The role of tumbling in bacterial scattering at convex obstacles

Active propulsion, as performed by bacteria and Janus particles, in combination with hydrodynamic interaction results in the accumulation of bacteria at a flat wall. However, in microfluidic devices with cylindrical pillars of sufficiently small radius, self-propelled particles can slide along and scatter off the surface of a pillar, without becoming trapped over long times. This non-equilibrium scattering process has been predicted to result in large diffusivities, even at high obstacle density, unlike particles that undergo classical specular reflection. Here, we test this prediction by experimentally studying the non-equilibrium scattering of pusher-like swimmers in microfluidic obstacle lattices. To explore the role of tumbles in the scattering process, we microscopically tracked wild-type (run and tumble) and smooth-swimming (run only) mutants of the bacterium Escherichia coli scattering off microfluidic pillars. We quantified key scattering parameters and related them to previously proposed models that included a prediction for the diffusivity, discussing their relevance. Finally, we discuss potential interpretations of the role of tumbles in the scattering process and connect our work to the broader study of swimmers in porous media.Comment: 9 pages, 8 figure

Gyrotactic swimmer dispersion in pipe flow: testing the theory

Suspensions of microswimmers are a rich source of fascinating new fluid mechanics. Recently we predicted the active pipe flow dispersion of gyrotactic microalgae, whose orientation is biased by gravity and flow shear. Analytical theory predicts that these active swimmers disperse in a markedly distinct manner from passive tracers (Taylor dispersion). Dispersing swimmers display non-zero drift and effective diffusivity that is non-monotonic with Péclet number. Such predictions agree with numerical simulations, but hitherto have not been tested experimentally. Here, to facilitate comparison, we obtain new solutions of the axial dispersion theory accounting both for swimmer negative buoyancy and a local nonlinear response of swimmers to shear, provided by two alternative microscopic stochastic descriptions. We obtain new predictions for suspensions of the model swimming alga Dunaliella salina, whose motility and buoyant mass we parametrise using tracking video microscopy. We then present a new experimental method to measure gyrotactic dispersion using fluorescently stained D. salina and provide a preliminary comparison with predictions of a non-zero drift above the mean flow for each microscopic stochastic description. Finally, we propose further experiments for a full experimental characterisation of gyrotactic dispersion measures and discuss the implications of our results for algal dispersion in industrial photobioreactors

Diffusion of active particles in a complex environment: Role of surface scattering.

Experiments have shown that self-propelled particles can slide along the surface of a circular obstacle without becoming trapped over long times. Using simulations and theory, we study the impact of boundary conditions on the diffusive transport of active particles in an obstacle lattice. We find that particle dynamics with sliding boundary conditions result in large diffusivities even at high obstacle density, unlike classical specular reflection. These dynamics are very well described by a model based on run-and-tumble particles with microscopically derived reorientation functions arising from obstacle-induced tumbles. This model, however, fails to describe fine structure in the diffusivity at high obstacle density predicted by simulations for pusherlike collisions. Using a simple deterministic model, we show that this structure results from particles being guided by the lattice. Our results thus show how nonclassical surface scattering introduces a dependence on the lattice geometry at high densities. We discuss implications for the study of bacteria in complex environments

Dispersion of swimming algae in laminar and turbulent channel flows: consequences for photobioreactors

Shear flow significantly affects the transport of swimming algae in suspension. For example, viscous and gravitational torques bias bottom-heavy cells to swim towards regions of downwelling fluid (gyrotaxis). It is necessary to understand how such biases affect algal dispersion in natural and industrial flows, especially in view of growing interest in algal photobioreactors. Motivated by this, we here study the dispersion of gyrotactic algae in laminar and turbulent channel flows using direct numerical simulation (DNS) and the analytical swimming dispersion theory of Bees and Croze (2010). Time-resolved dispersion measures are evaluated as functions of the Peclet and Reynolds numbers in upwelling and downwelling flows. For laminar flows, DNS results are compared with theory using competing descriptions of biased swimming cells in shear flow. Excellent agreement is found for predictions that employ generalized-Taylor-dispersion. The results highlight peculiarities of gyrotactic swimmer dispersion relative to passive tracers. In laminar downwelling flow the cell distribution drifts in excess of the mean flow, increasing in magnitude with Peclet number. The cell effective axial diffusivity increases and decreases with Peclet number (for tracers it merely increases). In turbulent flows, gyrotactic effects are weaker, but discernable and manifested as non-zero drift. These results should significantly impact photobioreactor design.Comment: 31 pages, 15 figures (includes supplementary materials

Migration and accumulation of bacteria with chemotaxis and chemokinesis

Abstract: Bacteria can chemotactically migrate up attractant gradients by controlling run-and-tumble motility patterns. In addition to this well-known chemotactic behaviour, several soil and marine bacterial species perform chemokinesis; they adjust their swimming speed according to the local concentration of chemoeffector, with higher speed at higher concentration. A field of attractant then induces a spatially varying swimming speed, which results in a drift towards lower attractant concentrations—contrary to the drift created by chemotaxis. Here, to explore the biological benefits of chemokinesis and investigate its impact on the chemotactic response, we extend a Keller–Segel-type model to include chemokinesis. We apply the model to predict the dynamics of bacterial populations capable of chemokinesis and chemotaxis in chemoeffector fields inspired by microfluidic and agar plate migration assays. We find that chemokinesis combined with chemotaxis not only may enhance the population response with respect to pure chemotaxis, but also modifies it qualitatively. We conclude presenting predictions for bacteria around dynamic finite-size nutrient sources, simulating, e.g. a marine particle or a root. We show that chemokinesis can reduce the measuring bias that is created by a decaying attractant gradient. Graphic abstract

Microbial mutualism at a distance: The role of geometry in diffusive exchanges

The exchange of diffusive metabolites is known to control the spatial patterns formed by microbial populations, as revealed by recent studies in the laboratory. However, the matrices used, such as agarose pads, lack the structured geometry of many natural microbial habitats, including in the soil or on the surfaces of plants or animals. Here we address the important question of how such geometry may control diffusive exchanges and microbial interaction. We model mathematically mutualistic interactions within a minimal unit of structure: two growing reservoirs linked by a diffusive channel through which metabolites are exchanged. The model is applied to study a synthetic mutualism, experimentally parametrized on a model algal-bacterial co-culture. Analytical and numerical solutions of the model predict conditions for the successful establishment of remote mutualisms, and how this depends, often counterintuitively, on diffusion geometry. We connect our findings to understanding complex behavior in synthetic and naturally occurring microbial communities.Gates Cambridge Trust The Winton Foundation for the Physics of Sustainability The Royal Society The Schlumberger Chair Fun

Combining SIMS and mechanistic modelling to reveal nutrient kinetics in an algal-bacterial mutualism

Funder: Raymond and Beverly Sackler ScholarshipFunder: Mines ParisTechFunder: Swedish Museum of Natural HistoryFunder: University of IcelandFunder: Consortium of Danish geoscience institutionsMicrobial communities are of considerable significance for biogeochemical processes, for the health of both animals and plants, and for biotechnological purposes. A key feature of microbial interactions is the exchange of nutrients between cells. Isotope labelling followed by analysis with secondary ion mass spectrometry (SIMS) can identify nutrient fluxes and heterogeneity of substrate utilisation on a single cell level. Here we present a novel approach that combines SIMS experiments with mechanistic modelling to reveal otherwise inaccessible nutrient kinetics. The method is applied to study the onset of a synthetic mutualistic partnership between a vitamin B12-dependent mutant of the alga Chlamydomonas reinhardtii and the B12-producing, heterotrophic bacterium Mesorhizobium japonicum, which is supported by algal photosynthesis. Results suggest that an initial pool of fixed carbon delays the onset of mutualistic cross-feeding; significantly, our approach allows the first quantification of this expected delay. Our method is widely applicable to other microbial systems, and will contribute to furthering a mechanistic understanding of microbial interactions

Migration of chemotactic bacteria in soft agar: role of gel concentration

We study the migration of chemotactic wild-type Escherichia coli populations in semisolid (soft) agar in the concentration range C = 0.15-0.5% (w/v). For C < 0.35%, expanding bacterial colonies display characteristic chemotactic rings. At C = 0.35%, however, bacteria migrate as broad circular bands rather than sharp rings. These are growth/diffusion waves arising because of suppression of chemotaxis by the agar and have not been previously reported experimentally to our knowledge. For C = 0.4-0.5%, expanding colonies do not span the depth of the agar and develop pronounced front instabilities. The migration front speed is weakly dependent on agar concentration at C < 0.25%, but decreases sharply above this value. We discuss these observations in terms of an extended Keller-Segel model for which we derived novel transport parameter expressions accounting for perturbations of the chemotactic response by collisions with the agar. The model makes it possible to fit the observed front speed decay in the range C = 0.15-0.35%, and its solutions qualitatively reproduce the observed transition from chemotactic to growth/diffusion bands. We discuss the implications of our results for the study of bacteria in porous media and for the design of improved bacteriological chemotaxis assays.Comment: 28 pages, 5 figures. Published online at http://www.sciencedirect.com/science/article/pii/S000634951100721

Migration and accumulation of bacteria with chemotaxis and chemokinesis

Bacteria can chemotactically migrate up attractant gradients by controlling run-and-tumble motility patterns. In addition to this well-known chemotactic behaviour, several soil and marine bacterial species perform chemokinesis: they adjust their swimming speed according to the local concentration of chemoattractant, with higher speed at higher concentration. A field of attractant then induces a spatially varying swimming speed, which results in a drift towards lower attractant concentrations - contrary to the drift created by chemotaxis. Here, to explore the biological benefits of chemokinesis and investigate its impact on the chemotactic response, we extend a Keller-Segel-type model to include chemokinesis. We apply the model to predict the dynamics of bacterial populations capable of chemokinesis and chemotaxis in chemoattractant fields inspired by microfluidic and agar plate migration assays. We find that chemokinesis combined with chemotaxis not only enhances the population response with respect to pure chemotaxis, but also modifies it qualitatively. We conclude presenting predictions for bacteria around dynamic finite-size nutrient sources, simulating, e.g., a marine particle or a root. We show that chemokinesis can reduce the measuring bias that is created by a decaying attractant gradient.ISSN:1292-8941ISSN:1292-895