Marine phytoplankton drive the biological CO₂ pump through photosynthesis, contributing to nearly half of global primary productivity. The intensifying effects of ocean deoxygenation (DeO₂), acidification (OA), and warming (OW) are expected to impact primary productivity and related ecological processes. However, the combined physiological effects of DeO₂, OA, and OW on phytoplankton remain poorly understood, despite their cascading relationships. Here, we integrated in situ investigations, outdoor mesocosm experiments, and laboratory studies, utilizing Chlorophyll a (Chl a) fluorescence, radioactive isotope tracing, and transcriptome analysis to examine how coastal diatoms and diatom-dominated phytoplankton assemblages respond to DeO₂, in combination with OA and OW, in terms of primary production processes. Under the combined influence of these three factors, the carbon concentrating mechanisms (CCMs), photorespiration, and mitochondrial respiration of Thalassiosira pseudonana were reduced, accompanied by a downregulation of related encoding genes, while genes associated with photosynthesis were upregulated. These findings support physiological consequences that reduced O₂ enhance the photosynthetic carbon fixation in phytoplankton assemblages and Thalassiosira weissflogii, though they contradict findings promotion of CCMs in T. weissflogii under low O₂ condition, indicating that the effects of DeO₂ on phytoplankton may be species-specific. Despite the combined effects of DeO₂ and OA exacerbating the failure of diatoms in darkness, the presence of DeO₂ and OA enhanced the Chl a-normalized photosynthesis of diatom-dominated phytoplankton assemblages under light by about 193%, remarkably re-oxygenated the deoxygenated waters.

Ocean deoxygenation, diatoms, coastal phytoplankton assemblages, primary production processes