Session D20: Bio: Bacteria Swimming

The swimming behavior of flagellated bacteria in viscous and viscoelastic media

The motility of bacteria E.coli in viscous and viscoelastic fluids has been widely studied although full understanding remains elusive. The swimming mode of wild-type E.coli is well-described by a run-and-tumble sequence in which periods of straight swimming at a constant speed are randomly interrupted by a tumble, defined as a sudden change of direction with a very low speed. Using a tracking microscope, we follow cells for extended periods of time and find that the swimming behavior can be more complex, and can include a wider variety of behaviors including a ``slow random walk'' in which the cells move at relatively low speed without the characteristic run. Significant variation between individual cells is observed, and furthermore, a single cell can change its motility during the course of a tracking event. Changing the viscosity and viscoelasticy of the swimming media also has profound effects on the average swimming speed and run-tumble nature of the cell motility, including changing the distribution, duration of tumbling and slow random walk events. The reasons for these changes are explained using a Purcell-style resistive force model for the cell and flagellar behavior as well as model for the changes in flagellar bundling in different fluid viscosities.   

Instability of hooks during bacterial flagellar swimming

In bacteria, a flexible hook transmits torque from the rotary motor at the cell body to the flagellum. Previously, the hook has been modeled as a Kirchhoff rod between the cell body and rotating flagellum. To study effects of the hook's flexibility on the bacteria's swimming speed and trajectory for wide range hook stiffnesses and flagellum configurations, we develop an efficient simplified spring model for the hook by linearizing the Kirchhoff rod. We treat the hydrodynamics of the cell body and helical flagellum using resistance matrices calculated by the method of regularized Stokeslets. We investigate flagellar and swimming dynamics for a range of hook flexibilities and flagellar orientations relative to the cell body and compare the results to models without hook flexibility. We investigate in detail parameters corresponding to E. coli and Vibrio alginolyticus. Generally, the flagellum changes orientation relative to the cell body, undergoing an orbit with the period of the motor rotation. We find that as the hook stiffness decreases, steady-state orbits of the flagellum first become unstable before the hook buckles, which may suggest a new mechanism of flick initiation in run-reverse-flick motility. We also find that for some parameter ranges, there are multiple stable steady state orbits, which may have implications for the tumbling and turning of bacteria.   

Polymorphic transformation of helical flagella of bacteria.

Bacteria such as \textit{E. coli} swim in an aqueous environment by utilizing the rotation of flagellar motors and alternate two modes of motility, \textit{runs} and \textit{tumbles}. Runs are steady forward swimming driven by bundles of flagellar filaments whose motors are turning CCW; tumbles involve a reorientation of the direction of swimming triggered by motor reversals. During tumbling, the helical flagellum undergoes polymorphic transformations, which is a local change in helical pitch, helical radius, and handedness. In this work, we investigate the underlying mechanism of structural conformation and how this polymorphic transition plays a role in bacterial swimming.   

Visualization of bacterial flagella dynamics in a viscous shear flow

We report on the dynamics of tethered bacterial flagella in an applied viscous shear flow and analyze their behavior using image processing. Flagellin proteins were repolymerized into flagellar filaments functionalized with biotin at their proximal end, and allowed to self-assemble within a micro channel coated with streptavidin. It was observed that all attached flagellar filaments aligned with the steady shear flow of various polymeric solutions. Furthermore it was observed that many of the filaments were stretched, and at elevated flow rates began to undergo polymorphic transformations, which were initiated at one end of the flagellum. When undergoing a change to a different helical form the flagellum was observed to transform to an oppositely handed helix, as to counteract the viscous torque imparted by the shear flow. It was also observed that some flagellar filaments did not undergo polymorphic transformations, but rotated about their helical axis. The rate of this rotation appears to be a function of the applied flow rate. These results expand on previous experimental work and aid in the development of a novel platform that harnesses the autonomic response of a `forest' of bacterial flagella for engineering applications.   

Barriers for active transport of bacteria in a microfluidic flow

We present experiments on the motion of swimming bacteria in a laminar, hyperbolic flow in a microfluidic cross channel. The bacteria used are a genetically-mutated ``smooth swimming''\footnote{R. Rusconi, J.S. Guasto and R. Stocker, Nature Physics {\bf 10}, 212 (2014).} bacillus subtilis. The movement of bacteria in the flow is bounded by {\em swimming invariant manifolds} (SWIMs) that act as one-way barriers. The SWIMs are similar to `burning invariant manifolds''\footnote{J. Mahoney, D. Bargteil, M. Kingsbury, K. Mitchell and T. Solomon, Europhys. Lett. {\bf 98}, 44005 (2012).} that act as one-way barriers that impede the motion of reaction fronts in a fluid flow. We explore the structure and bounding behavior of the SWIMs and how their separation from the passive manifolds depends on the bacteria swimming speed, normalized by the characteristic fluid speeds.   

Bacterial Trapping in Porous Media Flows

Swimming bacteria inhabit heterogeneous, microstructured environments that are often characterized by complex, ambient flows. Understanding the physical mechanisms underlying cell transport in these systems is key to controlling important processes such as bioremediation in porous soils and infections in human tissues. We study the transport of swimming bacteria (\textit{Bacillus subtilis}) in quasi-two-dimensional porous microfluidic channels with a range of periodic microstructures and flow strengths. Measured cell trajectories and the local cell number density reveal the formation of filamentous cell concentration patterns within the porous structures. The local cell densification is maximized at shear rates in the range 1-10 s$^{\mathrm{-1}}$, but widely varies with pore geometry and flow topology. Experimental observations are complemented by Langevin simulations to demonstrate that the filamentous patterns result from a coupling of bacterial motility to the complex flow fields via Jeffery orbits, which effectively `trap' the bacteria on streamlines. The resulting microscopic heterogeneity observed here suppresses bacterial transport and likely has implications for both mixing and cell nutrient uptake in porous media flows.   

Bacteria rolling: motilities of rosette colonies in Caulobacter crescentus

The aquatic bacterium \textit{Caulobacter crescentus} has two life cycle stages with distinct motilities: freely swimming swarmer cells and immotile stalked cells. Here, we show a new type of movement performed by freely suspended rosettes, spontaneous aggregates of stalked cells aligned radially relative to each other. Reproductive rosette members generate predivisional daughter cells with flagella, inducing rotations of the rosette as a whole. Such rotations exhibit dynamic angular velocities and lead to intermittent linear movements along liquid-solid interfaces, resembling rolling movements. We reconstructed the translational and rotational dynamics of the rosette movements from high-speed filming and long-term tracking. A mechanical model was developed to explain the hydrodynamic mechanism underlying such motilities. Our study illustrated a nontrivial mechanism for clustered bacteria to achieve motilities and sheds light on the adaptive significance of the collective behaviors of microorganisms in complex fluid environments.   

Motility and peristaltic flow in maintaining microbiome populations.

Bacteria are an important component of the microbiome in the digestive tract, and must be able to maintain their population despite the fact that the contents of the intestines are constantly flowing towards evacuation. Many bacteria accomplish this by colonizing the surfaces of the intestines where flows diminish, but some species live in the lumen. We attempt to address whether swimming motility of these species plays an important role in maintaining bacterial population in the face of peristaltic pumping out of the intestine. Using a two-dimensional model of peristaltic flows induced by small-amplitude traveling waves we examine the Lagrangian trajectories of passive bacteria as well as motile bacteria, which are treated as Brownian particles undergoing enhanced diffusion due to the bacteria's run-and-tumble motility. We examine how the densities of growing populations of bacteria depend on the combination of motility and peristaltic flow.   

Instabilities in the Swimming of Bacteria

Peritrichously flagellated bacteria, such as E. coli and B. subtillis, have flagella randomly distributed over their body. These flagella rotate to generate a pushing force that causes the cell to swim body first. For changes in direction these flagella return to their randomly distributed state where the flagella point in many different directions. The main observed state of swimming peritrichously flagellated bacteria however is one where all their flagella gathered or bundled at one end of the body. In this work we address this problem from the point of view of fluid-structure interactions and show theoretically and numerically how the conformation of flagella depends on the mechanics of the cell.   

Bacteria dispersion in microchanel containing random obstacles

Dispersion of particles in porous media is a classical problem well studied where physical laws are well established and show good agreement with experimental observations. Recently, contrary to what is thought, observations revealed that self-propelled particles under flow, orient their swimming, what is designated by the term of rheotaxis. But less is known about what happen for self-propelled particles under flow in presence of obstacles. For this purpose, we developed a specific experimental setup in order to show the coupling of bacteria {\it E. Coli} RP437 strain swimming with the presence of obstacles in the dispersion process. We chose to develop a micro-fluidic device of rectangular section of $0.05~\mu m^2$ containing obstacles of different sizes($10-150~\mu m$) when a bacteria size is about $1~\mu m$. Thanks to the transparency of the flow we can track hundreds of trajectories of bacteria, the analysis of which revealed that their swimming influences the dispersion when the flow velocity is of the order of their swimming velocity ($10~ \mu m/s$).