Self-Driven Jamming of Growing Microbial Populations


1Departments of Physics and Integrative Biology, University of California Berkeley, USA. 2Max Planck Institute for Dynamics and SelfOrganization Göttingen, Germany. 3Biophysics Graduate Group, University of California Berkeley, USA. 4Department of Bioengineering, University of California Berkeley, USA. † MD and JH equally contributed to this work. In natural settings, microbes tend to grow in dense populations [1–4] where they need to push against their surroundings to accommodate space for new cells. The associated contact forces play a critical role in a variety of population-level processes, including biofilm formation [5– 7], the colonization of porous media [8, 9], and the invasion of biological tissues [10–12]. Although mechanical forces have been characterized at the single cell level [13–16], it remains elusive how collective pushing forces result from the combination of single cell forces. Here, we reveal a collective mechanism of confinement, which we call selfdriven jamming, that promotes the build-up of large mechanical pressures in microbial populations. Microfluidic experiments on budding yeast populations in space-limited environments show that self-driven jamming arises from the gradual formation and sudden collapse of force chains driven by microbial proliferation, extending the framework of driven granular matter [17–20]. The resulting contact pressures can become large enough to slow down cell growth by delaying the cell cycle in the G1 phase and to strain or even destroy the microenvironment through crack propagation. Our results suggest that self-driven jamming and build-up of large mechanical pressures is a natural tendency of microbes growing in confined spaces, contributing to microbial pathogenesis and biofouling [21–26]. The simulataneous measurement of the physiology and mechanics of microbes is enabled by a microfluidic bioreactor [27–30] that we have designed to culture microbes under tightly controlled chemical and mechanical conditions. The setup, shown in Fig. 1A, is optimized for budding yeast (S. cerevisiae). We use this device to measure mechanical forces generated by partially-confined growing populations and the impact of those forces on both the population itself and its micro-environment. At the beginning of each experiment, we trap a single yeast cell in the growth chamber of the device, which can hold up to about 100 cells. The cells are fed by a continuous flow of culture medium, provided by a narrow set of channels that are impassable for cells. While cells first proliferate exponentially as in liquid culture, growth dynamics change dramatically once the chamber is filled. At high density, cells move in a stop-and-go manner and increasingly push against the chamber walls. The population develops a contact pressure∗ that increases over time until it reaches steady state, subject to large fluctuations. Depending on the geometry of the device (Fig. 1B and C), the mean steady-state pressure can reach up to 1 MPa. This pressure is larger than the≈ 0.2 MPa turgor pressure measured in budding yeast (stationary phase [31]) and much larger than the ≈ 1 mPa needed for the cells to overcome viscous friction (supplementary text). Both the intermittent flow and pressure build-up are counterintuitive because the outlet channel is wide enough for cells to pass. In principle, excess cells could flow like a liquid out of the chamber. Time lapse movies (here) reveal that blockages in the device stabilize the cell packing and prevent flow. Cells proliferate until a sudden avalanche flushes them through the outlet (Fig. 1D and E). Another jamming event occurs, and the process repeats. These dynamics generate characteristic slow pressure increases followed by sudden pressure drops (Fig. 1C). Jamming, intermittency and avalanches are familiar aspects of flowing sand, grains or even jelly beans [24]. To test whether the interplay of growth, collective rearrangement, and outflow of cells from the chamber can be explained by the mechanics of granular materials, we set up coarse-grained computer simulations with cells represented as elastic particles that grow exponentially and reproduce by budding. In our simulations, cells move via frictionless overdamped dynamics with repulsive contact interactions between neighbors. Our simulations indeed reproduce the intermittent dynamics observed in the experiments (Fig. 2A–C). We find that the pressure drops are roughly exponentially-distributed for both experiments and simulations (Fig. 2D) for P > 〈P〉, consistent with hopper flows [32]. Highly intermittent cell flows might reflect spatially heterogeneous mechanical stresses, a hallmark of driven granular materials [17–20]. Assuming that cell shape deformation is indicative of the forces between cells, we developed a non-invasive method to infer these forces (Fig. 2F, supplementary text, and fig. S1). Using this approach, we analyzed microscopy images to determine stress distributions of crowded populations. Both S. cerevisiae experiments and our coarse-grained simulations

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@inproceedings{Delarue2016SelfDrivenJO, title={Self-Driven Jamming of Growing Microbial Populations}, author={Morgan Delarue and J{\"{o}rn Hartung and Carl J. Schreck and Pawel Gniewek and Lucy Hu and Stephan Herminghaus and Oskar Hallatschek}, year={2016} }