Swimming Bacteria Research Articles

Bacterial activity hinders particle sedimentation.

Sedimentation in active fluids has come into focus due to the ubiquity of swimming micro-organisms in natural and industrial processes. Here, we investigate sedimentation dynamics of passive particles in a fluid as a function of bacteria E. coli concentration. Results show that the presence of swimming bacteria significantly reduces the speed of the sedimentation front even in the dilute regime, in which the sedimentation speed is expected to be independent of particle concentration. Furthermore, bacteria increase the dispersion of the passive particles, which determines the width of the sedimentation front. For short times, particle sedimentation speed has a linear dependence on bacterial concentration. Mean square displacement data shows, however, that bacterial activity decays over long experimental (sedimentation) times. An advection-diffusion equation coupled to bacteria population dynamics seems to capture concentration profiles relatively well. A single parameter, the ratio of single particle speed to the bacteria flow speed can be used to predict front sedimentation speed.

Direct versus indirect hydrodynamic interactions during bundle formation of bacterial flagella

Peritrichous bacteria swim through rotation of a helical bundle of filaments. Here, physical mechanisms that contribute to its formation in terms of direct and indirect hydrodynamic interactions are categorized. A simple analytical singularity model shows that indirect effects generically dominate at all except the very last stages of bundling. A numerical elastohydrodynamic model allows for a detailed analysis along the entire length of the filaments.

Intermicrobial Hitchhiking: How Nonmotile Microbes Leverage Communal Motility.

Motility allows many microbes to traverse their environment to find nutrient sources or escape unfavorable environments. However, some microbes are nonmotile and are restricted to their immediate conditions. Intriguingly, sporadic reports have demonstrated that many nonmotile microbes can utilize the motility machinery of other microbes in their vicinity. This form of transportation, called hitchhiking, has been observed with both prokaryotic and eukaryotic microbes. Importantly, many hitchhiking microbes are pathogenic to humans or plants. Here, we discuss reports of intermicrobial hitchhiking to generate a comprehensive view of hitchhiking mechanisms and how such interactions may influence human and plant health. We hypothesize that microbial hitchhiking is ubiquitous in nature and may become the subject of an independent subfield of research in microbiology.

Helical locomotion in a porous medium

Microorganisms and artificial microswimmers often need to swim through environments that are more complex than purely viscous liquids in their natural habitats or operational environments, such as gel-like mucus, wet soil, and aquifers. The question of how the properties of these complex environments affect locomotion has attracted considerable recent attention. In this paper, we present a theoretical model to examine how the additional resistance due to the network of stationary obstacles in a porous medium affects helical locomotion. Here, we focus on helical locomotion for its ubiquity as a propulsion mechanism adopted by many swimming bacteria and artificial microswimmers. We show that the additional resistance can have qualitatively different effects on various scenarios of helical locomotion: (1) a helical propeller driven by an external torque, (2) a free swimming bacterium consisting of a helical flagellum and a head, and (3) a cargo-carrying helical propeller driven by an external torque. Our results elucidate the subtle and significant differences between torqued helical propulsion versus force-free and torque-free swimming in a porous medium. We also remark on the limitations as well as potential connections of our results with experimental measurements of bacterial swimming speeds in polymeric solutions.

Adaptive behaviors of planktonic Pseudomonas aeruginosa in response to the surface-deposited dead siblings

In this study, the 3D motion behaviors and the underlying adaptation mechanism of planktonic Pseudomonas aeruginosa (PAO1) in response to the deposited dead siblings nearby were explored. Utilizing a real-time 3D tracking technique, digital holographic microscopy (DHM), we demonstrate that planktonic cells near the surface covered with dead siblings have a lower density and a reduced 3D velocity compared with those upon viable ones. As a sign of chemosensory responses, bacteria swimming near the dead siblings exhibit increase in frequency of the ‘flick’ motion. Transcriptomic analysis by RNA–seq reveals an upregulated expression of dgcM and dgcE inhibited the movement of PAO1, accompanied by increased transcriptional levels of the virulence factor-related genes hcp1, clpV1, and vgrG1. Moreover, the decrease in l-glutamate and the increase in succinic acid in the metabolites of the dead bacteria layer promote the dispersion of planktonic bacteria. As a result, the dead siblings on a surface inhibit the bacterial accumulation and activate the adaptive defensive responses of planktonic PAO1 in the vicinity.

Phylogenetic origin and sequence features of MreB from the wall-less swimming bacteria Spiroplasma

Spiroplasma are wall-less bacteria which belong to the phylum Tenericutes that evolved from Firmicutes including Bacillus subtilis. Spiroplasma swim by a mechanism unrelated to widespread bacterial motilities, such as flagellar motility, and caused by helicity switching with kinks traveling along the helical cell body. The swimming force is likely generated by five classes of bacterial actin homolog MreBs (SMreBs 1–5) involved in the helical bone structure. We analyzed sequences of SMreBs to clarify their phylogeny and sequence features. The maximum likelihood method based on around 5000 MreB sequences showed that the phylogenetic tree was divided into several radiations. SMreBs formed a clade adjacent to the radiation of MreBH, an MreB isoform of Firmicutes. Sequence comparisons of SMreBs and Bacillus MreBs were also performed to clarify the features of SMreB. Catalytic glutamic acid and threonine were substituted to aspartic acid and lysine, respectively, in SMreB3. In SMreBs 2 and 4, amino acids involved in inter- and intra-protofilament interactions were significantly different from those in Bacillus MreBs. A membrane-binding region was not identified in most SMreBs 1 and 4 unlike many walled-bacterial MreBs. SMreB5 had a significantly longer C-terminal region than the other MreBs, which possibly forms protein-protein interactions. These features may support the functions responsible for the unique mechanism of Spiroplasma swimming.

Directional self-locomotion of active droplets enabled by nematic environment

Active matter comprised of self-propelled interacting units holds a major promise for extraction of useful work from its seemingly chaotic out-of-equilibrium dynamics. Streamlining active matter to produce work is especially important at microscale, where the viscous forces prevail over inertia and the useful modes of transport require very specific non-reciprocal type of motion. Here we report that microscopic active droplets representing aqueous dispersions of swimming bacteria Bacillus subtilis show unidirectional propulsion when placed in an inactive nematic medium. Random motion of bacteria inside the droplet is rectified into a directional self-locomotion of the droplet by the polar director structure that the droplet itself creates in the surrounding nematic through anisotropic molecular interactions at its surface. Droplets without swimming bacteria show no net displacement. The trajectory of the active droplet can be predesigned as rectilinear or curvilinear by patterning the molecular orientation of the nematic medium. The effect demonstrates that swimming at microscale can be achieved at the expense of broken spatial symmetry of the medium; it can be used in development of micromachines.

Optical Force Measurements Illuminate Dynamics of Escherichia coli in Viscous Media

Escherichia coli and many other bacteria swim through media with the use of flagella, which are deformable helical propellers. When the viscosity of media is increased, a peculiar phenomenon can be observed in which the organism's motility appears to improve. This improvement in the cell's swimming speed has previously been explained by modified versions of resistive force theory (RFT) which accounts for the interaction between flagella and molecules associated with the viscosity increase. Using optical tweezers, we measure the swimming force of individual E. coli in solutions of varying viscosity. By using probe-free force measurements, we are able to quantitatively validate and compare RFT and proposed modifications to the theory. We find that the force produced by the flagellum remains relatively constant even when the viscosity of the medium increases by approximately two orders of magnitude, contrary to predictions of RFT and variants. We conclude that the observed swimming forces can be explained by allowing the flagella geometry to deform as the viscosity of the surrounding medium is increased.

A Trace Amount of Surfactants Enables Diffusiophoretic Swimming of Bacteria.

From birth to health, surfactants play an essential role in our lives. Due to the importance, their environmental impacts are well understood. One of the aspects that has been extensively studied is their impact on bacteria, particularly on their motility. Here, we uncover an alternate chemotactic strategy triggered by surfactants-diffusiophoresis. We show that even a trace amount of ionic surfactants, down to a single ppm level, can promote the bacterial diffusiophoresis by boosting the surface charge of the cells. Because diffusiophoresis is driven by the surface-solute interactions, surfactant-enhanced diffusiophoresis is observed regardless of the types of bacteria. Whether Gram-positive or -negative, flagellated or nonflagellated, the surfactants enable fast migration of freely suspended bacteria, suggesting a ubiquitous locomotion mechanism that has been largely overlooked. We also demonstrate the implication of surfactant-enhanced bacterial diffusiophoresis on the rapid formation of biofilms in flow networks, suggesting environmental and biomedical implications.

Large deformations of the hook affect free-swimming singly flagellated bacteria during flick motility.

Hook dynamics are important in the motility of singly flagellated bacteria during flick motility. Although the hook is relatively short, during reorientation events it may undergo large deformations, leading to nonlinear behavior. Here, we explore when these nonlinear and large deformations are important for the swimming dynamics in different ranges of hook flexibilities and flagellar motor torques. For this purpose, we investigate progressively more faithful models for the hook, starting with linear springs, then models that incorporate nonlinearities due to larger hook deformations. We also employ these models both with and without hydrodynamic interactions between the flagellum and cell body to test the importance of those hydrodynamic interactions. We show that for stiff hooks, bacteria swim with a flagellum rotating on-axis in orbits and hydrodynamic interactions between the cell body and flagellum change swimming speeds by about 40%. As the hook stiffness decreases, there is a critical hook stiffness that predicts the initiation of the dynamic instability causing flicks. We compare the transition value of stiffnesses predicted by our models to experiments and show that nonlinearity and large deflections do not significantly affect critical transition values, while hydrodynamic interactions can change transition values by up to 13%. Below the transition value, we observe precession of the flagellum, in which it deflects off-axis to undergo nearly circular stable trajectories. However, only slightly below the transition stiffness, nonlinearity in hook response destabilizes precession, leading to unstable deflections of the flagellum. We conclude that while the linear hook response can qualitatively predict transition stiffnesses, nonlinear models are necessary to capture the behavior of hooks for stiffnesses below transition. Furthermore, we show that for the lower range of hook stiffnesses observed in actual bacteria, models which capture the full deformations of hooks are necessary. Inclusion of the hydrodynamic interactions of the cell body, hook, and flagellum is required to quantitatively simulate nonlinear dynamics of soft hooks during flick motility.

Control of microswimmers by spiral nematic vortices: Transition from individual to collective motion and contraction, expansion, and stable circulation of bacterial swirls

The authors introduce a method to control swimming bacteria by a liquid crystal environment. The paper shows that a liquid crystal nematic patterned as a spiral vortex causes an individual-to-collective transition as the bacterial concentration increases, in which non-polar swimming of individual bacteria is replaced by a unipolar circular swirling of condensed swarms.

Chirality-induced bacterial rheotaxis in bulk shear flows.

Interaction of swimming bacteria with flows controls their ability to explore complex environments, crucial to many societal and environmental challenges and relevant for microfluidic applications such as cell sorting. Combining experimental, numerical, and theoretical analysis, we present a comprehensive study of the transport of motile bacteria in shear flows. Experimentally, we obtain with high accuracy and, for a large range of flow rates, the spatially resolved velocity and orientation distributions. They are in excellent agreement with the simulations of a kinematic model accounting for stochastic and microhydrodynamic properties and, in particular, the flagella chirality. Theoretical analysis reveals the scaling laws behind the average rheotactic velocity at moderate shear rates using a chirality parameter and explains the reorientation dynamics leading to saturation at large shear rates from the marginal stability of a fixed point. Our findings constitute a full understanding of the physical mechanisms and relevant parameters of bacteria bulk rheotaxis.

Effects of shear-thinning viscosity and viscoelastic stresses on flagellated bacteria motility

The behavior of flagellated bacteria swimming in non-Newtonian media remains an area with contradictory and conflicting results. We report on the behavior of wild-type and smooth-swimming E. coli in Newtonian, shear thinning and viscoelastic media, measuring their trajectories and swimming speed using a three dimensional real-time tracking microscope. We conclude that the speed enhancement in Methocel solution at higher concentration is due to shear-thinning and an analytical model is used to support our experimental result. We argue that shear-induced normal stresses reduce the wobbling behavior during cell swimming but do not significantly affect swimming speed. However, the normal stresses play an important role in decreasing the flagellar bundling time which changes the swimming speed distribution. A dimensionless number, the "Strangulation number" (Str) is proposed and used to characterize this effect.

Spatiotemporal dynamics of bacterial collective migration

Collective migration is a highly ordered collective behavior exhibited by species in response to a stimulus. Such behavior can help a population to gain a competitive advantage ahead of environmental changes. However, the process that shapes collective migration is complicated by the involvement of multiple factors, including genetics, phenotypic diversity, and the environment. In the last 50 years, mathematical models, computerized simulations, and quantitative experiments have all contributed to significant progress in the study of spatiotemporal dynamics in bacterial population migration. In this review, we first summarize the fundamental research on single-cell behavior of bacteria and collective migration, then overview recent work on the spatiotemporal dynamics of bacterial population migration and the applications of quantitative synthetic biology in collective migration research. Common bacteria such as Escherichia coli undergo random walks when grown in suspension in bulk liquid, consisting of successions of “runs” and “tumbles”. To find favorable environments for survival, bacteria process chemical stimuli by swimming towards (or away from) the sources of attractants (or repellents). Bacteria evaluate changes in signal concentrations by a well-characterized chemotaxis pathway, and then modulate the tumble frequency accordingly. Increasing levels of a chemoattractant decrease the tumble frequency, allowing the bacteria to approach the source of chemoattractant. Bacteria tend to live in groups in the natural environment and exhibit collective migration. Two forms of bacterial collective migration, chemotactic migration and swarming, have been extensively studied. In a capillary or semisolid medium containing a chemoattractant, the bacterial population consumes the attractant to form a gradient. Such a gradient attracts more bacteria to concentrate at the location of higher attractant concentration, allowing the population to re-establish the gradient. The attractant-consumption loop results in chemotactic collective migration of bacteria. By contrast, on the moist surface of a solid medium, highly compact bacteria swim on a thin layer above the surface to form a swarm. The population growth and collision between bacterial cells pushes the groups to expand and results in swarming. To understand the spatiotemporal dynamics of bacterial collective motion, mathematical models were developed together with single-cell tracking techniques. Based on the classic Keller-Segel model, which describes the macroscopic movement of chemotactic collective migration, recent studies have incorporated the chemotaxis pathway of single cells or have examined the effects of phenotypic diversity. The details of chemotactic collective migration in bacteria are becoming increasingly clear. Using another approach, recent studies of bacterial swarming combined the Vichek model of collective motion with fluid dynamics to reveal coordinated behaviors within the swarm. Furthermore, interactions between bacteria and physical obstacles were found to have significant impacts on bacterial motion. Developments in synthetic biology have provided tools to alter bacterial behavior through synthetic gene circuits. Scientists can then alter bacterial motility quantitatively to better understand bacterial collective migration, or to create collective patterns using specially designed gene circuits. These studies show great potential for the application of synthetic biology in studies of bacterial collective migration.

TaxisPy: A Python-based software for the quantitative analysis of bacterial chemotaxis

Several species of bacteria are able to modify their swimming behavior in response to chemical attractants or repellents. Methods for the quantitative analysis of bacterial chemotaxis such as quantitative capillary assays are tedious and time-consuming. Computer-based video analysis of swimming bacteria represents a valuable method to directly assess their chemotactic response. Even though multiple studies have used this approach to elucidate various aspects of bacterial chemotaxis, to date, no computer software for such analyses is freely available. Here, we introduce TaxisPy, a Python-based software for the quantitative analysis of bacterial chemotaxis. The software comes with an intuitive graphical user interface and can be accessed easily through Docker on any operating system. Using a video of freely swimming cells as input, TaxisPy estimates the culture's average tumbling frequency over time. We demonstrate the utility of the software by assessing the effect of different concentrations of the attractant shikimate on the swimming behavior of Pseudomonas putida F1 and by capturing the adaptation process that Escherichia coli undergoes after being exposed to l-aspartate.

The effect of flow on swimming bacteria controls the initial colonization of curved surfaces

The colonization of surfaces by bacteria is a widespread phenomenon with consequences on environmental processes and human health. While much is known about the molecular mechanisms of surface colonization, the influence of the physical environment remains poorly understood. Here we show that the colonization of non-planar surfaces by motile bacteria is largely controlled by flow. Using microfluidic experiments with Pseudomonas aeruginosa and Escherichia coli, we demonstrate that the velocity gradients created by a curved surface drive preferential attachment to specific regions of the collecting surface, namely the leeward side of cylinders and immediately downstream of apexes on corrugated surfaces, in stark contrast to where nonmotile cells attach. Attachment location and rate depend on the local hydrodynamics and, as revealed by a mathematical model benchmarked on the observations, on cell morphology and swimming traits. These results highlight the importance of flow on the magnitude and location of bacterial colonization of surfaces.

Active control of bacteria swimming orientation in a liquid crystal matrix by using UV light

Bacteria are omnipresent in nature. They also play a key role in biomedical industry and new technologies. A capability to control their movement may be very useful both for their study and applications. Here we explore the possibility of such active control of the movement of flagellated bacteria (a bacterium that can swim thanks to the rotation of its long screw-like helix). We demonstrate that we can dynamically change the swimming direction of bacteria by incorporating them into a liquid crystal media where the phase transition is locally controlled by UV illumination. This work opens new avenues to develop lab-on-a-chip devices that could be used as a micro-farm to “harvest” and study bacteria.

Bundled slender-body theory for elongated geometries in swimming bacteria

An elongated but finite body is represented by a bundle of thin filaments for redeeming the theoretical treatment of the slender-body theory, validated by comparing its predictions with known solutions. As an immediate application, this bundled slender-body theory is used to model swimming microorganisms that consist of both thin motile organelles and cell bodies with finite aspect ratios.

Geometrical Constraints on the Tangling of Bacterial Flagellar Filaments

Many species of bacteria swim through viscous environments by rotating multiple helical flagella. The filaments gather behind the cell body and form a close helical bundle, which propels the cell forward during a “run”. The filaments inside the bundle cannot be continuously actuated, nor can they easily unbundle, if they are tangled around one another. The fact that bacteria can passively form coherent bundles, i.e. bundles which do not contain tangled pairs of filaments, may appear surprising given that flagella are actuated by uncoordinated motors. In this article, we establish the theoretical conditions under which a pair of rigid helical filaments can form a tangled bundle, and we compare these constraints with experimental data collected from the literature. Our results suggest that bacterial flagella are too straight and too far apart to form tangled bundles based on their intrinsic, undeformed geometry alone. This makes the formation of coherent bundles more robust against the passive nature of the bundling process, where the position of individual filaments cannot be controlled.

Investigating Flagella-Driven Motility in Escherichia coli by Applying Three Established Techniques in a Series.

Motility is crucial to the survival and success of many bacterial species. Many methodologies exist to exploit motility to understand signaling pathways, to elucidate the function and assembly of flagellar parts, and to examine and understand patterns of movement. Here we demonstrate a combination of three of these methodologies. Motility in soft agar is the oldest, offering a strong selection for isolating gain-of-function suppressor mutations in motility-impaired strains, where motility is restored through a second mutation. The cell-tethering technique, first employed to demonstrate the rotary nature of the flagellar motor, can be used to assess the impact of signaling effectors on the motor speed and its ability to switch rotational direction. The "border-crossing" assay is more recent, where swimming bacteria can be primed to transition into moving collectively as a swarm. In combination, these protocols represent a systematic and powerful approach to identifying components of the motility machinery, and to characterizing their role in different facets of swimming and swarming. They can be easily adapted to study motility in other bacterial species.