UC Berkeley

Microbes proliferate and migrate to take over territories. The dynamics of population growth canbe classified by the rate of proliferation and migration. When proliferation is predominant, the population density tends to saturate, and cells form expanding clusters. On the other hand, when migration is more active than the timescale of proliferation, the populations get almost well-mixed like a liquid culture in a shaken test tube. Both extreme cases have been extensively studied in previous research. However, the intermediate regime, where proliferation and migration consort with each other, has not been understood well. With this thesis, I attempt to provide an overarching insight into the interplay of proliferation and migration using microfluidic experiments and computer simulations. In Chapter 2, we show that the balance of proliferation and diffusion results in the sharp transition between two density states, gaseous and jammed states, using a newly-developed microfluidic device named microfluidic panflute. The density dependence of the diffusivity is shown to be fundamental to producing bifurcating behaviors with hysteresis. We further discuss the ecological impact of the density transition on invasion resistance. Chapter 3 characterizes the clone size distribution of jammed populations by fluctuation tests and lineage tracing with microfluidics. We show the characteristic power-law decay of the site frequency spectrum. We further discussed applying our results to cancer research: the site frequency spectrum can be reconstructed by sampling tumors spatially. In chapters 4 and 5, characteristic behaviors of jammed and gaseous populations are discussed. Chapter 4 shows the impact of the shape of physical boundaries on the population dynamics in a jammed state. In chapter 5, gaseous populations in various types of flow are investigated. This thesis contributes to the understanding of microbial population dynamics in spatial structure. Also, experimental techniques developed in this thesis, especially microfluidic systems, have the potential to be a platform for microbial experiments to investigate the ecological and evolutionary dynamics under spatial constraints.