Emergent spatiotemporal population dynamics with cell-length control of synthetic microbial consortia

Abstract

The increased complexity of synthetic microbial biocircuits highlights the need for distributed cell functionality due to concomitant increases in metabolic and regulatory burdens imposed on single-strain topologies. Distributed systems, however, introduce additional challenges since consortium composition and spatiotemporal dynamics of constituent strains must be robustly controlled to achieve desired circuit behaviors. Here, we address these challenges with a modeling-based investigation of emergent spatiotemporal population dynamics using cell-length control in monolayer, two-strain bacterial consortia. We demonstrate that with dynamic control of a strain’s division length, nematic cell alignment in close-packed monolayers can be destabilized. We find that this destabilization confers an emergent, competitive advantage to smaller-length strains—but by mechanisms that differ depending on the spatial patterns of the population. We used complementary modeling approaches to elucidate underlying mechanisms: an agent-based model to simulate detailed mechanical and signaling interactions between the competing strains, and a reductive, stochastic lattice model to represent cell-cell interactions with a single rotational parameter. Our modeling suggests that spatial strain-fraction oscillations can be generated when cell-length control is coupled to quorum-sensing signaling in negative feedback topologies. Our research employs novel methods of population control and points the way to programming strain fraction dynamics in consortial synthetic biology.

Controlling microbial co-culture based on substrate pulsing can lead to stability through differential fitness advantages

“…Finally, cells can February 18, 2022 9/23 switch between the different states, and the rates of these transitions are functions of the environmental conditions [29,36,37]. Therefore it becomes possible to vary the distribution of cells between various states as a function of the environment and time [11,34]. Furthermore, while co-cultured, interactions between inter and intra-specific metabolic states may change the microorganism interactions and its population equilibrium and stability.…”

“…However, S.cerevisiae could benefit from a more heterogeneous metabolism during substrate limitation or transitory metabolite shifts. Metabolic heterogeneity is relevant for promoting the interactions needed for establishing microbial communities [33,34]. Thattai and van Oudenaarden [11] established that cell-to-cell differences in gene expression and protein translation (enzymes concentration and activity) could split the population into two or more groups, each one presenting different phenotypic behaviour.…”

“…It is relevant C) and D) Hi-frequency pulsed profile cultivation FSC-A vs SSC-A FC plot and micrography samples, respectively, at time 80 h. On all micrographies, example marked cells have been magnified. to notice that the intermittent feeding profiles exert more than metabolic changes into the individual cells but also seem to change the microorganism's morphology and social behaviour, probably impacting co-culture dynamics, and strain fixation to a great extent [34]. The latter, in turn, could impact their fitness and survival in a fermentation process by coupling or decoupling specific metabolic profiles and functions and some microbial behaviour profiles and their interactions.…”

“…Therefore the cells and the Continuous culture would seem more prominent than sole S.cerevisiae cells and would have a wider size distribution given the degree of aggregation, while on intermittent experiments, the absence of this effect would compress the size distribution into a relatively smaller mean size. It is relevant February 18, 2022 17/23 to notice that the intermittent feeding profiles exert more than metabolic changes into the individual cells but also seem to change the microorganism's morphology and social behaviour, probably impacting co-culture dynamics, and strain fixation to a great extent [34]. The latter, in turn, could impact their fitness and survival in a fermentation process by coupling or decoupling specific metabolic profiles and functions and some microbial behaviour profiles and their interactions.…”

“…However, in this case, an essential requirement for stability is that successive diauxic shifts must occur with a given periodicity during the continuous culture through, for example, GLU pulsing. Such periodic perturbation approach has been previously acknowledged as an efficient control strategy for microbial co-cultures [9,11,12] and typically leads to oscillations in cell number, each strain exhibiting period of growth and decay according to their respective metabolic capabilities [21][22][23]. In order to be able to predict such population behavior emerging from complex metabolic interactions, mathematical models are needed.…”