Session A07: Biological Active Matter I: Microorganisms

Active nematics and topological defects in colonies of gliding bacteria

The developmental cycle of Myxococcus xanthus involves the coordination of many hundreds of thousands of cells aggregating to form mounds known as fruiting bodies. This aggregation process begins with the sequential formation of cell layers on top of each other. We study this layer formation process by observing the formation of holes and second layers within a base monolayer of M xanthus cells. We find that these new holes and layers form at topological defects where the cell orientation field is undefined, and is driven by the bacteria acting as an active nematic liquid crystal through cell motility and substrate friction. We also track all of the individual cells within the monolayer to study the connection between individual cell motion and mean field activity within the system.   

Mechanical stress fluctuations in Myxococcus xanthus monolayers revealed by traction force microscopy

During development, a population of Myxococcus xanthus cells transitions from a two-dimensional monolayer to three-dimensional fruiting bodies. The initial motion of cells into the third dimension occurs at special points in the monolayer where there is a topological defect in the cellular alignment field. To understand how these defects are related to three-dimensional motion, we need to observe both how cells move and the relevant mechanical forces. Using traction force microscopy, we map out the spatial distribution of forces exerted by M. xanthus cells on a soft hydrogel substrate and link the position of defects to the distribution of stresses. We reveal strong stress fluctuations within the system, which ultimately drive the initial stage of fruiting body development.   

Capillary attraction facilitates bacterial collective dynamics: Experiment

When placed on an agar gel, small groups of the soil-dwelling bacteria M. xanthus move, merge with other groups, and eventually coarsen into a single monolayer. Here, we use surface profilometry to quantify the water meniscus that wets surface-attached cells, and show that the capillary attraction mediated by these menisci shapes the structure and dynamics of M. xanthus group motility. We construct a device that allows us to systematically vary the meniscus length of wetted cells and use time-lapse microscopy to quantify how changes in cell-cell capillary attraction effect both the mobility, shape, and lifetime of cell groups. We further show how such changes in the behavior of small groups manifest themselves in the eventual coarsening behavior of the population. Together with a computational model, our results, establish a basic mechanism for how environmental fluctuations in soil hydration may affect the collective behaviors of natural populations of M. xanthus.   

Capillary attraction facilitates bacterial collective dynamics: Theory

Myxococcus xanthus is a bacterium that lives in soil which often traps and stores water, and where capillary forces can be substantial. Key to the life cycle of M. xanthus cells is the formation of collective groups: they feed on prey in swarms and aggregate upon starvation. In the latter case, small motile groups of cells coarsen into large cell monolayers, ultimately forming three-dimensional aggregates called fruiting bodies. However, the physical mechanisms that drive the early coarsening process remain unclear. Here, we developed a computational model to study the role of capillary forces in this process. Our results demonstrate that water menisci forming around M. xanthus cells mediate a strong attraction between cells. Such capillary attraction, combined with cell motility, results in a variety of phases of collective motion, including “streams” and “diffusing droplets.” In agreement with experiment, our results show that capillary attraction facilitates mergers of cell groups and hinders their splitting, hence influencing large-scale coarsening dynamics.   

A mechanism for migrating bacterial populations to non-genetically adapt to new environments

Populations of bacteria can rapidly expand into new territory by consuming and chasing an attractant cue in the environment, but the consequences of non-genetic diversity for this process are unknown. Through theory and simulations, we predict that expanding populations non-genetically adapt their phenotype compositions to migrate effectively through multiple physical environments. Swimming phenotypes in the migrating group are spatially sorted by their chemotactic performance, but the mapping from phenotype to performance depends on the environment. Therefore, phenotypes that perform poorly localize to the back of the group and selectively fall behind. Thus, the group composition dynamically enriches for high performers, enhancing migration speed and overall growth. Furthermore, non-genetic inheritance controls a trade-off between large composition shifts and slow responsiveness to new environments. These results demonstrate that phenotypic diversity and collective behavior can synergize to produce emergent functionalities. Furthermore, non-genetic inheritance may generically enable bacterial populations to transiently adapt without mutations, emphasizing that genotype-to-phenotype mappings are context-dependent.   

Roughening instability of growing three-dimensional bacterial colonies in complex environments

How do growing bacterial colonies get their shape? While this process of morphogenesis is well-studied in 2D, many bacterial colonies thrive in 3D environments, such as gels and tissues in the body, or soils, sediments, and subsurface media. Here, we describe a morphological instability exhibited by large dense colonies of bacteria growing in 3D. Using experiments in transparent 3D media, we show that colonies of Escherichia coli and Vibrio cholerae generically roughen as they consume nutrients and grow, eventually forming branched, finger-like patterns. This behavior reflects a key difference between 2D and 3D colonies: while 2D colonies may access the nutrients needed for growth from the third dimension, the 3D colonies inevitably become nutrient-limited in their interior, driving a transition to rough, branched growth at the periphery of the colony. We elucidate this behavior using linear stability analysis and numerical simulations of a continuum active fluid model. We find that when the dimensions of the growing colony substantially exceed the nutrient penetration length, nutrient depletion drives a transition to roughening.   

Topological traps control material flux in self-organizing active filament spirals

Biological active systems regularly construct robust yet dynamic self-organizing structures where individual building blocks can flow in and out while the architecture remains stable over long time scales. Utilizing a novel active matter system of filamentous cyanobacteria spread on two-dimensional agar, we explore the role of topology in controlling material flux in self-organizing systems. We discover a persistent emergent architecture - active spirals - formed by the collective motility of long filaments, with each filament being a chain of up to thousands of bacterial cells that move cooperatively as a single filament. These spiral objects, once formed, remain stable and persist over long times. Within a spiral, wound filaments move in either clockwise or counterclockwise directions, and can reverse direction spontaneously. Through directional reversals and adhesion forces, filaments are able to interweave and exchange order. Using individual filament tracking, we describe the rich material flux within an active spiral and find discrete topological rules of filament interactions that encode these dynamics. We further discover the existence of a "topological trap" formed purely from the geometric chirality of neighboring wound filaments which creates a material flux boundary. Through analogy between filament tips and dislocations on a periodic polar lattice, we devise a simulation framework for an active spiral. In-silico, we demonstrate optimal strategies for how reversal dynamics control material exchange, which may shed light on the physiological role of this dynamical behavior in bacteria.   

Active Decentralized Transport in Biological Networks

Supply networks are essential for transport in living systems, such as blood flow and fungal mycelia, or in human made systems, such as power grids and sewage systems. Many transport systems use centrally controlled pumps to disperse their resources. In contrast, we study the slime mold Physarum polycephalum, which employs a decentralized strategy to disperse nutrients, transport mass, and propagate signals across its networked body. The decentralized strategy is driven by a network of elastic tubes that rhythmically contract and expand to shuttle cytoplasmic flow. While this mechanism has been studied for single tubes, no full network study has been conducted. In this work, we combine experimental data from real Physarum networks with simulations of the active mechanism that drives flow. We find that the model predicts excitation of contractile modes that span the entire network in agreement with our data. Beyond the understanding of Physarum, our results could be used to design other decentralized transport infrastructures.   

Collective Dynamics of Active Filaments

Gliding filamentous cyanobacteria provide an experimental realization of long, flexible, and self-propelled polymers on surfaces.  In addition, their motion is influenced by direction reversal and responses to light, different from previous studies of active polymers. 

To study the patterns formed by these active polymers, we combine simulations and experiments of cyanobacteria in quasi-2D confinement. We explore the patterns they form by tuning the key physical parameters such as the bending stiffness, activity, and reversal rate at low density of filaments. The simulations demonstrate the existence of various patterns including spirals and clusters displaying collective motion, in agreement with our experimental observations. Stochastic reversals tend to suppress both types of patterns.

At high densities of the filaments, our simulation shows dense swarms of filaments with both polar and nematic order. The long-range nematic and polar order are also confirmed by the experiments. Analysis of the dynamics and mechanics of individual filaments (propulsion, bending, buckling)  allows to fully parameterize the simulations for a quantitative comparison of the patterns.   

Microphase Separation in Scalar Active Matter

Continuous consumption of energy in systems of active particles generate novel collective behaviours and structures that are generically not observed in systems at thermal equilibrium. Motile active matter has been studied extensively, however non-motile (and so truly scalar in a sense) minimal models of active matter are crucially lacking in the literature and present a wide range of non-equilibrium collective phenomena.

We present a microscopic model inspired by the bacteria Neisseria Meningitidis in which diffusive agents feel intermittent attractive forces determined by an internal variable that switches stochastically. We solve the microscopic equations numerically to study the emergence of phase separation and demixing in the system. Through a formal coarse-graining procedure, we then derive an evolution equation for the particle density and show that our model pertains to the Active Model B+ class, confirming the presence of microphase separation by solving the kinetic equations numerically. We conclude on good agreement between the known results on the field theory and the current system. 

This is the first truly scalar model of active matter whose dynamics have been coarse-grained to produce both time-reversal-symmetry breaking terms predicted by this field theory.    

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Microalgae involve complex chemical reactions both for photosynthesis and internal metabolism. It is attractive while challenging to comprehensively understand the orchestration of these processes which act as the building blocks to construct the living systems. Here in our study, taking Chlorella Vulgaris as an example, we observed the “active color noises” produced by microalgae due to the external photoactivation which then affects their dynamical behaviors correspondingly. By tracing these “active color noises”, we may shade light into the cells which help us further understand the complex behaviors of living materials.   

Bioluminescent Breaking Waves

Bioluminescence (light generation in living organisms) is a phenomenon first documented thousands of years ago. Its many independent evolutionary pathways are reflected in the huge variety of attack or defence mechanisms of bioluminescent marine organisms. Intriguingly, a large group of organisms react towards mechanical stimulation with bioluminescent flashes. Among those are dinoflagellates: single-celled microorganisms that generate light via a complex mechano-sensing process (Jalaal et al. PRL 125 (2), 028102, 2020).  

Here, we go beyond single-cell analysis and present a lab-scale model of bioluminescent breaking waves. We conduct lock-release wave chamber experiments with cell-laden water. The turbulent gravity current impacts a solid wall, and consequently, a breaking wave forms. We perform the experiments at various conditions and record the light production. To explain the experimental results, we provide the counterpart theory and direct numerical simulations.      

Trajectory analysis of single microswimmer behaviour

Movement trajectories can be an informative measure of the behaviour and physiology of biological active matter at all scales. Even single cells can display complex motility patterns in order to navigate their surroundings and respond to environmental cues. Recent advances in tracking and analysis frameworks enable behavioural characteristics to be revealed from microscopy data. Here, we combine droplet microfluidics, high-speed imaging and computational analysis to achieve unprecedented long-term monitoring of individual cells of two algal species that display highly distinct behavioural signatures (namely the ‘run-and-tumble' like motility of the freshwater biflagellate Chlamydomonas reinhardtii and the ‘run-stop-shock' motion of the marine octoflagellate Pyramimonas octopus). We study the distributions of single-cell swimming speed, motility state transitions, and perform probability flux analysis to reveal the emergence of steady-state flux cycles in confined microswimmers. We propose novel motility measures to deduce how swimming behaviour changes and adapts in response to increasing physical confinement, light stimulation and sudden chemical perturbations. Our results emphasize the need for recording long-time statistics and trajectories for revealing non-equilibrium and non-stationary features in organismal behaviour.