Swimming Bacteria Research Articles

Ostwald-like ripening in the two-dimensional clustering of passive particles induced by swimming bacteria.

Clustering passive particles by active agents is a promising route for fabrication of colloidal structures. Here, we report the dynamic clustering of micrometric beads in a suspension of motile bacteria. We characterize the coarsening dynamics for various bead sizes, surface fractions, and bacterial concentrations. We show that the time scale τ for the onset of clustering is governed by the time of first encounter of diffusing beads. At large time (t≫τ), we observe a robust cluster growth as t^{1/3}, similar to the Ostwald ripening mechanism. From bead tracking measurements, we extract the short-range bacteria-induced attractive force at the origin of this clustering.

Cable bacteria with electric connection to oxygen attract flocks of diverse bacteria

Cable bacteria are centimeter-long filamentous bacteria that conduct electrons via internal wires, thus coupling sulfide oxidation in deeper, anoxic sediment with oxygen reduction in surface sediment. This activity induces geochemical changes in the sediment, and other bacterial groups appear to benefit from the electrical connection to oxygen. Here, we report that diverse bacteria swim in a tight flock around the anoxic part of oxygen-respiring cable bacteria and disperse immediately when the connection to oxygen is disrupted (by cutting the cable bacteria with a laser). Raman microscopy shows that flocking bacteria are more oxidized when closer to the cable bacteria, but physical contact seems to be rare and brief, which suggests potential transfer of electrons via unidentified soluble intermediates. Metagenomic analysis indicates that most of the flocking bacteria appear to be aerobes, including organotrophs, sulfide oxidizers, and possibly iron oxidizers, which might transfer electrons to cable bacteria for respiration. The association and close interaction with such diverse partners might explain how oxygen via cable bacteria can affect microbial communities and processes far into anoxic environments.

Numerical modeling of dispersion of swimming bacteria in a Poiseuille flow

Bacteria have long been assumed to behave as a passive colloid. In this paper, we show that the alignment of bacteria in the flow modifies their dispersion dynamics. We determine here the resulting relation between the macroscopic longitudinal dispersion coefficient and the P\'eclet number.

Swimming of Buoyant Bacteria in Quiescent Medium and Shear Flows.

Gravity has an unavoidable effect on all living organisms inhabiting fluidic surroundings. To investigate the spatial distribution of bacteria in quiescent fluids and their rheotactic behavior in shear flows under buoyancy, we adjust the buoyant force to regulate bacterial swimming in a microfluidic channel. It is found that swimming bacteria of Escherichia coli exhibit an obvious vertical separation when exposed to a medium with high density and gradually gather close to the up wall within minutes. The bacterial population presents a net upward number flux, which enhances the trapping of motile bacteria onto the up surface as a result of buoyancy force apart from the hydrodynamic and kinematic interactions in quiescent fluids. When flow is imposed into the channel, the buoyancy effect is however significantly suppressed. Additionally, the drift velocity perpendicular to the buoyancy vector as a result of chirality-induced transverse swimming decreases with buoyancy force. However, this transverse drift capability is recovered after excluding the intrinsic swimming motility in a quiescent medium. Failing to escape from the trapping as a result of buoyant force allows for a facile separation of bacteria along the vertical direction. The findings also offer a controllable way to redisperse and homogenize the bacteria distribution close to walls by imposing a weak shear flow.

Rotary biomolecular motor-powered supramolecular colloidal motor.

Cells orchestrate the motion and force of hundreds of protein motors to perform various mechanical tasks over multiple length scales. However, engineering active biomimetic materials from protein motors that consume energy to propel continuous motion of micrometer-sized assembling systems remains challenging. Here, we report rotary biomolecular motor-powered supramolecular (RBMS) colloidal motors that are hierarchically assembled from a purified chromatophore membrane containing FOF1-ATP synthase molecular motors, and an assembled polyelectrolyte microcapsule. The micro-sized RBMS motor with asymmetric distribution of FOF1-ATPases can autonomously move under light illumination and is collectively powered by hundreds of rotary biomolecular motors. The propulsive mechanism is that a transmembrane proton gradient generated by a photochemical reaction drives FOF1-ATPases to rotate for ATP biosynthesis, which creates a local chemical field for self-diffusiophoretic force. Such an active supramolecular architecture endowed with motility and biosynthesis offers a promising platform for intelligent colloidal motors resembling the propulsive units in swimming bacteria.

Persistent flocks of diverse motile bacteria in long-term incubations of electron-conducting cable bacteria, Candidatus Electronema aureum.

Cable bacteria are centimeters-long filamentous bacteria that oxidize sulfide in anoxic sediment layers and reduce oxygen at the oxic-anoxic interface, connecting these reactions via electron transport. The ubiquitous cable bacteria have a major impact on sediment geochemistry and microbial communities. This includes diverse bacteria swimming around cable bacteria as dense flocks in the anoxic zone, where the cable bacteria act as chemotactic attractant. We hypothesized that flocking only appears when cable bacteria are highly abundant and active. We set out to discern the timing and drivers of flocking over 81 days in an enrichment culture of the freshwater cable bacterium Candidatus Electronema aureum GS by measuring sediment microprofiles of pH, oxygen, and electric potential as a proxy of cable bacteria activity. Cable bacterial relative abundance was quantified by 16S rRNA amplicon sequencing, and microscopy observations to determine presence of flocking. Flocking was always observed at some cable bacteria, irrespective of overall cable bacteria rRNA abundance, activity, or sediment pH. Diverse cell morphologies of flockers were observed, suggesting that flocking is not restricted to a specific, single bacterial associate. This, coupled with their consistent presence supports a common mechanism of interaction, likely interspecies electron transfer via electron shuttles. Flocking appears exclusively linked to the electron conducting activity of the individual cable bacteria.

Dynamic mode structure of active turbulence

The collective motion of dense suspensions of swimming bacteria is typical of a broad class of active materials, which serve an array of important biological and ecological functions. This work combines microfluidic experiments with modal analysis, typically reserved for inertial turbulence, to quantify the active turbulence of bacterial suspensions. Our results unveil the underlying constituent flow structures responsible for the interactions of chaotic bacterial motion with solid boundaries and external flows, and establish an analysis framework to facilitate new experimental and modeling approaches in active matter systems.

Probing spiroplasma's cytoskeletal motility mechanism through hydrodynamic modelling and experiment.

Nearly all swimming bacteria have evolved to utilize external, helical, rotating appendages called flagella to achieve motility. These flagella are anchored into a cell wall which provides a structural rigidity during the swimming process. Contrary to this, a unique helical bacterium called spiroplasma has neither a cell wall nor flagella, yet still swims in water. Instead, this bacterium utilizes a set of actively deformable cytoskeletal filaments, internal to the cell, which allow for swimming motility. These filaments force the cell's bilayer membrane to deform, however, the interaction between the membrane and these filaments is unclear. Using this information, we have created an algorithm to handle this motility using the regularized stokeslet method which accurately describes spiroplasma's motion and used microscopy at varying viscosities to prove this description. We describe how our simulations found unique features of spiroplasma's motility and what this means for the interaction between spiroplasma's cytoskeleton and membrane.

Impact of viscoelastic ooze slime on complex wavy gliders near a solid boundary

• Fluid mechanics of bacterial motion is discussed numerically. • Glider is approximated as a 2D complex wavy sheet. • To capture the viscoelastic properties of slime FENE-P fluid model is utilized. • The gliding motion is highly dependent on slime rheology and wave amplitudes. Prokaryote propulsion is bewilderingly diverse. Many bacteria swim through the fluid medium via rotating a long helical flagellum driven by a rotary motor, some possesses helical shaped bodies and use mechanochemical filaments. Rod-shaped Bacteria (present near the solid wall) practice another mechanism of locomotion, generally called gliding motility. It is hypothesized that rod-shaped bacteria propel it selves by producing waves in their body and leave an adhesive slime trail. Based on these observations, we use a mathematical model (of complex undulating sheet) to examine the gliding motility of bacteria on a layer of non-Newtonian slime. FENE-P fluid model is approximated as a layer of non-Newtonian slime. Navier-Stokes equation is simplified using the lubrication assumption which results in a second-order differential equation. The speed of organism, flow rate and energy loss at larger values of the involved parameters are simulated using a blended numerical technique. The streamlines pattern and velocity of the slime are also drawn for the realistic pairs of speed and flow rate and are thoroughly explained.

Self-transport of swimming bacteria is impaired by porous microstructure

Motility is a fundamental survival strategy of bacteria to navigate porous environments, where they mediate essential biogeochemical processes in quiescent wetlands and sediments. However, a comprehensive understanding of the mechanisms regulating self-transport in the confined interstices of porous media is lacking, and determining the interactions between cells and surfaces of the solid matrix becomes paramount. Here, we precisely track the movement of bacteria (Magnetococcus marinus) through a series of microfluidic porous media with broadly varying geometries and show how successive scattering events from solid surfaces decorrelate cell motion. Ordered versus disordered media impact the cells’ motility over short ranges, but their large-scale transport properties are regulated by the cutoff of their persistent motility. An effective mean free path is established as the key geometrical parameter controlling cell transport, and we implement a theoretical model that universally predicts the effective cell diffusion for the diverse geometries studied here. These results aid in our understanding of the physical ecology of swimming cells, and their role in environmental and health hazards in stagnant porous media.

Influence of flagella and their property on the initial attachment behaviors of bacteria onto plastics

Flagella and their property would influence the initial attachment of bacteria onto plastics, yet their impacts have not been investigated. In present study, four types of E. coli with or without flagella as well as with normal or sticky flagella were utilized to investigate the effects of flagella and their property on the initial attachment behaviors of bacteria onto six types of plastics in freshwater systems. We found that E. coli with flagella exhibited better initial attachment performance onto all six types of plastics than strain without flagella. Flagella could help bacteria swim near to plastics, pierce the energy barrier, and subsequently attach onto plastics. With stronger adhesive force, sticky flagella could further facilitate bacterial attachment onto plastics. Moreover, flagella especially sticky flagella could help bacteria form more rigid attachment layer on plastics. Even with humic acid in suspensions or in river water, flagellar E. coli showed greater attachment onto plastics than E. coli without flagella. Humic acid might adsorb onto sticky flagella and thus decreased the attachment of bacteria with sticky flagella onto plastics. Obviously, flagella as well as their property would impact the initial attachment of bacteria onto plastics and the subsequent formation of plastisphere in freshwater.

Phase separation phenomenon in mixed system composed of low- and high-inertia active particles

Active matter refers to a class of substance capable of autonomously moving by harnessing energy from its surrounding environment. The substance exhibits unique non-equilibrium phenomenon, and hence has attracted great attention in the scientific community. Many active matters, such as bacteria, cells, micro-swimmers, and self-propelled colloidal particles, operate in viscous environments and their motions are described usually by using overdamped models. Examples include overdamped active Brownian particle (ABP) model for self-propelled colloidal particles in solution and run-and-tumble (RTP) model for swimming bacteria. In recent years, increasing studies focus on the influence of inertia on the behavior of active matter. Vibrating robots, runners, flying insects, and micro-fliers are typical of active systems under the underdamped condition. The motions of these active matters can be modelled by underdamped Langevin equation, known as the active inertial particle (AIP) model. Previous studies have demonstrated that like the scenarios in ABP systems, motility-induced phase separation (MIPS) phenomena also happen in AIP systems under certain density conditions. However, due to the strong collision-and-rebound effect, aggregation of AIP particles and hence the MIPS are impeded. In complex living/application environments, mixture of different active agents is often seen. Some studies on mixed systems of active matter show that the composition is an important quantity, which influences the phase separation phenomena. In this paper, we study the phase separation phenomena in a mixed system composed of low- and high-inertia active particles by underdamped Langevin dynamics simulations. We find that compared with single-component system, the mixed system is unexpectedly favorable for the occurrence of phase separation at a moderate overall concentration and a certain range of component fraction, while unfavorable for phase separation at a high overall concentration. The underlying mechanism is that the presence of a small number of the high-inertia particles could accelerate the motion of the low-inertia particles, thus facilitating their aggregation and promoting the phase separation. However, when the fraction of the high-inertia particles is large, frequent elastic collisions would disturb the aggregation of the low-inertia particles and suppress the occurrence of phase separation. Our results provide a new insight into the collective behavior of active materials and also a reference for their design and applications.

Analysis of Adhesion and Surface Motility of a Spirochete Bacterium.

Spirochetes are Gram-negative bacteria with helical or flat wave morphology and move using flagella residing beneath the outer membrane. Most commonly, flagellated bacteria swim in liquid. Meanwhile, some species of spirochete not only swim but keep moving after adhering to solid surfaces, and such amphibious motility is believed to be significant for pathogenicity. This chapter focuses on the zoonotic spirochete Leptospira and describes the method for measuring the spirochete adhesion and surface motility.

Confinement, chaotic transport, and trapping of active swimmers in time-periodic flows.

Microorganisms encounter complex unsteady flows, including algal blooms in marine settings, microbial infections in airways, and bioreactors for vaccine and biofuel production. Here, we study the transport of active swimmers in two-dimensional time-periodic flows using Langevin simulations and experiments with swimming bacteria. We find that long-term swimmer transport is controlled by two parameters, the pathlength of the unsteady flow and the normalized swimmer speed. The pathlength nonmonotonically controls swimmer dispersion dynamics, giving rise to three distinct dispersion regimes. Weak flows hinder swimmer transport by confining cells toward flow manifolds. As pathlength increases, chaotic transport along flow manifolds initiates, maximizing the number of unique flow cells traveled. Last, strong flows trap swimmers at the vortex core, suppressing dispersal. Experiments with Vibrio cholerae showed qualitative agreement with model dispersion patterns. Our results reveal that nontrivial chaotic transport can arise in simple unsteady flows and suggest a potentially optimal dispersal strategy for microswimmers in nature.

Non-symmetric pinning of topological defects in living liquid crystals

Topological defects, such as vortices and disclinations, play a crucial role in spatiotemporal organization of equilibrium and non-equilibrium systems. The defect immobilization or pinning is a formidable challenge in the context of the out-of-equilibrium system, like a living liquid crystal, a suspension of swimming bacteria in lyotropic liquid crystal. Here we control the emerged topological defects in a living liquid crystal by arrays of 3D-printed microscopic obstacles (pillars). Our studies show that while −1/2 defects may be easily immobilized by the pillars, +1/2 defects remain motile. Due to attraction between oppositely charged defects, positive defects remain in the vicinity of pinned negative defects, and the diffusivity of positive defects is significantly reduced. Experimental findings are rationalized by computational modeling of living liquid crystals. Our results provide insight into the engineering of active systems via targeted immobilization of topological defects.

Porous Pellicle Formation of a Filamentous Bacterium, Leptothrix.

The bacterium Leptothrix cholodnii generates filaments encased in a sheath comprised of woven nanofibrils. In static liquid culture, L. cholodnii moves toward the air-liquid interface, where it forms porous pellicles. Observations of aggregation at the interface reveal that clusters consisting of only a few bacteria primarily grow by netting free cells. These growing clusters hierarchically enlarge through the random docking of other small clusters. We find that the bacteria swim using their polar flagellum toward the interface, where their sheath assists them in intertwining with others and thereby promotes the formation of small clusters. In contrast, sheathless hydrophobic mutant cells get stuck to the interface. We find that the nanofibril sheath is vital for robust pellicle formation as it lowers cell surface hydrophobicity by 60%, thereby reducing their adsorption and enabling cells to move toward and stick together at the air-liquid interface. IMPORTANCE Efficient and sustainable management of water resources is becoming a fundamental issue for supporting growing populations and for developing economic activity. Fundamental to this management is the treatment of wastewater. Microorganisms are the active component of activated sludge that is employed in the biodegradation process of many wastewater treatment facilities. However, uncontrolled growth of filamentous bacteria such as Sphaerotilus often results in filamentous bulking, lowering the efficiency of water treatment systems. To prevent this undesirable condition, strategies based on a fundamental understanding of the ecology of filamentous bacteria are required. Although the filamentous bacterium Leptothrix cholodnii, which is closely related to Sphaerotilus, is a minor inhabitant of activated sludge, its complete genome sequence is known, making gene manipulation relatively easy. Moreover, L. cholodnii generates porous pellicles under static conditions, which may be a characteristic of filamentous bulking. We show that both swimming motility and nanofibril-mediated air-liquid interface attachment are required for porous pellicle formation. These insights are critical for a better understanding of the characteristics of filamentous bulking and might improve strategies to control activated sludge.

Multi-scale organization in communicating active matter

The emergence of collective motion among interacting, self-propelled agents is a central paradigm in non-equilibrium physics. Examples of such active matter range from swimming bacteria and cytoskeletal motility assays to synthetic self-propelled colloids and swarming microrobots. Remarkably, the aggregation capabilities of many of these systems rely on a theme as fundamental as it is ubiquitous in nature: communication. Despite its eminent importance, the role of communication in the collective organization of active systems is not yet fully understood. Here we report on the multi-scale self-organization of interacting self-propelled agents that locally process information transmitted by chemical signals. We show that this communication capacity dramatically expands their ability to form complex structures, allowing them to self-organize through a series of collective dynamical states at multiple hierarchical levels. Our findings provide insights into the role of self-sustained signal processing for self-organization in biological systems and open routes to applications using chemically driven colloids or microrobots.

Mixing in chaotic flows with swimming bacteria

This is a manuscript accepted for publication on Physical Review Fluids, Gallery of Fluid Motion special issue. The manuscript is associated with a poster winner of the 39th Annual Gallery of Fluid Motion Award, for work presented at the 74th Annual Meeting of the American Physical Society's Division of Fluid Dynamics (Phoenix, AZ, USA 2021).

Interaction of microswimmers in viscoelastic liquid crystals

Swimming bacteria successfully colonize complex non-Newtonian environments exemplified by viscoelastic media and liquid crystals. While there is a significant body of research on microswimmer motility in viscoelastic liquids, the motion in anisotropic fluids still lacks clarity. This paper studies how individual microswimmers (e.g., bacteria) interact in a mucus-like environment modeled by a visco-elastic liquid crystal. We have found that an individual swimmer moves faster along the same track after the direction reversal, in faithful agreement with the experiment. This behavior is attributed to the formation of the transient tunnel due to the visco-elastic medium memory. We observed that the aft swimmer has a higher velocity for two swimmers traveling along the same track and catches up with the leading swimmer. Swimmers moving in a parallel course attract each other and then travel at a close distance. A pair of swimmers launched at different angles form a "train”: after some transient, the following swimmers repeat the path of the "leader”. Our results shed light on bacteria penetration in mucus and colonization of heterogeneous liquid environments.

Reduced surface accumulation of swimming bacteria in viscoelastic polymer fluids

Surface-associated bacterial communities flourish in nature and in the body of animal hosts with abundant macromolecular polymers. It is unclear how the endowed viscoelasticity of polymeric fluids influences bacterial motile behavior in such environments. Here, we combined experiment and theory to study near-surface swimming of flagellated bacteria in viscoelastic polymer fluids. In contrast to the swimming behavior in Newtonian fluids, we discovered that cells swim in less curved trajectories and display reduced near-surface accumulation. Using a theoretical analysis of the non-Newtonian hydrodynamic forces, we demonstrated the existence of a generic lift force acting on a rotating filament near a rigid surface, which arises from the elastic tension generated along curved flow streamlines. This viscoelastic lift force weakens the hydrodynamic interaction between flagellated swimmers and solid surfaces and contributes to a decrease in surface accumulation. Our findings reveal previously unrecognized facets of bacterial transport and surface exploration in polymer-rich environments that are pertinent to diverse microbial processes and may inform the design of artificial microswimmers capable of navigating through complex geometries.