Fitness cost associated with cell phenotypic switching drives population diversification dynamics and controllability

Abstract

Isogenic cell populations can cope with stress conditions by switching to alternative phenotypes. Even if it can lead to increased fitness in a natural context, this feature is typically unwanted for a range of applications (e.g., bioproduction, synthetic biology, and biomedicine) where it tends to make cellular response unpredictable. However, little is known about the diversification profiles that can be adopted by a cell population. Here, we characterize the diversification dynamics for various systems (bacteria and yeast) and for different phenotypes (utilization of alternative carbon sources, general stress response and more complex development patterns). Our results suggest that the diversification dynamics and the fitness cost associated with cell switching are coupled. To quantify the contribution of the switching cost on population dynamics, we design a stochastic model that let us reproduce the dynamics observed experimentally and identify three diversification regimes, i.e., constrained (at low switching cost), dispersed (at medium and high switching cost), and bursty (for very high switching cost). Furthermore, we use a cell-machine interface called Segregostat to demonstrate that different levels of control can be applied to these diversification regimes, enabling applications involving more precise cellular responses.

WITHDRAWN: Release of extracellular DNA byPseudomonasspecies as a major determinant for biofilm switching and an early indicator for cell population control

“…This regime is characterized by the appearance of spontaneous flux of cells (called bursts) phenotypically switching, these cells being progressively washed-out from the continuous cultivation device due to the loss of growth associated with the fitness cost. This specific diversification regime was previously reported during cultivation performed in a device called Segregostat 27 . In short, the Segregostat cultivation protocol relies on the use of reactive flow cytometry (Figure 4A) to detect the bursts of diversification (in a way similar to the determination of the fluxes of cells shown in Figure 2J).…”

“…When a burst of diversification is detected, a pulse of glucose is added in order to interfere with the natural diversification process i.e., by giving a fitness advantage to the cells that are not differentiating. This concept is illustrated in the case of the sporulation in Bacillus subtilis (Figure 4B) 27 . In this case, a PspoIIE:GFP transcriptional reporter was used in order to detect the cells deciding to trigger sporulation.…”

“…In microbial ecology, phenotypic switching is often associated with a fitness cost 25,32 . We recently demonstrated that this cost is the main driver for diversification dynamics of the whole population 27 . To illustrate this concept, we will take one of our previously characterized cellular system as an example.…”

“…In the previous section, we observed that the diversification dynamics associated with biofilm switching was bursty. Our previous experiences with other bursty systems, like the sporulation in Bacillus subtilis or the T7-based expression system in E. coli, pointed out that these systems can be easily perturbed based on glucose pulsing since the differentiated fraction of cells exhibits a significantly reduced fitness by comparison with the non-differentiated one 27 . This approach seems also to hold in the case of biofilm switching, given the fitness cost observed at this level (Figure 3).…”

“…Massive release of eDNA increases the probability of binding to cells and the number of eDNA-bound cells, in turn, increases the probability of cell aggregation and biofilm formation. In this work, we will use these characteristics to characterize the dynamics of P. putida population upon continuous cultivation based on automated flow cytometry (FC) 27 . In a second, reactive FC strategies 28,29 will be implemented for acting on the cell phenotypic switching mechanisms associated with biofilm formation in an attempt to either reduce or enhance biofilm formation.…”