Ursell, TristanHoeger, Kentaro2020-12-082020-12-082020-12-08https://hdl.handle.net/1794/25904Microbes have been found to inhabit a myriad of natural and artificial environments on earth, many of which are chemically complex and physically anisotropic – such as wet soils, the oceans, or mammalian guts. In order to navigate these environments many bacteria rely on self-propulsion to expand their colonies or traverse chemical gradients. While swimming through these viscous environments, they encounter physical anisotropies such as other swimming cells, and steric objects across a wide range of sizes. At high densities, bacteria display behaviors which are distinct from dilute individual motion and are often better described by the collective motion of the bulk population yet are defined by the motion of individuals within the bulk. In natural systems, inter-species and intra-species diversity is the norm within cell populations. To study the effects of phenotypic diversity, we imaged the collective motion of wild-type Bacillus Subtilis with varied concentrations of a non-motile mutant doped into the population. We observed a transition from turbulent behavior to constrained semi-ballistic motion as the fraction of non-motile cells increased and found evidence for a non-linear relation between mean cell speed and the fraction of non-motile cells. Swimming bacteria couple hydrodynamically to large, flat planar and low-curvature convex surfaces that create an attractive force that deviates their trajectories. Current hydrodynamic models reproduce this behavior but their validity when considering small obstacles is unknown. We developed a novel method for the fabrication of microfluidic devices to overcome key limits presented by classic ‘soft lithography’ devices to image hundreds-of-thousands of high-curvature scattering interactions between swimming bacteria and micro-fabricated pillars with radii from ~ 1 to ~10 cell lengths. The results of these interactions were poorly described by current hydrodynamic models but well-fit by a sterics-only model we developed. Thus, we conclude that on these length scales cell-surface interactions are primarily steric and as curvature decreases, hydrodynamics begins to play an increasingly important role. We also observed cell motion in triangular arrays of such pillars and found that at high density, these pillars tightly constrained the direction of motion highlighting the importance of obstacle placement in their effects on cell motility.en-USAll Rights Reserved.BacteriaMicrofluidicsMicroswimmerElectronic Thesis or Dissertation