africa, we found that upwelling promoted phytoplankton omega‐3 production and that the community relied mainly on upwelled nitrate. Additionally, community composition changed rapidly during the study in response to upwelling, which was reflected in the amount and kind of omega‐3 produced. We observed quantities of omega‐3 that were 10 times higher than previous measurements from the region, suggesting that global omega‐3 production may be underestimated. Key Points: Upwelling promoted phytoplankton long chain omega‐3 production which was tightly coupled to the introduction of new nitrate during upwellingPre‐upwelling, non‐diatom trophic markers were dominant, with a rapid switch over just 2 days to diatom trophic markers post‐upwellingLong chain omega‐3 concentrations were 10 times higher than previous records suggesting that their global production has been underestimated [ABSTRACT FROM AUTHOR]

The well‐established importance of Agulhas Current "leakage" for Indian‐Atlantic Ocean exchange of heat and salt raises the question of the relevance of Agulhas eddies for carbon and nitrogen cycling. We measured net primary production (NPP), nitrate and ammonium uptake, and nitrification along a transect of the Cape Basin (CB) in winter 2017, including across an anticyclonic Agulhas eddy sampled at high‐resolution. Euphotic zone‐integrated rates of NPP and nitrogen uptake were more than three‐fold lower at the eddy center than at its edges, with intermediate rates measured outside the eddy. Additionally, proportionally more nitrate was consumed at the eddy edges than at its center. Mixed‐layer integrated nitrification rates were highest at the eddy‐center, with lower rates at the edges and in the surrounding basin. Accounting for phytoplankton consumption of newly nitrified nitrate in the eddy decreased the carbon export potential inferred from nitrate uptake (i.e., the f‐ratio) by 66% ± 37% (vs. a 14% ± 22% decrease across the rest of the transect). At most stations, NPP and total measured nitrogen uptake were decoupled relative to stoichiometric expectations, with roughly a third of NPP possibly supported by regenerated dissolved organic nitrogen (DON). Accounting for DON uptake decreased the average f‐ratio from 0.28 ± 0.26 to 0.22 ± 0.21, with the highest f‐ratio estimated for an eddy‐edge station (0.64) and the lowest for its center (0.00). While the low productivity metrics measured in the eddy‐center could imply that Agulhas leakage decreases carbon export potential in the CB, enhanced nutrient supply and consumption at eddy edges may (partly) offset this reduction. Plain Language Summary: Mesoscale eddies are abundant in the ocean, transporting physical, chemical, and biological properties from the eddy source region. Eddies can also cause small‐scale upwelling and/or downwelling, which affect the local biogeochemistry and biology (e.g., altering phytoplankton growth by changing the nutrient and/or light conditions). Large anticyclonic eddies that pinch off the Agulhas Current south of Africa transfer warm, salty waters from the Indian to the Atlantic Ocean, thereby playing a crucial role in ocean circulation. By contrast, little is known of the role of Agulhas eddies in carbon and nitrogen cycling. We find that the physical perturbations caused by the passage of an Agulhas eddy into the southeastern Atlantic stimulate primary production and nitrate uptake at the eddy edges, implying enhanced CO2 removal to depth, while productivity (and CO2 removal) is depressed at the eddy center. Additionally, the deep mixed layers created by the eddy's anticyclonic circulation favor high rates of nitrification, which produces recycled nitrate. Phytoplankton consumption of this nitrate yields no net removal of CO2, exacerbating the dampening effect of the eddy on Atlantic productivity. It is possible, however, that the reduction in productivity may be partly offset by the elevated supply and consumption of subsurface nutrients at the eddy edges. Key Points: Primary production and carbon export potential are elevated at Agulhas eddy edges and reduced at their centersAgulhas eddies host high rates of mixed‐layer nitrification that can supply 100% of phytoplankton nitrateDissolved organic nitrogen appears to fuel a significant fraction of primary production in Agulhas eddies and the Cape Basin [ABSTRACT FROM AUTHOR]