Bacterial stress rewires diatom chronobiology and ecosystem function.

Diatoms are vital primary producers in marine ecosystems and play a key role in blue carbon sequestration. Although their circadian rhythms have been studied in isolation, how these rhythms are modulated by co-occurring bacteria remains unknown. Using a defined co-culture of the diatom Phaeodactylum tricornutum with the marine bacterium Aliivibrio fischeri, we observed time-dependent physiological and transcriptomic changes in P. tricornutum, including a 16.3% reduction in rhythmic genes with prolonged culture time. Genome-scale metabolic modeling suggested a biphasic response, with predicted biomass flux increasing by 81% at the early co-culture stage but decreasing by 87% during prolonged co-culture. Deconvolution of the transcriptome via AI-driven independent component analysis identified gene modules associated with silica transport and senescence-related responses under co-culture conditions. Together, these findings establish a systems-level framework that links interspecies interactions between diatoms and bacteria, providing mechanistic insights into how microbial associations influence phytoplankton chronobiology and rhythmic regulation.