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The Benguela Upwelling System (BUS) is one of the world’s most productive ecosystems, supporting globally relevant pelagic fisheries. BUS marine community can change as a function of nutrients and omega-3 long chain polyunsaturated fatty acids (hereafter, omega-3) availability. Phytoplankton growth is supported by upwelled nitrate, a new source of nitrogen (N), or by recycled N forms such as ammonium. Preferential assimilation of one N form over another may lead to differences in omega-3 production between high and low food-quality species. This study evaluates how upwelling and the N source(s) used by phytoplankton influence omega-3 production. Sampling was conducted in the BUS at an anchor station sampled daily for 10 consecutive days. An upwelling event on days 5-6-7 supplied high concentrations of nutrients to surface waters, while pre- and post- upwelling the water column was well-stratified with low nutrient concentrations. Omega-3 and phytoplankton concentrations declined to ⁓zero during the upwelling event. Nanoplankton (2.7-10µm) were responsible for most of the productivity (30-95%) and relied on nitrate for their growth. Omega-3 concentrations at the surface reached peaks of 215.5 and 175.3µgL-1 pre- and post-upwelling, which were up to 10-times higher than previous measurements from the BUS. Pre-upwelling, non-diatom trophic markers were dominant, with a rapid switch (over just two days) to diatom trophic markers post-upwelling. This study defines the key role of upwelling in promoting phytoplankton omega-3 production, which is tightly coupled to the introduction of new-N during upwelling. The high concentrations of omega-3 reported suggest that global omega-3 production is largely underestimated.

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 (2.7‐10µm) dominated primary production (30‐95%), relying mainly on nitrate to support their growth. Surface LC omega‐3 concentrations reached peaks of 215 and 175 µgL‐1 pre‐ and post‐upwelling, up to 10‐times higher than previous measurements from the BUS (<5 µgL‐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.