Multi-omics and stable isotopic reveal coordinated carbon-nitrogen metabolic reprogramming sustaining diatom cellular homeostasis under CO2 limitation.

Algal blooms frequently trigger CO2 limitation, under which diatoms not only survive but dominate. However, the cellular metabolic adaptations underlying this ecological phenomenon remain poorly understood. This study systematically investigated the coordinated carbon-nitrogen metabolic response of the typical diatom Skeletonema costatum (S. costatum) to CO2 limitation (300 ppm, 100 ppm) via stable isotope and multi-omics analysis. CO2 limitation triggered the carbon concentrating mechanism (CCM) and attenuated nitrogen isotope fractionation, redirecting carbon flux towards amino acid biosynthesis rather than fatty acid biopathway. Integrated transcriptomic and metabolomic profiling revealed that carbon fixation and the tricarboxylic acid (TCA) cycle were activated, while fatty acid synthesis was inhibited. This redirected carbon skeletons from acetyl-CoA into the TCA cycle to support amino acid production. Concurrent upregulation of nitrogen assimilation genes, particularly those involved in glutamine/glutamate synthesis, facilitated ammonium incorporation. The alanine-aspartate-glutamate pathway served as a central hub, integrating carbon skeletons and amino groups to drive amino acid synthesis and maintain cellular homeostasis. These findings systematically delineate the metabolic reprogramming that enables diatoms to adapt to CO2 limitation, providing key insights into their dominance during algal blooms.