Abstract
Introduction Fluctuations in nitrogen and phosphorus availability are key drivers of harmful algal bloom dynamics, yet the molecular mechanisms enabling the paralytic shellfish toxin-producing dinoflagellate Gymnodinium catenatum to persist under nutrient limitation remain insufficiently resolved. Methods Here, we integrated batch culture experiments under nutrient-replete, nitrogen-depleted, and phosphorus-depleted conditions with measurements of physiological characteristics, and label-free quantitative proteomics to elucidate nutrient-specific acclimation strategies. Results Both deficiencies inhibited growth, but nitrogen depletion caused immediate growth arrest and a pronounced late-stage decline in cellular chlorophyll a , whereas phosphorus-depleted cells maintained slow growth and relatively stable pigment contents. Among 11, 255 identified proteins, 2, 558 and 532 were differentially expressed under nitrogen and phosphorus deprivation, respectively, indicating a substantially more extensive proteomic response under nitrogen stress. Under nitrogen limitation, cells coordinately repressed nitrate transport and reduction systems while increasing the abundance of proteins associated with ammonium uptake and assimilation, amino acid catabolism, and purine degradation, suggesting enhanced nitrogen recycling and remobilization under nitrogen deficiency. In contrast, phosphorus-depleted cells exhibited enhanced phosphate acquisition and redistribution, polyphosphate metabolism, and organic compounds scavenging pathways. Both deficiencies suppressed photosynthetic apparatus components and Calvin cycle enzymes, with more obvious effects under nitrogen deprivation, while central carbon metabolism exhibited treatment-specific responses, whereas central carbon metabolism showed stronger glycolytic and TCA-cycle responses to N deficiency and a shared branch-specific remodeling of the pentose phosphate pathway under both nutrient stresses. Discussion These findings demonstrated distinct, nutrient-specific metabolic allocation strategies in G. catenatum , providing a mechanistic framework for understanding its ecological success and bloom potential in nutrient-variable coastal environments.