Emergent probability fluxes in confined microbial navigation

Preparation, maintenance and propagation of synchronous cultures of photoactive Chlamydomonas cells

The systematic cultivation of species of photosynthetically active 'green' microorganisms in research labs started in the 1940s. Among these microorganisms, Chlamydomonas represents a genus of green biciliated microalgae, of which Chlamydomonas reinhardtii has become the main describing species. For decades C. reinhardtii has been used as an established model organism in biology, including research areas such as molecular biology of eukaryotes, photosynthesis, light receptors, cell metabolism, the dynamics of microtubule assembly and protein transport along cilia. More recently, the use of suspensions of light-responsive living microorganisms has seen a major expansion from the life sciences to the biophysics, statistical physics, fluid dynamics and bioengineering communities. Studies that substantially advance the state of the art in these research areas require the reliable preparation and maintenance of viable, monodisperse and synchronous cell cultures. Although some technical aspects are shared with standard procedures in cell biology and microbiology, Chlamydomonas and its relatives are photosensitive and, simultaneously, motile, meaning this microorganism requires tailored cultivation protocols that are specific to this species. Here we provide guidance on which Chlamydomonas wild-type and mutant strains are suitable for specific experiments and provide detailed step-by-step procedures to measure culture synchronicity, growth rate of the population, average cell size and motility features. The reliable preparation of cell cultures may facilitate future interdisciplinary research using living suspensions of photoactive microorganisms.

Collective self-caging of active filaments in virtual confinement

Motility coupled to responsive behavior is essential for many microorganisms to seek and establish appropriate habitats. One of the simplest possible responses, reversing the direction of motion, is believed to enable filamentous cyanobacteria to form stable aggregates or accumulate in suitable light conditions. Here, we demonstrate that filamentous morphology in combination with responding to light gradients by reversals has consequences far beyond simple accumulation: Entangled aggregates form at the boundaries of illuminated regions, harnessing the boundary to establish local order. We explore how the light pattern, in particular its boundary curvature, impacts aggregation. A minimal mechanistic model of active flexible filaments resembles the experimental findings, thereby revealing the emergent and generic character of these structures. This phenomenon may enable elongated microorganisms to generate adaptive colony architectures in limited habitats or guide the assembly of biomimetic fibrous materials.

Stationary particle currents in sedimenting active matter wetting a wall

Recently it was predicted, on the basis of a lattice gas model, that scalar active matter in a gravitational field would rise against gravity up a confining wall or inside a thin capillary-in spite of repulsive particle-wall interactions [Phys. Rev. Lett. 124, 048001 (2020)0031-900710.1103/PhysRevLett.124.048001]. In this paper we confirm this prediction with sedimenting active Brownian particles (ABPs) in a box numerically and elucidate the mechanism leading to the formation of a meniscus rising above the bulk of the sedimentation region. The height of the meniscus increases with the activity of the system, algebraically with the Péclet number. The formation of the meniscus is determined by a stationary circular particle current, a vortex, centered at the base of the meniscus, whose size and strength increase with the ABP activity. The origin of these vortices can be traced back to the confinement of the ABPs in a box: already the stationary state of ideal (noninteracting) ABPs without gravitation displays circular currents that arrange in a highly symmetric way in the eight octants of the box. Gravitation distorts this vortex configuration downward, leaving two major vortices at the two side walls, with a strong downward flow along the walls. Repulsive interactions between the ABPs change this situation only as soon as motility induced phase separation (MIPS) sets in and forms a dense, sedimented liquid region at the bottom, which pushes the center of the vortex upwards towards the liquid-gas interface. Self-propelled particles therefore represent an impressive realization of scalar active matter that forms stationary particle currents being able to perform visible work against gravity or any other external field, which we predict to be observable experimentally in active colloids under gravitation.

Methods and Measures for Investigating Microscale Motility

Motility is an essential factor for an organism's survival and diversification. With the advent of novel single-cell technologies, analytical frameworks, and theoretical methods, we can begin to probe the complex lives of microscopic motile organisms and answer the intertwining biological and physical questions of how these diverse lifeforms navigate their surroundings. Herein, we summarize the main mechanisms of microscale motility and give an overview of different experimental, analytical, and mathematical methods used to study them across different scales encompassing the molecular-, individual-, to population-level. We identify transferable techniques, pressing challenges, and future directions in the field. This review can serve as a starting point for researchers who are interested in exploring and quantifying the movements of organisms in the microscale world.

Active Spaghetti: Collective Organization in Cyanobacteria

Filamentous cyanobacteria can show fascinating examples of nonequilibrium self-organization, which, however, are not well understood from a physical perspective. We investigate the motility and collective organization of colonies of these simple multicellular lifeforms. As their area density increases, linear chains of cells gliding on a substrate show a transition from an isotropic distribution to bundles of filaments arranged in a reticulate pattern. Based on our experimental observations of individual behavior and pairwise interactions, we introduce a nonreciprocal model accounting for the filaments' large aspect ratio, fluctuations in curvature, motility, and nematic interactions. This minimal model of active filaments recapitulates the observations, and rationalizes the appearance of a characteristic length scale in the system, based on the Péclet number of the cyanobacteria filaments.

Spatial Distribution of Flagellated Microalgae Chlamydomonas reinhardtii in a Quasi-Two-Dimensional Space

Although the phenomenon of collective order formation by cell-cell interactions in motile cells, microswimmers, has been a topic of interest, most studies have been conducted under conditions of high cell density, where the space occupancy of a cell population relative to the space size ϕ>0.1 (ϕ is the area fraction). We experimentally determined the spatial distribution (SD) of the flagellated unicellular green alga Chlamydomonas reinhardtii at a low cell density (ϕ≈0.01) in a quasi-two-dimensional (thickness equal to cell diameter) restricted space and used the variance-to-mean ratio to investigate the deviation from the random distribution of cells, that is, do cells tend to cluster together or avoid each other? The experimental SD is consistent with that obtained by Monte Carlo simulation, in which only the excluded volume effect (EV effect) due to the finite size of cells is taken into account, indicating that there is no interaction between cells other than the EV effect at a low cell density of ϕ≈0.01. A simple method for fabricating a quasi-two-dimensional space using shim rings was also proposed.

Light-regulated adsorption and desorption of Chlamydomonas cells at surfaces

Microbial colonization of surfaces represents the first step towards biofilm formation, which is a recurring phenomenon in nature with beneficial and detrimental implications in technological and medical settings. Consequently, there is interest in elucidating the fundamental aspects of the initial stages of biofilm formation of microorganisms on solid surfaces. While most of the research is oriented to understand bacterial surface colonization, the fundamental principles of surface colonization of motile, photosynthetic microbes remain largely unexplored so far. Recent single-cell studies showed that the flagellar adhesion of Chlamydomonas reinhardtii is switched on in blue light and switched off under red light [Kreis et al., Nat. Phys., 2018, 14, 45-49]. Here, we study this light-switchable surface association on the population level and measure the kinetics of adsorption and desorption of suspensions of motile C. reinhardtii cells on glass surfaces using bright-field optical microscopy. We observe that both processes exhibit a response lag relative to the time at which the blue- and red-light conditions are set and model this feature using time-delayed Langmuir-type kinetics. We find that cell adsorption occurs significantly faster than desorption, which we attribute to the protein-mediated molecular adhesion mechanism of the cells. Adsorption experiments using phototactically blind C. reinhardtii mutants demonstrate that phototaxis does not affect the cell adsorption kinetics. Hence, this framework can be used as an assay for characterizing the dynamics of the surface colonization of microbial species exhibiting light-regulated surface adhesion under precisely controlled environmental conditions.

Phenotyping single-cell motility in microfluidic confinement

The movement trajectories of organisms serve as dynamic read-outs of their behaviour and physiology. For microorganisms this can be difficult to resolve due to their small size and fast movement. Here, we devise a novel droplet microfluidics assay to encapsulate single micron-sized algae inside closed arenas, enabling ultralong high-speed tracking of the same cell. Comparing two model species - Chlamydomonas reinhardtii (freshwater, 2 cilia), and Pyramimonas octopus (marine, 8 cilia), we detail their highly-stereotyped yet contrasting swimming behaviours and environmental interactions. By measuring the rates and probabilities with which cells transition between a trio of motility states (smooth-forward swimming, quiescence, tumbling or excitable backward swimming), we reconstruct the control network that underlies this gait switching dynamics. A simplified model of cell-roaming in circular confinement reproduces the observed long-term behaviours and spatial fluxes, including novel boundary circulation behaviour. Finally, we establish an assay in which pairs of droplets are fused on demand, one containing a trapped cell with another containing a chemical that perturbs cellular excitability, to reveal how aneural microorganisms adapt their locomotor patterns in real-time.

A multi-adenylate cyclase regulator at the flagellar tip controls African trypanosome transmission

Signaling from ciliary microdomains controls developmental processes in metazoans. Trypanosome transmission requires development and migration in the tsetse vector alimentary tract. Flagellar cAMP signaling has been linked to parasite social motility (SoMo) in vitro, yet uncovering control of directed migration in fly organs is challenging. Here we show that the composition of an adenylate cyclase (AC) complex in the flagellar tip microdomain is essential for tsetse salivary gland (SG) colonization and SoMo. Cyclic AMP response protein 3 (CARP3) binds and regulates multiple AC isoforms. CARP3 tip localization depends on the cytoskeletal protein FLAM8. Re-localization of CARP3 away from the tip microdomain is sufficient to abolish SoMo and fly SG colonization. Since intrinsic development is normal in carp3 and flam8 knock-out parasites, AC complex-mediated tip signaling specifically controls parasite migration and thereby transmission. Participation of several developmentally regulated receptor-type AC isoforms may indicate the complexity of the in vivo signals perceived.

Trypanosomes can sense signal molecules and coordinate their movement in response to such signals, a phenomenon termed social motility (SoMo). Here, Bachmaier et al show that cyclic AMP response protein 3 (CARP3) localization to the flagellar tip and its interaction with a number of different adenylate cyclases is essential for migration to tsetse fly salivary glands and for SoMo, therewith linking SoMo and cAMP signaling to trypanosome transmission.

Confinement-induced accumulation and de-mixing of microscopic active-passive mixtures

Understanding the out-of-equilibrium properties of noisy microscale systems and the extent to which they can be modulated externally, is a crucial scientific and technological challenge. It holds the promise to unlock disruptive new technologies ranging from targeted delivery of chemicals within the body to directed assembly of new materials. Here we focus on how active matter can be harnessed to transport passive microscopic systems in a statistically predictable way. Using a minimal active-passive system of weakly Brownian particles and swimming microalgae, we show that spatial confinement leads to a complex non-monotonic steady-state distribution of colloids, with a pronounced peak at the boundary. The particles’ emergent active dynamics is well captured by a space-dependent Poisson process resulting from the space-dependent motion of the algae. Based on our findings, we then realise experimentally the de-mixing of the active-passive suspension, opening the way for manipulating colloidal objects via controlled activity fields.

Understanding how order emerges in active matter may facilitate macroscopic control of microscopic objects. Here, Williams et al. show how to control the transport of passive microscopic particles in presence of motile algae in conjunction with boundary-induced accumulation of microswimmers.

Spatial confinement toward creating artificial living systems

Lifeforms are regulated by many physicochemical factors, and these factors could be controlled to play a role in the construction of artificial living systems. Among these factors, spatial confinement is an important one, which mediates biological behaviors at multiscale levels and participates in the biomanufacturing processes accordingly. This review describes how spatial confinement, as a fundamental biological phenomenon, provides cues for the construction of artificial living systems. Current knowledge about the role of spatial confinement in mediating individual cell behavior, collective cellular behavior, and tissue-level behavior are categorized. Endeavors on the synthesis of biomacromolecules, artificial cells, engineered tissues, and organoids in spatially confined bioreactors are then emphasized. After that, we discuss the cutting-edge applications of spatially confined artificial living systems in biomedical fields. Finally, we conclude by assessing the remaining challenges and future trends in the context of fundamental science, technical improvement, and practical applications.

Controlling Collective Motion of Kinesin-Driven Microtubules via Patterning of Topographic Landscapes

Biomolecular motor proteins that generate forces by consuming chemical energy obtained from ATP hydrolysis play pivotal roles in organizing cytoskeletal structures in living cells. An ability to control cytoskeletal structures would benefit programmable protein patterning; however, our current knowledge is limited because of the underdevelopment of engineering approaches for controlling pattern formation. Here, we demonstrate the controlling of self-assembled patterns of microtubules (MTs) driven by kinesin motors by designing the boundary shape in fabricated microwells. By manipulating the collision angle of gliding MTs defined by the boundary shape, the self-assembly of MTs can be controlled to form protruding bundle and bridge patterns. Corroborated by the theory of self-propelled rods, we further show that the alignment of MTs determines the transition between the assembled patterns, providing a blueprint to reconstruct bridge structures in microchannels. Our findings introduce the tailoring of the self-organization of cytoskeletons and motor proteins for nanotechnological applications.

Emergent probability fluxes in confined microbial navigation

When the motion of a motile cell is observed closely, it appears erratic, and yet the combination of nonequilibrium forces and surfaces can produce striking examples of organization in microbial systems. While most of our current understanding is based on bulk systems or idealized geometries, it remains elusive how and at which length scale self-organization emerges in complex geometries. Here, using experiments and analytical and numerical calculations, we study the motion of motile cells under controlled microfluidic conditions and demonstrate that probability flux loops organize active motion, even at the level of a single cell exploring an isolated compartment of nontrivial geometry. By accounting for the interplay of activity and interfacial forces, we find that the boundary's curvature determines the nonequilibrium probability fluxes of the motion. We theoretically predict a universal relation between fluxes and global geometric properties that is directly confirmed by experiments. Our findings open the possibility to decipher the most probable trajectories of motile cells and may enable the design of geometries guiding their time-averaged motion.