Effect of Cell Aspect Ratio on Swarming Bacteria

Immobility of isolated swarmer cells due to local liquid depletion

Bacterial swarming is a complex phenomenon in which thousands of self-propelled rod-shaped cells move coherently on surfaces, providing an excellent example of active matter. However, bacterial swarming is different from most studied examples of active systems because single isolated cells do not move, while clusters do. The biophysical aspects underlying this behavior are unclear. In this work we explore the case of low local cell densities, where single cells become temporarily immobile. We show that immobility is related to local depletion of liquid. In addition, it is also associated with the state of the flagella. Specifically, the flagellar bundles at (temporarily) liquid depleted regions are completely spread-out. Our results suggest that dry models of self-propelled agents, which only consider steric alignments and neglect hydrodynamic effects, are oversimplified and are not sufficient to describe swarming bacteria.

Anomalous diffusion of active Brownian particles in responsive elastic gels: Nonergodicity, non-Gaussianity, and distributions of trapping times

Understanding actual transport mechanisms of self-propelled particles (SPPs) in complex elastic gels-such as in the cell cytoplasm, in in vitro networks of chromatin or of F-actin fibers, or in mucus gels-has far-reaching consequences. Implications beyond biology/biophysics are in engineering and medicine, with a particular focus on microrheology and on targeted drug delivery. Here, we examine via extensive computer simulations the dynamics of SPPs in deformable gellike structures responsive to thermal fluctuations. We treat tracer particles comparable to and larger than the mesh size of the gel. We observe distinct trapping events of active tracers at relatively short times, leading to subdiffusion; it is followed by an escape from meshwork-induced traps due to the flexibility of the network, resulting in superdiffusion. We thus find crossovers between different transport regimes. We also find pronounced nonergodicity in the dynamics of SPPs and non-Gaussianity at intermediate times. The distributions of trapping times of the tracers escaping from "cages" in our quasiperiodic gel often reveal the existence of two distinct timescales in the dynamics. At high activity of the tracers these timescales become comparable. Furthermore, we find that the mean waiting time exhibits a power-law dependence on the activity of SPPs (in terms of their Péclet number). Our results additionally showcase both exponential and nonexponential trapping events at high activities. Extensions of this setup are possible, with the factors such as anisotropy of the particles, different topologies of the gel network, and various interactions between the particles (also of a nonlocal nature) to be considered.

Diverse morphology and motility induced emergent order in bacterial collectives

Microbial communities exhibit complex behaviors driven by species interactions and individual characteristics. In this study, we delve into the dynamics of a mixed bacterial population comprising two distinct species with different morphology and motility aspects. Employing agent-based modeling and computer simulations, we analyze the impacts of size ratios and packing fractions on dispersal patterns, aggregate formation, clustering, and spatial ordering. Notably, we find that motility and anisotropy of elongated bacteria significantly influence the distribution and spatial organization of nonmotile spherical species. Passive spherical cells display a superdiffusive behavior, particularly at larger size ratios in the ballistic regime. As the size ratio increases, clustering of passive cells is observed, accompanied by enhanced alignment and closer packing of active cells in the presence of higher passive cell area fractions. In addition, we identify the pivotal role of passive cell area fraction in influencing the response of active cells toward nematicity, with its dependence on size ratio. These findings shed light on the significance of morphology and motility in shaping the collective behavior of microbial communities, providing valuable insights into complex microbial behaviors with implications for ecology, biotechnology, and bioengineering.

Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment

Collective alignment of cell populations is a commonly observed phenomena in biology. An important example are aligning fibroblasts in healthy or scar tissue. In this work we derive and simulate a mechanistic agent-based model of the collective behaviour of actively moving and interacting cells, with a focus on understanding collective alignment. The derivation strategy is based on energy minimisation. The model ingredients are motivated by data on the behaviour of different populations of aligning fibroblasts and include: Self-propulsion, overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces. We find that there is an optimal ratio of self-propulsion speed and overlap avoidance that maximises collective alignment. Further we find that deformability aids alignment, and that cell-cell junctions by themselves hinder alignment. However, if cytoskeletal forces are transmitted via cell-cell junctions we observe strong collective alignment over large spatial scales.

Nonequilibrium hyperuniform states in active turbulence

We demonstrate that the complex spatiotemporal structure in active fluids can feature characteristics of hyperuniformity. Using a hydrodynamic model, we show that the transition from hyperuniformity to nonhyperuniformity and antihyperuniformity depends on the strength of active forcing and can be related to features of active turbulence without and with scaling characteristics of inertial turbulence. Combined with identified signatures of Levy walks and nonuniversal diffusion in these systems, this allows for a biological interpretation and the speculation of nonequilibrium hyperuniform states in active fluids as optimal states with respect to robustness and strategies of evasion and foraging.

Topological defects in multi-layered swarming bacteria

Topological defects, which are singular points in a director field, play a major role in shaping active systems. Here, we experimentally study topological defects and the flow patterns around them, that are formed during the highly rapid dynamics of swarming bacteria. The results are compared to the predictions of two-dimensional active nematics. We show that, even though some of the assumptions underlying the theory do not hold, the swarm dynamics is in agreement with two-dimensional nematic theory. In particular, we look into the multi-layered structure of the swarm, which is an important feature of real, natural colonies, and find a strong coupling between layers. Our results suggest that the defect-charge density is hyperuniform, i.e., that long range density-fluctuations are suppressed.

Anisotropic Diffusion of Elongated Particles in Active Coherent Flows

The study of particle diffusion, a classical conundrum in scientific inquiry, holds manifold implications for various real-world applications. Particularly within the domain of active flows, where the motion of self-propelled particles instigates fluid movement, extensive research has been dedicated to unraveling the dynamics of passive spherical particles. This scrutiny has unearthed intriguing phenomena, such as superdiffusion at brief temporal scales and conventional diffusion at longer intervals. In contrast to the spherical counterparts, anisotropic particles, which manifest directional variations, are prevalent in nature. Although anisotropic behavior in passive fluids has been subject to exploration, enigmatic aspects persist in comprehending the interplay of anisotropic particles within active flows. This research delves into the intricacies of anisotropic passive particle diffusion, exposing a notable escalation in translational and rotational diffusion coefficients, as well as the superdiffusion index, contingent upon bacterial concentration. Through a detailed examination of particle coordinates, the directional preference of particle diffusion is not solely dependent on the particle length, but rather determined by the ratio of the particle length to the associated length scale of the background flow field. These revelations accentuate the paramount importance of unraveling the nuances of anisotropic particle diffusion within the context of active flows. Such insights not only contribute to the fundamental understanding of particle dynamics, but also have potential implications for a spectrum of applications.

Interplay of cell motility and self-secreted extracellular polymeric substance induced depletion effects on spatial patterning in a growing microbial colony

Reproducing bacteria self-organize to develop patterned biofilms in various conditions. Various factors contribute to the shaping of a multicellular bacterial organization. Here we investigate how motility force and self-secreted extracellular polymeric substances (EPS) influence bacterial cell aggregation, leading to phase-separated colonies using a particle-based/individual-based model. Our findings highlight the critical role of the interplay between motility force and depletion effects in regulating phase separation within a growing colony under far-from-equilibrium conditions. We observe that increased motility force hinders depletion-induced cell aggregation and phase segregation, necessitating a higher depletion effect for highly motile bacteria to undergo phase separation within a growing biofilm. We present a phase diagram illustrating the systematic variation of motility force and repulsive mechanical force, shedding light on the combined contributions of these two factors: self-propulsive motion and aggregation due to the depletion effect, resulting in the presence of small to large bacterial aggregates. Furthermore, our study reveals the dynamic nature of clustering, marked by changes in cluster size over time. Additionally, our findings suggest that differential dispersion among the components can lead to the localization of EPS at the periphery of a growing colony. Our study enhances the understanding of the collective dynamics of motile bacterial cells within a growing colony, particularly in the presence of a self-secreted polymer-driven depletion effect.

A mechanistic understanding of microcolony morphogenesis: coexistence of mobile and sessile aggregates

Most bacteria in the natural environment self-organize into collective phases such as cell clusters, swarms, patterned colonies, or biofilms. Several intrinsic and extrinsic factors, such as growth, motion, and physicochemical interactions, govern the occurrence of different phases and their coexistence. Hence, predicting the conditions under which a collective phase emerges due to individual-level interactions is crucial. Here we develop a particle-based biophysical model of bacterial cells and self-secreted extracellular polymeric substances (EPS) to decipher the interplay of growth, motility-mediated dispersal, and mechanical interactions during microcolony morphogenesis. We show that the microcolony dynamics and architecture significantly vary depending upon the heterogeneous EPS production. In particular, microcolony shows the coexistence of both motile and sessile aggregates rendering a transition towards biofilm formation. We identified that the interplay of differential dispersion and the mechanical interactions among the components of the colony determines the fate of the colony morphology. Our results provide a significant understanding of the mechano-self-regulation during biofilm morphogenesis and open up possibilities of designing experiments to test the predictions.

Efflux-linked accelerated evolution of antibiotic resistance at a population edge

Efflux is a common mechanism of resistance to antibiotics. We show that efflux itself promotes accumulation of antibiotic-resistance mutations (ARMs). This phenomenon was initially discovered in a bacterial swarm where the linked phenotypes of high efflux and high mutation frequencies spatially segregated to the edge, driven there by motility. We have uncovered and validated a global regulatory network connecting high efflux to downregulation of specific DNA-repair pathways even in non-swarming states. The efflux-DNA repair link was corroborated in a clinical "resistome" database: genomes with mutations that increase efflux exhibit a significant increase in ARMs. Accordingly, efflux inhibitors decreased evolvability to antibiotic resistance. Swarms also revealed how bacterial populations serve as a reservoir of ARMs even in the absence of antibiotic selection pressure. High efflux at the edge births mutants that, despite compromised fitness, survive there because of reduced competition. This finding is relevant to biofilms where efflux activity is high.

Swarming behavior of a novel strain of Brevibacillus thermoruber

Brevibacillus thermoruber strain Nabari was isolated from compost and identified based on 16 S rRNA gene sequencing and DNA-DNA hybridization using B. thermoruber DSM 7064 ^T as the standard, despite some differences in their physiological and structural characteristics. When B. thermoruber Nabari was cultivated on various solid media containing 1.5% agar at 60°C, it rapidly propagated over the entire plate. In particular, on R2A-agar medium, it formed fine dendritic colonies. Macroscopic and microscopic observations of peripheral regions of the colonies indicated that the dendritic patterns were formed by bacterial swarming of some of the cells; large flows of bacterial cell populations were observed in the peripheral regions of the dendritic colonies. The cells were highly flagellated, but no extreme elongation of cells was observed. When B. thermoruber Nabari cells were cultivated at 37°C on R2A-agar plates, most colonies were nonmotile, but some colonies were motile. For example, a wandering colony moved on the plate and split into two, and then they collided to become one again. Additionally, a simple incubation system was devised to record the movement of colonies at high temperatures in this study while protecting the cameras from thermal damage.

Mixed-species bacterial swarms show an interplay of mixing and segregation across scales

Bacterial swarms are a highly-researched example of natural active matter. In particular, the interplay between biological interactions and the physics underlying the swarming dynamics is of both biological and physical interest. In this paper, we study mixed swarms of Bacillus subtilis and Pseudomonas aeruginosa. We find intricate interactions between the species, showing both cooperation and segregation across different spatial and temporal scales. On one hand, even though axenic colonies grow on disparate time scale, an order of magnitude apart, the two-species swarm together, forming a single, combined colony. However, the rapidly moving populations are locally segregated, with different characteristic speeds and lengths (or cluster sizes) that depend on the ratio between the species. Comparison with controlled mutant strains suggest that both the physical and known biological differences in species characteristics may not be enough to explain the segregation between the species in the mixed swarm. We hypothesize that the heterogeneous spatial distribution is due to some mechanism that enables bacteria to recognize their own kind, whose precise origin we could not identify.

Antibiotic Resistance via Bacterial Cell Shape-Shifting

Bacteria have evolved to develop multiple strategies for antibiotic resistance by effectively reducing intracellular antibiotic concentrations or antibiotic binding affinities, but the role of cell morphology in antibiotic resistance remains poorly understood. By analyzing cell morphological data for different bacterial species under antibiotic stress, we find that bacteria increase or decrease the cell surface-to-volume ratio depending on the antibiotic target. Using quantitative modeling, we show that by reducing the surface-to-volume ratio, bacteria can effectively reduce the intracellular antibiotic concentration by decreasing antibiotic influx. The model further predicts that bacteria can increase the surface-to-volume ratio to induce the dilution of membrane-targeting antibiotics, in agreement with experimental data. Using a whole-cell model for the regulation of cell shape and growth by antibiotics, we predict shape transformations that bacteria can utilize to increase their fitness in the presence of antibiotics. We conclude by discussing additional pathways for antibiotic resistance that may act in synergy with shape-induced resistance.

Physical characteristics of mixed-species swarming colonies

In nature, bacterial collectives typically consist of multiple species, which are interacting both biochemically and physically. Nonetheless, past studies on the physical properties of swarming bacteria were focused on axenic (single-species) populations. In bacterial swarming, intricate interactions between the individuals lead to clusters, rapid jets, and vortices that depend on cell characteristics such as speed and length. In this work, we show the first results of rapidly swarming mixed-species populations of Bacillus subtilis and Serratia marcescens, two model swarm species that are known to swarm well in axenic situations. In mixed liquid cultures, both species have higher reproduction rates. We show that the mixed population swarms together well and that the fraction between the species determines all dynamical scales-from the microscopic (e.g., speed distribution), mesoscopic (vortex size), and macroscopic (colony structure and size). Understanding mixed-species swarms is essential for a comprehensive understanding of the bacterial swarming phenomenon and its biological and evolutionary implications.

Surveying a Swarm: Experimental Techniques to Establish and Examine Bacterial Collective Motion

The survival and successful spread of many bacterial species hinges on their mode of motility. One of the most distinct of these is swarming, a collective form of motility where a dense consortium of bacteria employ flagella to propel themselves across a solid surface. Surface environments pose unique challenges, derived from higher surface friction/tension and insufficient hydration. Bacteria have adapted by deploying an array of mechanisms to overcome these challenges. Beyond allowing bacteria to colonize new terrain in the absence of bulk liquid, swarming also bestows faster speeds and enhanced antibiotic resistance to the collective. These crucial attributes contribute to the dissemination, and in some cases pathogenicity, of an array of bacteria. This mini-review highlights; 1) aspects of swarming motility that differentiates it from other methods of bacterial locomotion. 2) Facilitatory mechanisms deployed by diverse bacteria to overcome different surface challenges. 3) The (often difficult) approaches required to cultivate genuine swarmers. 4) The methods available to observe and assess the various facets of this collective motion, as well as the features exhibited by the population as a whole.

Multiple functions of flagellar motility and chemotaxis in bacterial physiology

Most swimming bacteria are capable of following gradients of nutrients, signaling molecules and other environmental factors that affect bacterial physiology. This tactic behavior became one of the most-studied model systems for signal transduction and quantitative biology, and underlying molecular mechanisms are well characterized in Escherichia coli and several other model bacteria. In this review, we focus primarily on less understood aspect of bacterial chemotaxis, namely its physiological relevance for individual bacterial cells and for bacterial populations. As evident from multiple recent studies, even for the same bacterial species flagellar motility and chemotaxis might serve multiple roles, depending on the physiological and environmental conditions. Among these, finding sources of nutrients and more generally locating niches that are optimal for growth appear to be one of the major functions of bacterial chemotaxis, which could explain many chemoeffector preferences as well as flagellar gene regulation. Chemotaxis might also generally enhance efficiency of environmental colonization by motile bacteria, which involves intricate interplay between individual and collective behaviors and trade-offs between growth and motility. Finally, motility and chemotaxis play multiple roles in collective behaviors of bacteria including swarming, biofilm formation and autoaggregation, as well as in their interactions with animal and plant hosts.

Bacterial motility: machinery and mechanisms

Bacteria have developed a large array of motility mechanisms to exploit available resources and environments. These mechanisms can be broadly classified into swimming in aqueous media and movement over solid surfaces. Swimming motility involves either the rotation of rigid helical filaments through the external medium or gyration of the cell body in response to the rotation of internal filaments. On surfaces, bacteria swarm collectively in a thin layer of fluid powered by the rotation of rigid helical filaments, they twitch by assembling and disassembling type IV pili, they glide by driving adhesins along tracks fixed to the cell surface and, finally, non-motile cells slide over surfaces in response to outward forces due to colony growth. Recent technological advances, especially in cryo-electron microscopy, have greatly improved our knowledge of the molecular machinery that powers the various forms of bacterial motility. In this Review, we describe the current understanding of the physical and molecular mechanisms that allow bacteria to move around.

Mechanistic underpinning of cell aspect ratio-dependent emergent collective motions in swarming bacteria

Self-propelled bacteria can exhibit a large variety of non-equilibrium self-organized phenomena. Swarming is one such fascinating dynamical scenario where a number of motile individuals group into dynamical clusters and move in synchronized flows and vortices. While precedent investigations into rod-like particles confirm that an increased aspect-ratio promotes alignment and order, recent experimental studies in bacteria Bacillus subtilis show a non-monotonic dependence of the cell-aspect ratio on their swarming motion. Here, by computer simulations of an agent-based model of self-propelled, mechanically interacting, rod-shaped bacteria under overdamped conditions, we explore the collective dynamics of a bacterial swarm subjected to a variety of cell-aspect ratios. When modeled with an identical self-propulsion speed across a diverse range of cell aspect ratios, simulations demonstrate that both shorter and longer bacteria exhibit slow dynamics whereas the fastest speed is obtained at an intermediate aspect ratio. Our investigation highlights that the origin of this observed non-monotonic trend of bacterial speed and vorticity with the cell-aspect ratio is rooted in the cell-size dependence of motility force. The swarming features remain robust for a wide range of surface density of the cells, whereas asymmetry in friction attributes a distinct effect. Our analysis identifies that at an intermediate aspect ratio, an optimum cell size and motility force promote alignment, which reinforces the mechanical interactions among neighboring cells leading to the overall fastest motion. Mechanistic underpinning of the collective motions reveals that it is a joint venture of the short-range repulsive and the size-dependent motility forces, which determines the characteristics of swarming.

Heterogeneous bacterial swarms with mixed lengths

Heterogeneous systems of active matter exhibit a range of complex emergent dynamical patterns. In particular, it is difficult to predict the properties of the mixed system based on its constituents. These considerations are particularly significant for understanding realistic bacterial swarms, which typically develop heterogeneities even when grown from a single cell. Here, mixed swarms of cells with different aspect ratios are studied both experimentally and in simulations. In contrast with previous theory, there is no macroscopic phase segregation. However, locally, long cells act as nucleation cites, around which aggregates of short, rapidly moving cells can form, resulting in enhanced swarming speeds. On the other hand, high fractions of long cells form a bottleneck for efficient swarming. Our results suggest a physical advantage for the spontaneous heterogeneity of bacterial swarm populations.

Bacterial surface motility is modulated by colony-scale flow and granular jamming

Microbes routinely face the challenge of acquiring territory and resources on wet surfaces. Cells move in large groups inside thin, surface-bound water layers, often achieving speeds of 30 µm s^-1 within this environment, where viscous forces dominate over inertial forces (low Reynolds number). The canonical Gram-positive bacterium Bacillus subtilis is a model organism for the study of collective migration over surfaces with groups exhibiting motility on length-scales three orders of magnitude larger than themselves within a few doubling times. Genetic and chemical studies clearly show that the secretion of endogenous surfactants and availability of free surface water are required for this fast group motility. Here, we show that: (i) water availability is a sensitive control parameter modulating an abiotic jamming-like transition that determines whether the group remains fluidized and therefore collectively motile, (ii) groups self-organize into discrete layers as they travel, (iii) group motility does not require proliferation, rather groups are pulled from the front, and (iv) flow within expanding groups is capable of moving material from the parent colony into the expanding tip of a cellular dendrite with implications for expansion into regions of varying nutrient content. Together, these findings illuminate the physical structure of surface-motile groups and demonstrate that physical properties, like cellular packing fraction and flow, regulate motion from the scale of individual cells up to length scales of centimetres.

Chemotactic behaviour of Escherichia coli at high cell density

At high cell density, swimming bacteria exhibit collective motility patterns, self-organized through physical interactions of a however still debated nature. Although high-density behaviours are frequent in natural situations, it remained unknown how collective motion affects chemotaxis, the main physiological function of motility, which enables bacteria to follow environmental gradients in their habitats. Here, we systematically investigate this question in the model organism Escherichia coli, varying cell density, cell length, and suspension confinement. The characteristics of the collective motion indicate that hydrodynamic interactions between swimmers made the primary contribution to its emergence. We observe that the chemotactic drift is moderately enhanced at intermediate cell densities, peaks, and is then strongly suppressed at higher densities. Numerical simulations reveal that this suppression occurs because the collective motion disturbs the choreography necessary for chemotactic sensing. We suggest that this physical hindrance imposes a fundamental constraint on high-density behaviours of motile bacteria, including swarming and the formation of multicellular aggregates and biofilms.

Single Cells Exhibit Differing Behavioral Phases during Early Stages of Pseudomonas aeruginosa Swarming

Pseudomonas aeruginosa is among the many bacteria that swarm, where groups of cells coordinate to move over surfaces. It has been challenging to determine the behavior of single cells within these high-cell-density swarms. To track individual cells within P. aeruginosa swarms, we imaged a fluorescently labeled subset of the larger population. Single cells at the advancing swarm edge varied in their motility dynamics as a function of time. From these data, we delineated four phases of early swarming prior to the formation of the tendril fractals characteristic of P. aeruginosa swarming by collectively considering both micro- and macroscale data. We determined that the period of greatest single-cell motility does not coincide with the period of greatest collective swarm expansion. We also noted that flagellar, rhamnolipid, and type IV pilus motility mutants exhibit substantially less single-cell motility than the wild type.IMPORTANCE Numerous bacteria exhibit coordinated swarming motion over surfaces. It is often challenging to assess the behavior of single cells within swarming communities due to the limitations of identifying, tracking, and analyzing the traits of swarming cells over time. Here, we show that the behavior of Pseudomonas aeruginosa swarming cells can vary substantially in the earliest phases of swarming. This is important to establish that dynamic behaviors should not be assumed to be constant over long periods when predicting and simulating the actions of swarming bacteria.

Surface-to-volume scaling and aspect ratio preservation in rod-shaped bacteria

Rod-shaped bacterial cells can readily adapt their lengths and widths in response to environmental changes. While many recent studies have focused on the mechanisms underlying bacterial cell size control, it remains largely unknown how the coupling between cell length and width results in robust control of rod-like bacterial shapes. In this study we uncover a conserved surface-to-volume scaling relation in Escherichia coli and other rod-shaped bacteria, resulting from the preservation of cell aspect ratio. To explain the mechanistic origin of aspect-ratio control, we propose a quantitative model for the coupling between bacterial cell elongation and the accumulation of an essential division protein, FtsZ. This model reveals a mechanism for why bacterial aspect ratio is independent of cell size and growth conditions, and predicts cell morphological changes in response to nutrient perturbations, antibiotics, MreB or FtsZ depletion, in quantitative agreement with experimental data.

Cell Shape and Population Migration Are Distinct Steps of Proteus mirabilis Swarming That Are Decoupled on High-Percentage Agar

Swarming on rigid surfaces requires movement of cells as individuals and as a group of cells. For the bacterium Proteus mirabilis, an individual cell can respond to a rigid surface by elongating and migrating over micrometer-scale distances. Cells can form groups of transiently aligned cells, and the collective population is capable of migrating over centimeter-scale distances. To address how P. mirabilis populations swarm on rigid surfaces, we asked whether cell elongation and single-cell motility are coupled to population migration. We first measured the relationship between agar concentration (a proxy for surface rigidity), single-cell phenotypes, and swarm colony phenotypes. We find that cell elongation and single-cell motility are coupled with population migration on low-percentage hard agar (1% to 2.5%) and become decoupled on high-percentage hard agar (>2.5%). Next, we evaluate how disruptions in lipopolysaccharide (LPS), specifically the O-antigen components, affect responses to hard agar. We find that LPS is not essential for elongation and motility of individual cells, as predicted, and instead functions to broaden the range of agar concentrations on which cell elongation and motility are coupled with population migration. These findings demonstrate that cell elongation and motility are coupled with population migration under a permissive range of surface conditions; increasing agar concentration is sufficient to decouple these behaviors. Since swarm colonies cover greater distances when these steps are coupled than when they are not, these findings suggest that collective interactions among P. mirabilis cells might be emerging as a colony expands outwards on rigid surfaces.IMPORTANCE How surfaces influence cell size, cell-cell interactions, and population migration for robust swarmers like P. mirabilis is not fully understood. Here, we have elucidated how cells change length along a spectrum of sizes that positively correlates with increases in agar concentration, regardless of population migration. Single-cell phenotypes can be decoupled from collective population migration simply by increasing agar concentration. A cell's lipopolysaccharides function to broaden the range of agar conditions under which cell elongation and single-cell motility remain coupled with population migration. In eukaryotes, the physical environment, such as a surface matrix, can impact cell development, shape, and migration. These findings support the idea that rigid surfaces similarly act on swarming bacteria to impact cell shape, single-cell motility, and collective population migration.

Homogeneous and heterogeneous populations of active rods in two-dimensional channels

Active swarms, consisting of individual agents which consume energy to move or produce work, are known to generate a diverse range of collective behaviors. Many examples of active swarms are biological in nature (e.g., fish shoals and bird flocks) and have been modeled extensively by numerical simulations. Such simulations of swarms usually assume that the swarm is homogeneous; that is, every agent has exactly the same dynamical properties. However, many biological swarms are highly heterogeneous, such as multispecies communities of micro-organisms in soil, and individual species may have a wide range of different physical properties. Here we explore heterogeneity by developing a simple model for the dynamics of a swarm of motile heterogeneous rodlike bacteria in the absence of hydrodynamic effects. Using molecular dynamics simulations of active rods confined within a two-dimensional rectangular channel, we first explore the case of homogeneous swarms and show that the key parameter governing both dynamics is ratio of the motility force to the steric force. Next we explore heterogeneous or mixed swarms in which the constituent self-propelled rods have a range of motilities and steric interactions. Our results show that the confining boundaries play a strong role in driving the segregation of mixed populations.

Learning the space-time phase diagram of bacterial swarm expansion

Most living systems, from individual cells to tissues and swarms, display collective self-organization on length scales that are much larger than those of the individual units that drive this organization. A fundamental challenge is to understand how properties of microscopic components determine macroscopic, multicellular biological function. Our study connects intracellular physiology to macroscale collective behaviors during multicellular development, spanning five orders of magnitude in length and six orders of magnitude in time, using bacterial swarming as a model system. This work is enabled by a high-throughput adaptive microscopy technique, which we combined with genetics, machine learning, and mathematical modeling to reveal the phase diagram of bacterial swarming and that cell–cell interactions within each swarming phase are dominated by mechanical interactions.

Coordinated dynamics of individual components in active matter are an essential aspect of life on all scales. Establishing a comprehensive, causal connection between intracellular, intercellular, and macroscopic behaviors has remained a major challenge due to limitations in data acquisition and analysis techniques suitable for multiscale dynamics. Here, we combine a high-throughput adaptive microscopy approach with machine learning, to identify key biological and physical mechanisms that determine distinct microscopic and macroscopic collective behavior phases which develop as Bacillus subtilis swarms expand over five orders of magnitude in space. Our experiments, continuum modeling, and particle-based simulations reveal that macroscopic swarm expansion is primarily driven by cellular growth kinetics, whereas the microscopic swarming motility phases are dominated by physical cell–cell interactions. These results provide a unified understanding of bacterial multiscale behavioral complexity in swarms.

A statistical physics view of swarming bacteria

Bacterial swarming is a collective mode of motion in which cells migrate rapidly over surfaces, forming dynamic patterns of whirls and jets. This review presents a physical point of view of swarming bacteria, with an emphasis on the statistical properties of the swarm dynamics as observed in experiments. The basic physical principles underlying the swarm and their relation to contemporary theories of collective motion and active matter are reviewed and discussed in the context of the biological properties of swarming cells. We suggest a paradigm according to which bacteria have optimized some of their physical properties as a strategy for rapid surface translocation. In other words, cells take advantage of favorable physics, enabling efficient expansion that enhances survival under harsh conditions.

The 3D architecture of a bacterial swarm has implications for antibiotic tolerance

Swarming bacteria are an example of a complex, active biological system, where high cell density and super-diffusive cell mobility confer survival advantages to the group as a whole. Previous studies on the dynamics of the swarm have been limited to easily observable regions at the advancing edge of the swarm where cells are restricted to a plane. In this study, using defocused epifluorescence video imaging, we have tracked the motion of fluorescently labeled individuals within the interior of a densely packed three-dimensional (3D) region of a swarm. Our analysis reveals a novel 3D architecture, where bacteria are constrained by inter-particle interactions, sandwiched between two distinct boundary conditions. We find that secreted biosurfactants keep bacteria away from the swarm-air upper boundary, and added antibiotics at the lower swarm-surface boundary lead to their migration away from this boundary. Formation of the antibiotic-avoidance zone is dependent on a functional chemotaxis signaling system, in the absence of which the swarm loses its high tolerance to the antibiotics.

Geometry, packing, and evolutionary paths to increased multicellular size

The evolutionary transition to multicellularity transformed life on earth, heralding the evolution of large, complex organisms. Recent experiments demonstrated that laboratory-evolved multicellular "snowflake yeast" readily overcome the physical barriers that limit cluster size by modifying cellular geometry [Jacobeen et al., Nat. Phys. 14, 286 (2018)10.1038/s41567-017-0002-y]. However, it is unclear why this route to large size is observed, rather than an evolved increase in intercellular bond strength. Here, we use a geometric model of the snowflake yeast growth form to examine the geometric efficiency of increasing size by modifying geometry and bond strength. We find that changing geometry is a far more efficient route to large size than evolving increased intercellular adhesion. In fact, increasing cellular aspect ratio is on average ∼13 times more effective than increasing bond strength at increasing the number of cells in a cluster. Modifying other geometric parameters, such as the geometric arrangement of mother and daughter cells, also had larger effects on cluster size than increasing bond strength. Simulations reveal that as cells reproduce, internal stress in the cluster increases rapidly; thus, increasing bond strength provides diminishing returns in cluster size. Conversely, as cells become more elongated, cellular packing density within the cluster decreases, which substantially decreases the rate of internal stress accumulation. This suggests that geometrically imposed physical constraints may have been a key early selective force guiding the emergence of multicellular complexity.

Derivation of a hydrodynamic theory for mesoscale dynamics in microswimmer suspensions

In this paper, we systematically derive a fourth-order continuum theory capable of reproducing mesoscale turbulence in a three-dimensional suspension of microswimmers. We start from overdamped Langevin equations for a generic microscopic model (pushers or pullers), which include hydrodynamic interactions on both small length scales (polar alignment of neighboring swimmers) and large length scales, where the solvent flow interacts with the order parameter field. The flow field is determined via the Stokes equation supplemented by an ansatz for the stress tensor. In addition to hydrodynamic interactions, we allow for nematic pair interactions stemming from excluded-volume effects. The results here substantially extend and generalize earlier findings [S. Heidenreich et al., Phys. Rev. E 94, 020601 (2016)2470-004510.1103/PhysRevE.94.020601], in which we derived a two-dimensional hydrodynamic theory. From the corresponding mean-field Fokker-Planck equation combined with a self-consistent closure scheme, we derive nonlinear field equations for the polar and the nematic order parameter, involving gradient terms of up to fourth order. We find that the effective microswimmer dynamics depends on the coupling between solvent flow and orientational order. For very weak coupling corresponding to a high viscosity of the suspension, the dynamics of mesoscale turbulence can be described by a simplified model containing only an effective microswimmer velocity.

Role of tumbling in bacterial swarming

Typical wild-type bacteria swimming in sparse suspensions exhibit a movement pattern called "run and tumble," characterized by straight trajectories (runs) interspersed by shorter, random reorientation (tumbles). This is achieved by rotating their flagella counterclockwise, or clockwise, respectively. The chemotaxis signaling network operates in controlling the frequency of tumbles, enabling navigation toward or away from desired regions in the medium. In contrast, while in dense populations, flagellated bacteria exhibit collective motion and form large dynamic clusters, whirls, and jets, with intricate dynamics that is fundamentally different than trajectories of sparsely swimming cells. Although collectively swarming cells do change direction at the level of the individual cell, often exhibiting reversals, it has been suggested that chemotaxis does not play a role in multicellular colony expansion, but the change in direction stems from clockwise flagellar rotation. In this paper, the effects of cell rotor switching (i.e., the ability to tumble) and chemotaxis on the collective statistics of swarming bacteria are studied experimentally in wild-type Bacillus subtilis and two mutants-one that does not tumble and one that tumbles independently of the chemotaxis system. We show that while several of the parameters examined are similar between the strains, other collective and individual characteristics are significantly different. The results demonstrate that tumbling and/or flagellar directional rotor switching has an important role on the dynamics of swarming, and imply that swarming models of self-propelled rods that do not take tumbling and/or rotor switching into account may be oversimplified.