Bacterial respiration during stationary phase induces intracellular damage that leads to dormancy

Most bacteria frequently encounter nutrient-depleted conditions, necessitating regulatory mechanisms that alter cellular physiology and allow for survival of starvation. Here, we show that regrowth of Escherichia coli from prolonged stationary phase upon encountering fresh nutrients is heterogeneous, with one subpopulation suddenly regrowing after a delay (dormancy) and another of nongrowing cells that represented an increasing fraction as the culture aged. Moreover, a sizeable fraction of cells rejuvenated immediately, even when the inoculum was from very old cultures. The size of the dormant and nongrowing subpopulations depended on the time cells had endured stationary phase, as opposed to time-dependent changes to the medium. Regrowth of dormant cells was correlated with the dissolution of polar phase-bright foci that likely represent aggregates of damage, and a deep-learning algorithm was able to distinguish cellular fates based on a single stationary-phase image. Growth restarted in dormant cells after the upregulation of chaperones and DNA repair enzymes, and deletion of the chaperone DnaK resulted in compromised stationary-phase cell morphology and higher incidence of non-growing cells. A mathematical model of damage accumulation and division-mediated partitioning was in quantitative agreement with experimental data, including the small population of cells capable of immediate regrowth even in old cultures. Cells that endured stationary-phase without the ability to respire all immediately and homogeneously regrew in fresh nutrients, indicating that respiration in stationary phase is the driver of dormancy. These findings establish the importance of intracellular damage control when nutrients are sparse, and repair when nutrients are plentiful.