Life on Earth is affected by periodic fluctuations in light caused by our planet’s rotation. Circadian (24-h) rhythms enable living systems to adapt to environmental cycles and anticipate the changes in their surroundings. To perform their functions, the clocks must be sensitive to the entraining cues and simultaneously resilient to perturbations in their environments. It is unclear how clocks have evolved to find this balance in any species.

Here, we used the cyanobacterium Synechococcus elongatus to investigate the clock dynamics in individual cells otherwise masked in bulk studies. To do this, we developed a microfluidic setup, allowing us to carefully control cellular environments and quantify circadian gene expression and clock-modulated cell growth and division.

Using quantitative time-lapse microscopy, we measured the robustness of cyanobacterial circadian rhythms with previously inaccessible precision. We observed extremely robust timekeeping under various deterministic light environments. Using clock mutants, we revealed that the rhythm robustness under constant light is maintained even without individual regulators of the clock. In contrast, perturbations to the core clock genes affected free-running rhythms and clock entrainment in individual cells.

Exposed to variable light periods, the clock buffered the noise by shifting its phase only by a fraction of the perturbation. The clock also made cell cycle duration less variable under such conditions. However, the clock timing was sensitive to the meteorological fluctuations in light amplitude. Comparing wild-type and clock-less cells, we observed clock-induced growth acceleration during the day. This growth advantage was consistent in the absence of light amplitude fluctuations and remains to be understood under more natural conditions.

Overall, we provided a novel experimental framework for studying the robustness of individual clocks and revealed the principles of clock-environment interactions useful for informing strategies for altering natural and synthetic clocks for biotechnological applications.