Physical-biological interactions create heterogeneous sea-air CO2 fluxes on the northern Patagonian Shelf during the low-productivity season

The Patagonian Shelf is recognized for its high potential for carbon uptake, driven by intense biological productivity. While net CO2 uptake persists much of the year, the mechanisms shaping sea-air CO2 fluxes (FCO2) under low-productivity conditions remain unclear. We examined surface FCO2 during autumn 2022 on the northern Patagonian Shelf, influenced by the Brazil and Malvinas Currents, where submesoscale activity generates patchy flux regimes. Even under low productivity, chlorophyll-a (Chl-a) was the strongest predictor of seawater pCO2 and modulated FCO2: high Chl-a areas acted as CO2 sinks, whereas low-Chl-a regions were near equilibrium or sources. Bloom phenology explained coherent patterns, with sinks associated with off-season peaks and sources with late-stage declines. Strongest uptake occurred in a retention zone offshore the upwelling front, where Malvinas Current circulation concentrated pigmented cells. Conversely, adjacent upwelling areas with stronger advection promoted outgassing of aged, carbon-rich waters that offset biological uptake, underscoring the dual role of upwelling. Planktonic assemblages also modulated carbon cycling: Prochlorococcus dominated oligotrophic Brazil Current waters with low Chl-a, depleted microbes, and reduced fluorescent dissolved organic matter (DOM), reflecting limited sequestration and persistent outgassing. Conversely, Synechococcus, picoeukaryotes, and heterotrophic bacteria co-occurred in sink regions, where DOM showed signatures of recent production. On the shelf, abundant bacteria and viruses were linked to humic-like refractory DOM, suggesting microbial reworking as a pathway for long-term storage. These findings demonstrate that while temperature set the FCO2 landscape at the Brazil-Malvinas confluence, while physical transport, bloom dynamics, and microbial transformations interact to produce heterogeneous CO2 source-sink patterns.