Stabilization of Microbial Communities by Responsive Phenotypic Switching

Clonal microbes can switch between different phenotypes and recent theoretical work has shown that stochastic switching between these subpopulations can stabilize microbial communities. This phenotypic switching need not be stochastic, however, but can also be in response to environmental factors, both biotic and abiotic. Here, motivated by the bacterial persistence phenotype, we explore the ecological effects of such responsive switching by analyzing phenotypic switching in response to competing species. We show how the stability of microbial communities with responsive switching differs generically from that of communities with stochastic switching only. To understand this effect, we go on to analyse simple two-species models. Combining exact results and numerical simulations, we extend the classical stability results for models of two competing species without phenotypic variation to the case where one of the two species switches, stochastically and responsively, between two phenotypes. In particular, we show that responsive switching can stabilize coexistence even when stochastic switching on its own does not affect the stability of the community.

Role of bacterial persistence in spatial population expansion

Bacterial persistence, tolerance to antibiotics via stochastic phenotype switching provides a survival strategy and a fitness advantage in temporally fluctuating environments. Here we study its possible benefit in spatially varying environments using a Fisher wave approach. We study the spatial expansion of a population with stochastic switching between two phenotypes in spatially homogeneous conditions and in the presence of an antibiotic barrier. Our analytical results show that the expansion speed in growth-supporting conditions depends on the fraction of persister cells at the leading edge of the population wave. The leading edge contains a small fraction of persister cells, keeping the effect on the expansion speed minimal. The fraction of persisters increases gradually in the interior of the wave. This persister pool benefits the population when it is stalled by an antibiotic environment. In that case, the presence of persister enables the population to spread deeper into the antibiotic region and to cross an antibiotic region more rapidly. The interplay of population dynamics at the interface separating the two environments and phenotype switching in the antibiotic region results in a optimal switching rate. Overall, our results show that stochastic switching can promote population expansion in the presence of antibiotic barriers or other stressful environments.

Reducing phenotypic and genotypic instabilities of microbial population during continuous cultivation based on stochastic switching dynamics

Predicting the fate of a microbial population (i.e., growth, gene expression…) remains a challenge, especially when this population is exposed to very dynamic environmental conditions, such as those encountered during continuous cultivation processes. Indeed, the dynamic nature of continuous cultivation process implies the potential deviation of the microbial population involving genotypic and phenotypic diversification. This work has been focused on the induction of the arabinose operon in Escherichia coli as a model system. As a preliminary step, the GFP level triggered by an arabinose-inducible PBAD promoter has been tracked by flow cytometry in chemostat with glucose-arabinose co-feeding. Ampicillin was used as an “unstable” selective marker, allowing the simultaneous investigation of the effect of phenotypic diversification and genetic instability in continuous cultures. Under classical chemostat operation, the system was very unstable, with only a small fraction of cells (less than 10%) being able to accumulate GFP to a large extent, this fraction rapidly collapsing with time and going below 10% of the total population. On the long run, this phenotypic diversification was followed by an extensive loss of plasmid. In a second set of experiments, continuous cultivation was performed by adding either glucose or arabinose, based on the ability of individual cells for switching from low GFP to high GFP states, according to a technology called segregostat. In segregostat mode of cultivation, on-line flow cytometry analysis was used for adjusting the arabinose/glucose transitions based on the stochastic switching capabilities of the microbial population. This strategy allowed finding an appropriate arabinose pulsing frequency, leading to a prolonged maintenance of the induction level with limited impact of phenotypic diversification and genetic instability for more than 68 generations