Cellular populations in both nature and the laboratory are composed of phenotypically heterogeneous individuals that compete with each other resulting in complex population dynamics. Predicting population growth characteristics based on knowledge of heterogeneous single-cell dynamics remains challenging. By observing groups of cells for hundreds of generations at single-cell resolution, we reveal that growth noise causes clonal populations of Escherichia coli to double faster than the mean doubling time of their constituent single cells across a broad set of balanced-growth conditions. We show that the population-level growth rate gain as well as age structures of populations and of cell lineages in competition are predictable. Furthermore, we theoretically reveal that the growth rate gain can be linked with the relative entropy of lineage generation time distributions. Unexpectedly, we find an empirical linear relation between the means and the variances of generation times across conditions, which provides a general constraint on maximal growth rates. Together, these results demonstrate a fundamental benefit of noise for population growth, and identify a growth law that sets a "speed limit" for proliferation.growth noise | age-structured population model | cell lineage analysis | growth law | microfluidics C ell growth is an important physiological process that underlies the fitness of organisms. In exponentially growing cell populations, proliferation is usually quantified using the bulk population growth rate, which is assumed to represent the average growth rate of single cells within a population. In addition, basic growth laws exist that relate ribosome function and metabolic efficiency, macromolecular composition, and cell size of the culture as a whole to the bulk population growth rate (1-3). Population growth rate is therefore a quantity of primary importance that reports cellular physiological states and fitness.However, at the single-cell level, growth-related parameters such as the division time interval and division cell size are heterogeneous even in a clonal population growing at a constant rate (4-9). Such "growth noise" causes concurrently living cells to compete within the population for representation among its future descendants. For example, if two sibling cells born from the same mother cell had different division intervals, the faster dividing sibling is likely to have more descendants in the future population compared with its slower dividing sister, despite the fact that progenies of both siblings may proliferate equally well (Fig. 1). Intrapopulation competition complicates single-cell analysis because any growth-correlated quantities measured over the population deviate from intrinsic single-cell properties (10-12). In the case of the toy model described in Fig. 1, cells are assumed to determine their generation times (division interval) randomly by roll of a dice. The mean of intrinsic cellular generation time is thus ð1 + 2 + ⋯ + 6Þ=6 = 3.5 h, but population doubling time, which is...

Restriction-modification (RM) systems represent a minimal and ubiquitous biological system of self/non-self discrimination in prokaryotes [1], which protects hosts from exogenous DNA [2]. The mechanism is based on the balance between methyltransferase (M) and cognate restriction endonuclease (R). M tags endogenous DNA as self by methylating short specific DNA sequences called restriction sites, whereas R recognizes unmethylated restriction sites as non-self and introduces a double-stranded DNA break [3]. Restriction sites are significantly underrepresented in prokaryotic genomes [4-7], suggesting that the discrimination mechanism is imperfect and occasionally leads to autoimmunity due to self-DNA cleavage (self-restriction) [8]. Furthermore, RM systems can promote DNA recombination [9] and contribute to genetic variation in microbial populations, thus facilitating adaptive evolution [10]. However, cleavage of self-DNA by RM systems as elements shaping prokaryotic genomes has not been directly detected, and its cause, frequency, and outcome are unknown. We quantify self-restriction caused by two RM systems of Escherichia coli and find that, in agreement with levels of restriction site avoidance, EcoRI, but not EcoRV, cleaves self-DNA at a measurable rate. Self-restriction is a stochastic process, which temporarily induces the SOS response, and is followed by DNA repair, maintaining cell viability. We find that RM systems with higher restriction efficiency against bacteriophage infections exhibit a higher rate of self-restriction, and that this rate can be further increased by stochastic imbalance between R and M. Our results identify molecular noise in RM systems as a factor shaping prokaryotic genomes.

Microorganisms often live in symbiosis with their hosts, and some are considered mutualists, where all species involved benefit from the interaction. How free-living microorganisms have evolved to become mutualists is unclear. Here we report an experimental system in which non-symbiotic Escherichia coli evolves into an insect mutualist. The stinkbug Plautia stali is typically associated with its essential gut symbiont, Pantoea sp., which colonizes a specialized symbiotic organ. When sterilized newborn nymphs were infected with E. coli rather than Pantoea sp., only a few insects survived, in which E. coli exhibited specific localization to the symbiotic organ and vertical transmission to the offspring. Through transgenerational maintenance with P. stali, several hypermutating E. coli lines independently evolved to support the host’s high adult emergence and improved body colour; these were called ‘mutualistic’ E. coli. These mutants exhibited slower bacterial growth, smaller size, loss of flagellar motility and lack of an extracellular matrix. Transcriptomic and genomic analyses of ‘mutualistic’ E. coli lines revealed independent mutations that disrupted the carbon catabolite repression global transcriptional regulator system. Each mutation reproduced the mutualistic phenotypes when introduced into wild-type E. coli, confirming that single carbon catabolite repression mutations can make E. coli an insect mutualist. These findings provide an experimental system for future work on host–microbe symbioses and may explain why microbial mutualisms are omnipresent in nature.

Bacterial persistence is a phenomenon in which a small fraction of isogenic bacterial cells survives a lethal dose of antibiotics. It is generally assumed that persistence is caused by growth-arrested dormant cells generated prior to drug exposure. However, evidence from direct observation is scarce due to extremely low frequencies of persisters, and is limited to high persistence mutants or to conditions that significantly increase persister frequencies. Here, utilizing a microfluidic device with a membrane-covered microchamber array, we visualize the responses of more than 106 individual cells of wildtype Escherichia coli to lethal doses of antibiotics, sampling cells from different growth phases and culture media. We show that preexisting dormant persisters constitute only minor fractions of persistent cell lineages in populations sampled from exponential phase, and that most persistent cell lineages grew actively before drug exposure. Actively growing persisters exhibit radical morphological changes in response to drug exposure, including L-form-like morphologies or filamentation depending on antibiotic type, and restore their rod-like shape after drug removal. Incubating cells under stationary phase conditions increases both the frequency and the probability of survival of dormant cells. While dormant cells in late stationary phase express a general stress response regulator, RpoS, at high levels, persistent cell lineages tended to show low to moderate RpoS expression among the dormant cells. These results demonstrate that heterogeneous survival pathways may coexist within bacterial populations to achieve persistence and that persistence does not necessarily require dormant cells.