Bacterial respiration during stationary phase induces intracellular damage that leads to delayed regrowth

Bacterial survival is often challenged by nutrient-depleted conditions. Here, we show that Escherichia coli regrowth from prolonged stationary phase is heterogeneous. Some cells rejuvenated immediately, even after extended starvation, but others only restarted growth after a delay or not at all. The proportion of nongrowing cells increased with time spent in stationary phase, rather than time-dependent medium changes. Delayed regrowth was correlated with the dissolution of polar phase-bright foci likely representing damaged protein aggregates, and a deep learning algorithm distinguished cellular fates based on single images. Delayed regrowth initiated after upregulation of chaperones and DNA-repair enzymes, and deletion of a chaperone compromised stationary-phase morphology and increased the nongrowing cell proportion. Mathematical modeling of damage accumulation and division-mediated partitioning quantitatively predicted all rejuvenation statistics. Cells regrew immediately after starving in the absence of respiration. These findings reinforce the importance of intracellular damage control when nutrients are sparse, and repair when nutrients are plentiful.