We report a novel form of convection in suspensions of the bioluminiscent marine bacterium $Photobacterium~phosphoreum$. Suspensions of these bacteria placed in a chamber open to the air create persistent luminiscent plumes most easily visible when observed in the dark. These flows are strikingly similar to the classical bioconvection pattern of aerotactic swimming bacteria, which create an unstable stratification by swimming upwards to an air-water interface, but they are a puzzle since the strain of $P.~phosphoreum$ used does not express flagella and therefore cannot swim. Systematic experimentation with suspensions of microspheres reveals that these flow patterns are driven not by the bacteria but by the accumulation of salt at the air-water interface due to evaporation of the culture medium; even at room temperature and humidity, and physiologically relevant salt concentrations, the rate of water evaporation is sufficient to drive convection patterns. A mathematical model is developed to understand the mechanism of plume formation, and linear stability analysis as well as numerical simulations were carried out to support the conclusions. While evaporation-driven convection has not been discussed extensively in the context of biological systems, these results suggest that the phenomenon may be relevant in other systems, particularly those using microorganisms of limited motility.
Understanding flow and transport of bacteria in porous media is crucial to technologies such as bioremediation, biomineralization or enhanced oil recovery. While physicochemical bacteria filtration is well-documented, recent studies showed that bacterial motility plays a key role in the transport process. Flow and transport experiments performed in microfluidic chips containing randomly placed obstacles confirmed that the distributions of non-motile particles stays compact, whereas for the motile strains, the distributions are characterized by both significant retention as well as fast downstr…
Bacteria commonly live in structured communities that affect human health and influence ecological systems. Heterogeneous populations, such as motile and non-motile populations, often coexist in bacteria communities. Motile subpopulations in microbial communities are believed to be important to dispersal, quest for food, and material transport. However, except in circumstances where motile cells drive colony expansion (e.g. bacterial swarming), the physiological functions of motile subpopulations in bacterial communities are largely unclear. Here we discovered that motile cells in routinely cu…
Bacteria suspension exhibits a wide range of collective phenomena arising from interactions between individual cells. Here we show Serratia marcescens cells near an air-liquid interface spontaneously aggregate into dynamic clusters through surface-mediated hydrodynamic interactions. These long-lived clusters translate randomly and rotate in the counter-clockwise direction; they continuously evolve, merge with others and split into smaller ones. Measurements indicate that long-ranged hydrodynamic interactions have strong influences on cluster properties. Bacterial clusters change material and f…
The role of activity on the hydrodynamic dispersion of bacteria in a model porous medium is studied by tracking thousands of bacteria in a microfluidic chip containing randomly placed pillars. We first evaluate the spreading dynamics of two populations of motile and non-motile bacteria injected at different flow rates. In both cases, we observe that the mean and the variance of the distances covered by the bacteria vary linearly with time and flow velocity, a result qualitatively consistent with the standard geometric dispersion picture. However, quantitatively, the motiles bacteria display a …
We have measured the spatial distribution of motile Escherichia coli inside spherical water droplets emulsified in oil. At low cell concentrations, the cell density peaks at the water-oil interface; at increasing concentration, the bulk of each droplet fills up uniformly while the surface peak remains. Simulations and theory show that the bulk density results from a `traffic' of cells leaving the surface layer, increasingly due to cell-cell scattering as the surface coverage rises above $\sim 10\%$. Our findings show similarities with the physics of a rarefied gas in a spherical cavity with at…
External control of the swimming speed of `active particles' can be used to self assemble designer structures in situ on the micrometer to millimeter scale. We demonstrate such reconfigurable templated active self assembly in a fluid environment using light powered strains of Escherichia coli. The physics and biology controlling the sharpness and formation speed of patterns is investigated using a bespoke fast-responding strain.
Mixtures of active and passive particles are predicted to exhibit a variety of nonequilibrium phases. Here we report a dynamic clustering phase in mixtures of colloids and motile bacteria. We show that colloidal clustering results from a balance between bond breaking due to persistent active motion and bond stabilization due to torques that align active particle velocity tangentially to the passive particle surface. Furthermore, dynamic clustering spans a broad regime between diffusivity-based and motility-induced phase separation that subsumes typical bacterial motility parameters.
Microbiology is the science of microbes, particularly bacteria. Many bacteria are motile: they are capable of self-propulsion. Among these, a significant class execute so-called run-and-tumble motion: they follow a fairly straight path for a certain distance, then abruptly change direction before repeating the process. This dynamics has something in common with Brownian motion (it is diffusive at large scales), and also something in contrast. Specifically, motility parameters such as the run speed and tumble rate depend on the local environment and hence can vary in space. When they do so, eve…
We studied the swimming of \textit{Escherichia coli} bacteria in the vicinity of the critical point in a solution of the non-ionic surfactant \chem{C_{12}E_{5}} in buffer solution. In phase contrast microscopy, each swimming cell produces a transient trail behind itself lasting several seconds. Comparing quantitative image analysis with simulations show that these trails are due to local phase re-organisation triggered by differential adsorption. This contrasts with similar trails seen in bacteria swimming in liquid crystals, which are due to shear effects. We show how our trails are controlle…
Motile Bacteria Modify Salt Precipitation Patterns in Dried Sessile Droplet
Georgia Institute of Technology（佐治亚理工学院）；University of Nebraska - Lincoln（内布拉斯加大学林肯分校）；Illinois Institute of Technology（伊利诺伊理工学院）；Blue Valley North High School（蓝谷北高中）
We show, using differential dynamic microscopy, that the diffusivity of non-motile cells in a three-dimensional (3D) population of motile E. coli is enhanced by an amount proportional to the active cell flux. While non-motile mutants without flagella and mutants with paralysed flagella have quite different thermal diffusivities and therefore hydrodynamic radii, their diffusivities are enhanced to the same extent by swimmers in the regime of cell densities explored here. Integrating the advective motion of non-swimmers caused by swimmers with finite persistence-length trajectories predicts our …
We study the spreading of a bacterial colony undergoing turbulent like collective motion. We present two minimalistic models to investigate the interplay between population growth and coherent structures arising from turbulence. Using Direct Numerical Simulation (DNS) of the proposed models we find that turbulence has two prominent effects on the spatial growth of the colony: (a) the front speed is enhanced, and (b) the front gets crumpled. Both these effects, which we highlight by using statistical tools, are markedly different in our two models. We also show that the crumpled front structure…
How motile bacteria move near a surface is a problem of fundamental biophysical interest and is key to the emergence of several phenomena of biological, ecological and medical relevance, including biofilm formation. Solid boundaries can strongly influence a cell's propulsion mechanism, thus leading many flagellated bacteria to describe long circular trajectories stably entrapped by the surface. Experimental studies on near-surface bacterial motility have, however, neglected the fact that real environments have typical microstructures varying on the scale of the cells' motion. Here, we show tha…
As a paradigmatic model of active fluids, bacterial suspensions show intriguing rheological responses drastically different from their counterpart colloidal suspensions. Although the flow of bulk bacterial suspensions has been extensively studied, the rheology of bacterial suspensions under confinement has not been experimentally explored. Here, using a microfluidic viscometer, we systematically measure the rheology of dilute E. coli suspensions under different degrees of confinement. Our study reveals a strong confinement effect: the viscosity of bacterial suspensions decreases substantially …
Swimming microorganisms can influence the diffusion of passive particles. The effect of this swimmer-particle interaction depends on different properties, such as the hydrodynamic field of the swimmer and the relative sizes of microorganisms and particles. We investigated an enhancement of the diffusion of silica doublets in a suspension of microalgae Chlamydomonas reinhardtii in a flat capillary. Depending on the concentration of microswimmers, the translational and rotational diffusion constants increase by several orders of magnitude in the presence of the swimming algae. For low concentrat…
A simple model for simulating flows of active suspensions is investigated. The approach is based on dissipative particle dynamics. While the model is potentially applicable to a wide range of self-propelled particle systems, the specific class of self-motile bacterial suspensions is considered as a modeling scenario. To mimic the rod-like geometry of a bacterium, two dissipative particle dynamics particles are connected by a stiff harmonic spring to form an aggregate dissipative particle dynamics molecule. Bacterial motility is modeled through a constant self-propulsion force applied along the…
The rheological response under simple shear of an active suspension of Escherichia coli is determined in a large range of shear rates and concentrations. The effective viscosity and the time scales characterizing the bacterial organization under shear are obtained. In the dilute regime, we bring evidences for a low shear Newtonian plateau characterized by a shear viscosity decreasing with concentration. In the semi-dilute regime, for particularly active bacteria, the suspension display a "super-fluid" like transition where the viscous resistance to shear vanishes, thus showing that macroscopic…
An experimental study of flows of the green non-motile Chlorella micro-alga in a plane microchannel is presented. Depending on the value of the cell volume fraction, three distinct flow regimes are observed. For low values of the cell volume fraction a Newtonian flow regime characterised by a Poiseuille like flow field, absence of wall slip and hydrodynamic reversibility of the flow states is observed. For intermediate values of the cell volume fraction, the flow profiles are consistent with a Poiseuille flow of a shear thinning fluid in the presence of slip at the channel's wall. For even lar…
Adhesion of bacteria to liquid-liquid interfaces can play a role in the biodegradation of dispersed hydrocarbons and in biochemical and bioprocess engineering. Whereas thermodynamic factors underpinning adhesion are well studied, the role of bacterial activity on adhesion is less explored.Here, we show that bacterial motility enhances adhesion to surfactant-decorated oil droplets dispersed in artificial sea water. Motile Halomonas titanicae adhered to hexadecane droplets stabilized with dioctyl sodium sulfosuccinate (DOSS) more rapidly and at greater surface densities compared to nonmotile H. …
Drying of bacterial suspensions is frequently encountered in a plethora of natural and engineering processes. However, the evaporation-driven mechanical instabilities of dense consolidating bacterial suspensions have not been explored heretofore. Here, we report the formation of two different crack patterns of drying suspensions of \textit{Escherichia coli} (\textit{E. coli}) with distinct motile behaviors. Circular cracks are observed for wild-type \textit{E. coli} with active swimming, whereas spiral-like cracks form for immotile bacteria. Using the elastic fracture mechanics and the poroela…
Swimming bacteria create long-range velocity fields that stir a large volume of fluid and move around passive particles dispersed in the fluid. Recent experiments and simulations have shown that long-time mean-squared displacement of passive particles in a bath of swimming bacteria exhibits diffusive behaviour with the effective diffusion coefficient significantly larger than its thermal counterpart. Comprehensive theoretical prediction of this effective diffusion coefficient and understanding of the enhancement mechanism remain a challenge. Here, we adapt the kinetic theory by Lin et al., J. …
Non-motile active matter exhibits a wide range of non-equilibrium collective phenomena yet examples are crucially lacking in the literature. We present a microscopic model inspired by the bacteria {\it Neisseria Meningitidis} in which diffusive agents feel intermittent attractive forces. Through a formal coarse-graining procedure, we show that this truly scalar model of active matter exhibits the time-reversal-symmetry breaking terms defining the {\it Active Model B+} class. In particular, we confirm the presence of microphase separation by solving the kinetic equations numerically. We show th…
To survive in harsh conditions, motile bacteria swim in complex environment and respond to the surrounding flow. Here we develop a PDE model describing how the flagella bending affects macroscopic properties of bacterial suspensions. First, we show how the flagella bending contributes to the decrease of the effective viscosity observed in dilute suspension. Our results do not impose tumbling (random re-orientation) as it was done previously to explain the viscosity reduction. Second, we demonstrate a possibility of bacterium escape from the wall entrapment due to the self-induced buckling of f…
Aerotaxis is the ability of motile cells to navigate toward oxygen. A key question is the dependence of the aerotactic velocity with the local oxygen concentration c. Here we combine simultaneous bacteria tracking and local oxygen concentration measurements using Ruthenium encapsulated in micelles to characterize the aerotactic response of Burkholderia contaminans, a motile bacterium ubiquitous in the environment. In our experiments, an oxygen gradient is produced by the bacterial respiration in a sealed glass capillary permeable to oxygen at one end, producing a bacterial band traveling towar…
Swimming microorganisms rely on effective mixing strategies to achieve efficient nutrient influx. Recent experiments, probing the mixing capability of unicellular biflagellates, revealed that passive tracer particles exhibit anomalous non-Gaussian diffusion when immersed in a dilute suspension of self-motile Chlamydomonas reinhardtii algae. Qualitatively, this observation can be explained by the fact that the algae induce a fluid flow that may occasionally accelerate the colloidal tracers to relatively large velocities. A satisfactory quantitative theory of enhanced mixing in dilute active sus…
Active matter is a new class of material, intrinsically out-of equilibrium with intriguing properties. So far, the recent upsurge of studies has mostly focused on the spontaneous behavior of these systems --in the absence of external constraints or driving--. Yet, many real life systems evolve under constraints, being both submitted to flow and various taxis. In the present work, we demonstrate a new experimental system which opens up the way for quantitative investigations, and discriminating examinations, of the challenging theoretical description of such systems. We explore the behavior of …
Near field hydrodynamic interactions are essential to determine many important emergent behaviors observed in active suspensions, but have not been successfully modeled so far. In this work we propose an effective model capable of efficiently capturing the essence of the near field hydrodynamic interactions, validated numerically by a pedagogic model system consisting of an E. coli and a spherical tracer. The proposed model effectively captures all the details of near field hydrodynamics through only a tensorial coefficient of resistance, which is fundamentally different from, and thus cannot …
We probe non-equilibrium properties of an active bacterial bath through measurements of correlations of passive tracer particles and the response function of a driven, optically trapped tracer. These measurements demonstrate violation of the fluctuation-dissipation theorem and enable us to extract the power spectrum of the active stress fluctuations. In some cases, we observe $1/\sqrtω$ scaling in the noise spectrum which we show can be derived from a theoretical model incorporating coupled stress, orientation, and concentration fluctuations of the bacteria.
We describe a new kind of self-propelling motion of bacteria based on the cooperative action of rotating flagella on the surface of bacteria. Describing the ensemble of rotating flagella in the framework of the hydrodynamics with spin the reciprocal theorem of Stokesian hydrodynamics is generalized accordingly. The velocity of the self-propulsion is expressed in terms of the characteristics of the vector field of flagella orientation and it is shown that unusually high velocities of \textit{Thiovulum majus} bacteria may be explained by the cooperative action of the rotating flagella. The expre…
The viscosity of an active suspension of E-Coli bacteria is determined experimentally in the dilute and semi dilute regime using a Y shaped micro-fluidic channel. From the position of the interface between the pure suspending fluid and the suspension, we identify rheo-thickening and rheo-thinning regimes as well as situations at low shear rate where the viscosity of the bacteria suspension can be lower than the viscosity of the suspending fluid. In addition, bacteria concentration and velocity profiles in the bulk are directly measured in the micro-channel.
We analyse the time dependent non-linear rheology of a dilute bacterial suspension (e.g. E. coli) for a pair of impulsively started linear flows - simple shear and uniaxial extension. The rheology is governed by the bacterium orientation distribution which satisfies a kinetic equation that includes rotation by the imposed flow, and relaxation to isotropy via rotary diffusion and tumbling. The relevant dimensionless parameters are the Peclet number $Pe\equiv \dotγτ$, which dictates the importance of flow-induced orientation anisotropy, and $τD_r$, which quantifies the relative importance of the…
We investigate theoretically the collective dynamics of soft active particles living in a viscous fluid. We focus on a minimal model for active but non-motile particles consisting of $N>1$ elastic dimers deformed by active stresses and interacting hydrodynamically. We first derive a set of effective equations of motion for the positions of the particles. We then exploit these equations in two experimentally-relevant cases: uncorrelated random internal stresses, and uniform monochromatic external shaking. In both cases, we show that small groups of intrinsically non-motile particles can display…
Sedimentation in active fluids has come into focus due to the ubiquity of swimming micro-organisms in natural and artificial environments. Here, we experimentally investigate sedimentation of passive particles in water containing various concentrations of the bacterium E. coli. Results show that the presence of living bacteria reduces the velocity of the sedimentation front even in the dilute regime, where the sedimentation velocity is expected to be independent of particle concentration. Bacteria increase the effective diffusion coefficient of the passive particles, which determines the width…
Concentrated suspensions of swimming microorganisms and other forms of active matter are known to display complex, self-organized spatio-temporal patterns on scales large compared to those of the individual motile units. Despite intensive experimental and theoretical study, it has remained unclear the extent to which the hydrodynamic flows generated by swimming cells, rather than purely steric interactions between them, drive the self-organization. Here we utilize the recent discovery of a spiral-vortex state in confined suspensions of \textit{B. subtilis} to study this issue in detail. Those …
Active matter such as swarming bacteria and motile colloids exhibits exotic properties different from conventional equilibrium materials. Among these properties, the enhanced diffusion of tracer particles is generally deemed as a hallmark of active matter. Here, rather than spherical tracers, we investigate the diffusion of isolated ellipsoids in quasi-two-dimensional bacterial bath. Our study reveals a nonlinear enhancement of both translational and rotational diffusions. More importantly, we uncover an anomalous coupling between translation and rotation that is strictly prohibited in the cla…
Colloids coupled to a bath of swimming cells generically display enhanced diffusion. This transport dynamics stems from a subtle interplay between the active and passive particles that still resists our understanding despite decades of intense research. Here, we tackle the root of the problem by providing a quantitative characterisation of the single scattering events between a colloid and a bacterium. Based on our experiments, we build a minimal model that quantitatively predicts the geometry of the scattering trajectories, and enhanced colloidal diffusion at long times. This quantitative con…
Deposits from evaporating drops have shown to take a variety of shapes, depending on the physicochemical properties of both solute and solvent. Classically, the evaporation of drops of colloidal suspensions leads to the so-called coffee ring effect, caused by radially outward flows. Here we investigate deposits from evaporating drops containing living motile microalgae (Chlamydomonas reinhardtii), which are capable of resisting these flows. We show that utilizing their light-sensitivity allows to control the final pattern: adjusting the wavelength and incident angle of the light source enables…
We study the collective dynamics of elongated swimmers in a very thin fluid layer by devising long, filamentous, non-tumbling bacteria. The strong confinement induces weak nematic alignment upon collision, which, for large enough density of cells, gives rise to global nematic order. This homogeneous but fluctuating phase, observed on the largest experimentally-accessible scale of millimeters, exhibits the properties predicted by standard models for flocking such as the Vicsek-style model of polar particles with nematic alignment: true long-range nematic order and non-trivial giant number fluct…
The rheology of semidilute bacterial suspensions is studied with the tools of kinetic theory, considering binary interactions, going beyond the ideal gas approximation. Two models for the interactions are considered, which encompass both the steric and short range interactions. In these, swimmers can either align polarly regardless of the state previous to the collision or they can align axially, being possible the end up antiparallel if the relative angle between directors is large. In both cases, it is found that an ordered phase develops when increasing the density, where the shear stress o…
Motile bacteria are known to accumulate at surfaces, eventually leading to changes in bacterial motility and bio-film formation. We use a novel two-colour, three-dimensional Lagrangian tracking technique, to follow simultaneously the body and the flagella of a wild-type ${\it Escherichia~coli}$. We observe long surface residence times and surface escape corresponding mostly to immediately antecedent tumbling. A motility model accounting for a large behavioural variability in run-time duration, reproduces all experimental findings and gives new insights into surface trapping efficiency.
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 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 stochas…
Dense suspensions of swimming bacteria are known to exhibit collective behaviour arising from the interplay of steric and hydrodynamic interactions. Unconfined suspensions exhibit transient, recurring vortices and jets, whereas those confinedin circular domains may exhibit order in the form of a spiral vortex. Here we show that confinement into a long and narrow macroscopic `racetrack' geometry stabilises bacterial motion to form a steady unidirectional circulation. This motion is reproduced in simulations of discrete swimmers that reveal the crucial role that bacteria-driven fluid flows play …
We point out unconventional mechanical properties of confined active fluids, such as bacterial suspensions, under shear. Using a minimal model of an active liquid crystal with no free parameters, we predict the existence of a window of bacteria concentration for which a suspension of \textit{E.~Coli} effectively behaves, at steady-state, as a negative viscosity fluid and reach quantitative agreement with experimental measurements. Our theoretical analysis further shows that a negative apparent viscosity is due to a non-monotonic local velocity profile, and is associated with a non-monotonic st…
We examine the interplay of motility and information exchange in a model of run-and-tumble active particles where the particle's motility is encoded as a bit of information that can be exchanged upon contact according to the rules of AND and OR logic gates in a circuit. Motile AND particles become non-motile upon contact with a non-motile particle. Conversely, motile OR particles remain motile upon collision with their non-motile counterparts. AND particles that have become non-motile additionally "reawaken", i.e., recover their motility, at a fixed rate $μ$, as in the SIS (Susceptible, Infect…
Locomotion is essential for living cells. It enables bacteria and algae to explore space for food, cancer to spread, and immune system to fight infections. Motile cells display trajectories of intriguing complexity, from regular (e.g. circular, helical, and so on) to irregular motions (run-tumble), the origin of which has remained elusive for over a century. This dynamics versatility is conventionally attributed to the shape asymmetry of the motile entity, to the suspending media, and/or to stochastic regulation. We propose here a universal approach highlighting that these movements are generi…
