Spatiotemporal dynamics of metabolite gradients control the emergent morphology of a bacterial colony on hard agar

The growth of an E. coli colony on hard agar exhibits robust expansion kinetics and morphology despite the complex interactions between millions of cells experiencing compact confinement under a spatiotemporally varying nutrient gradient. To probe the mechanistic origins of such robust colony characteristics, an agent-based model along with a set of reaction-diffusion equations to model the spatiotemporal dynamics of extracellular metabolites is employed. For colonies grown on glucose minimal medium plates, we find glucose depletion driven by anaerobiosis to be the primary factor contributing to the experimentally observed saturation in vertical expansion, while the excreted fermentation products play a crucial role for cell maintenance at the aerated colony surface. We also establish that the well-known linear expansion of the colony radius is not limited by nutrient. Various physiological factors affecting colony morphology are also characterized. Overall, our study emphasizes that in addition to mechanical interactions, the spatiotemporally varying metabolite gradients and the mode of metabolism of the individual cells determine the emergent morphology and expansion kinetics of the macroscopic colony.