Temporal structure of chemical stress controls single-cell inhibition and recovery in photosynthetic microorganisms

Although fluctuating conditions are a hallmark of microbial habitats, how the timing of chemical stress influences single-cell inhibition and recovery is not well resolved. Using a microfluidic platform, we continuously tracked photosynthetic performance in thousands of individual cells of a coral-associated microalga ( Symbiodiniaceae sp.) exposed to identical cumulative doses of the photosystem II inhibitor diuron delivered either as constant or fluctuating profiles. Fluctuating exposure produced stronger early inhibition than constant exposure, but as concentrations declined it enabled partial recovery that did not occur under time-averaged constant conditions. These dynamics revealed distinct response subpopulations that differed in both the magnitude and timing of inhibition, including groups that regained activity exclusively under fluctuating stress. Quantifying per-cell decline kinetics showed that fluctuating exposure synchronizes the onset of inhibition across cells, creating a narrow temporal window in which a subset of cells can recover once stress levels fall, whereas constant exposure yields more heterogeneous but uniformly declining trajectories. These results demonstrate that stress timing, not cumulative dose alone, governs whether photosynthetic inhibition is reversible at the single-cell level. More broadly, our findings illustrate how temporal variability and intrinsic phenotypic heterogeneity jointly govern cellular function, highlighting stress timing as an important and often overlooked axis shaping microbial performance in dynamic environments. Significance statement Environmental stress in nature is rarely constant; instead, it fluctuates over minutes to days. Yet most laboratory assays rely on static exposures, leaving the role of stress timing poorly understood. Using microfluidics, we imposed precisely timed chemical stress on individual cells of a coral-associated microalga and monitored their photosynthetic performance continuously. Fluctuating exposure caused strong initial inhibition but later allowed partial recovery in a subset of cells, revealing functional heterogeneity that constant stress concealed. These results show that when stress occurs, its temporal structure can be as important as how much stress is delivered. By uncovering mechanisms that govern reversibility and heterogeneity in a key coral symbiont, this work provides a mechanistic basis for understanding microbial responses in dynamic environments.