Dynamic Regulation of Growth and Physiology of Microbes under Complex Changing Conditions

As microbes deplete local resources and transition from exponential to stationary phase they can change greatly in size, morphology, growth and expression-profiles. These responses can also vary importantly between individual cells, as shown by population snapshots. However, it has been difficult to track individual cells along the growth curve to determine the progression of events or correlations between how cells enter and exit dormancy. We have developed a platform for tracking >105 parallel cell lineages in dense and changing cultures, independently validating that the imaged cells closely track the batch population. This provides a microcosm of bulk growth with exceptional resolution and control, while enabling conventional bulk assays on the same culture. We used the platform to show that for both Escherichia coli and Bacillus subtilis, growth changes from an adder mode in exponential phase to a mixed adder-timer entering stationary phase, and then a near-perfect sizer upon exit — creating broadly distributed cell sizes in stationary phase — and rapid return to narrowly distributed sizes upon exit. By high-throughput tracking of single cells as they enter and exit stationary phase, we further show that the heterogeneity in entry and exit behavior has little consequence in regular wake up from overnight stationary phase but can play important role in determining population fitness after long periods of dormancy or survival against antibiotics.