Large scale zigzag pattern emerging from circulating active shakers

We report the emergence of large zigzag bands in a population of reversibly actuated magnetic rotors that behave as active shakers, namely squirmers that shake the fluid around them without moving. The shakers collectively organize into dynamic structures displaying self-similar growth and generate topological defects in the form of cusps that connect vortices of rolling particles with alternating chirality. By combining experimental analysis with particle-based simulation, we show that the special flow field created by the shakers is the only ingredient needed to reproduce the observed spatiotemporal pattern. We unveil a self-organization scenario in a collection of driven particles in a viscoelastic medium emerging from the reduced particle degrees of freedom, as here the frozen orientational motion of the shakers

3D spatial exploration by E. coli echoes motor temporal variability

Unraveling bacterial strategies for spatial exploration is crucial for understanding the complexity in the organization of life. Bacterial motility determines the spatio-temporal structure of microbial communities, controls infection spreading and the microbiota organization in guts or in soils. Most theoretical approaches for modeling bacterial transport rely on their run-and-tumble motion. For Escherichia coli, the run time distribution was reported to follow a Poisson process with a single characteristic time related to the rotational switching of the flagellar motors. However, direct measurements on flagellar motors show heavy-tailed distributions of rotation times stemming from the intrinsic noise in the chemotactic mechanism. Currently, there is no direct experimental evidence that the stochasticity in the chemotactic machinery affect the macroscopic motility of bacteria. In stark contrast with the accepted vision of run-and-tumble, here we report a large behavioral variability of wild-type \emph{E. coli}, revealed in their three-dimensional trajectories. At short observation times, a large distribution of run times is measured on a population and attributed to the slow fluctuations of a signaling protein triggering the flagellar motor reversal. Over long times, individual bacteria undergo significant changes in motility. We demonstrate that such a large distribution of run times introduces measurement biases in most practical situations. Our results reconcile the notorious conundrum between run time observations and motor switching statistics. We finally propose that statistical modeling of transport properties currently undertaken in the emerging framework of active matter studies, should be reconsidered under the scope of this large variability of motility features.Comment: 12 pages, 7 figures, Supplementary information include

Run-to-tumble variability controls the surface residence times of E. coli bacteria

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

Oscillatory surface rheotaxis of swimming E. coli bacteria

Bacterial contamination of biological conducts, catheters or water resources is a major threat to public health and can be amplified by the ability of bacteria to swim upstream. The mechanisms of this rheotaxis, the reorientation with respect to flow gradients, often in complex and confined environments, are still poorly understood. Here, we follow individual E. coli bacteria swimming at surfaces under shear flow with two complementary experimental assays, based on 3D Lagrangian tracking and fluorescent flagellar labelling and we develop a theoretical model for their rheotactic motion. Three transitions are identified with increasing shear rate: Above a first critical shear rate, bacteria shift to swimming upstream. After a second threshold, we report the discovery of an oscillatory rheotaxis. Beyond a third transition, we further observe coexistence of rheotaxis along the positive and negative vorticity directions. A full theoretical analysis explains these regimes and predicts the corresponding critical shear rates. The predicted transitions as well as the oscillation dynamics are in good agreement with experimental observations. Our results shed new light on bacterial transport and reveal new strategies for contamination prevention.Comment: 12 pages, 5 figure

Transport de bactéries actives : des processus à l’échelle microscopique à la dispersion hydrodynamique

In this thesis, I investigate the transport properties of Escherichia. Coli bacteria in a flow. First I introduce the Lagrangian 3D tracker that I used and improved. This apparatus allows to follow bacteria in 3 dimensions over long periods of time and large spaces in a quiescent fluid or under flow and is the suitable tool to study microscopic properties of bacteria. Then I focus on the motility of bacteria in the bulk of quiescent fluids. Especially, I focus on the "run and tumble" process and bridge the gap between the short-time and long-time approach. I then study the long time behavior of bacteria at surfaces as well as the exchange with the bulk. The flow is then turned on and the behavior of bacteria at surfaces, submitted to different shear, is studied. To have a general picture of bacterial transport, all the effects due to surfaces, shear and bacteria activity and shape are considered. I also focus on bacterial trajectory in the bulk under flow. I find new features and compare my experimental result to an active Bretherton-Jeffery model. In a last chapter, thanks to a theoretical framework, I build a method able to extract parameters from my experimental data. To conclude, I discuss the implication of my work in the framework of bacterial transport and dispersion.Dans cette thèse, je m’intéresse aux propriétés de transport de la bactérie Escherichia. Coli sous écoulement dans des micro-canaux. Tout d’abord, le dispositif de tracking lagrangien 3D est présenté. Cet appareil permet de suivre des bactéries nageant dans un espace à 3 dimensions et de reconstruire leurs trajectoires. Dans une première partie, grâce à une approche aux temps longs, le processus de « run and tumble » pour des bactéries nageant dans un fluide aux repos loin des surfaces est revisité. J’étudie ensuite le comportement des bactéries aux surfaces, via leurs temps de résidences, ainsi que les échanges avec les régions loin des parois. Dans une deuxième partie, les bactéries sont mises en écoulement et leurs différents comportements sont mis en évidence. Aux surfaces, plusieurs régimes rhéotactiques sont observés, dont un nouveau régime où l’orientation de la bactérie oscille. Loin des parois, les trajectoires des bactéries sont comparées à un modèle de Bretherton-Jeffery actif et de nouvelles caractéristiques, en accord avec le modèle, sont observées. Dans un dernier chapitre, je développe une méthode capable d’extraire des paramètres de mes trajectoires expérimentales. Pour conclure, je discute des conséquences des précédents résultats dans le cadre de la dispersion hydrodynamiques

Transport de bactéries actives : des processus à l’échelle microscopique à la dispersion hydrodynamique

Dans cette thèse, je m’intéresse aux propriétés de transport de la bactérie Escherichia. Coli sous écoulement dans des micro-canaux. Tout d’abord, le dispositif de tracking lagrangien 3D est présenté. Cet appareil permet de suivre des bactéries nageant dans un espace à 3 dimensions et de reconstruire leurs trajectoires. Dans une première partie, grâce à une approche aux temps longs, le processus de « run and tumble » pour des bactéries nageant dans un fluide aux repos loin des surfaces est revisité. J’étudie ensuite le comportement des bactéries aux surfaces, via leurs temps de résidences, ainsi que les échanges avec les régions loin des parois. Dans une deuxième partie, les bactéries sont mises en écoulement et leurs différents comportements sont mis en évidence. Aux surfaces, plusieurs régimes rhéotactiques sont observés, dont un nouveau régime où l’orientation de la bactérie oscille. Loin des parois, les trajectoires des bactéries sont comparées à un modèle de Bretherton-Jeffery actif et de nouvelles caractéristiques, en accord avec le modèle, sont observées. Dans un dernier chapitre, je développe une méthode capable d’extraire des paramètres de mes trajectoires expérimentales. Pour conclure, je discute des conséquences des précédents résultats dans le cadre de la dispersion hydrodynamiques.In this thesis, I investigate the transport properties of Escherichia. Coli bacteria in a flow. First I introduce the Lagrangian 3D tracker that I used and improved. This apparatus allows to follow bacteria in 3 dimensions over long periods of time and large spaces in a quiescent fluid or under flow and is the suitable tool to study microscopic properties of bacteria. Then I focus on the motility of bacteria in the bulk of quiescent fluids. Especially, I focus on the "run and tumble" process and bridge the gap between the short-time and long-time approach. I then study the long time behavior of bacteria at surfaces as well as the exchange with the bulk. The flow is then turned on and the behavior of bacteria at surfaces, submitted to different shear, is studied. To have a general picture of bacterial transport, all the effects due to surfaces, shear and bacteria activity and shape are considered. I also focus on bacterial trajectory in the bulk under flow. I find new features and compare my experimental result to an active Bretherton-Jeffery model. In a last chapter, thanks to a theoretical framework, I build a method able to extract parameters from my experimental data. To conclude, I discuss the implication of my work in the framework of bacterial transport and dispersion

Collective hydrodynamic transport of magnetic microrollers

We investigate the collective transport properties of microscopic magnetic rollers that propel close to a surface due to a circularly polarized, rotating magnetic field. The applied field exerts a torque to the particles, which induces a net rolling motion close to a surface. The collective dynamics of the particles result from the balance between magnetic dipolar interactions and hydrodynamic ones. We show that, when hydrodynamics dominate, i.e. for high particle spinning, the collective mean velocity linearly increases with the particle density. In this regime we analyse the clustering kinetics, and find that hydrodynamic interactions between the anisotropic, elongated particles, induce preferential cluster growth along a direction perpendicular to the driving one, leading to dynamic clusters that easily break and reform during propulsion

Oscillatory surface rheotaxis of swimming E. coli bacteria

International audienceBacterial contamination of biological channels, catheters or water resources is a major threat to public health, which can be amplified by the ability of bacteria to swim upstream. The mechanisms of this 'rheotaxis', the reorientation with respect to flow gradients, are still poorly understood. Here, we follow individual E. coli bacteria swimming at surfaces under shear flow using 3D Lagrangian tracking and fluorescent flagellar labelling. Three transitions are identified with increasing shear rate: Above a first critical shear rate, bacteria shift to swimming upstream. After a second threshold, we report the discovery of an oscillatory rheotaxis. Beyond a third transition, we further observe coexistence of rheotaxis along the positive and negative vorticity directions. A theoretical analysis explains these rheotaxis regimes and predicts the corresponding critical shear rates. Our results shed light on bacterial transport and reveal strategies for contamination prevention, rheotactic cell sorting, and microswimmer navigation in complex flow environments