The mechanistic basis of Myxococcus xanthus rippling behavior and its physiological role during predation

Role of non-exponential reversal times in aggregation models of bacterial populations

Individual bacteria typically follow somewhat simple rules of motion, but collective behavior can exhibit complex behavioral patterns. For instance, the formation and dispersal of aggregates of reversing bacteria in biofilms are primarily driven by coordinated motion among cells. Many mathematical models of aggregation assume that cells have no memory, e.g., the time between their behavior changes, such as direction reversals, is exponentially distributed. However, in practice, the distribution is quite distinct from exponential. Therefore, in this paper, we analyze numerically the importance of non-exponential reversal times in 1D agent-based and kinetic models of aggregation. In particular, we consider these models in a practical parameter regime by fitting a Gamma distribution to represent the run times of myxobacteria and study their collective behavior with exponential and non-exponential reversal times. We demonstrate that non-exponential reversal times aid aggregation and result in tighter aggregates. We compare and contrast the behavior of agent-based and kinetic models that consider aggregation driven by chemotaxis. Thus, incorporating non-exponential reversal times into models of aggregation can be particularly important for reproducing experimental data, such as aggregate persistence and dispersal. These results provide a simple example of how the existence of memory helps bacteria coordinate their behaviors.

The Limits of Our Explanation: A Case Study in Myxococcus xanthus Cooperation

In this article, I demonstrate two ways in which our major theories of the evolution of cooperation may fail to capture particular social phenomena. The first shortcoming of our current major theories stems from the possibility of mischaracterizing the cooperative problem in game theory. The second shortcoming of our current major theories is the insensitivity of these explanatory models to ecological and genomic context. As a case study to illustrate these points, I will use the cooperative interaction of a species of myxobacteria called Myxococcus xanthus. M. xanthus cooperate in many areas of their life cycle-in quorum sensing, social motility, fruiting body formation, and predation. I focus in particular on predation as we have not yet discovered an adequate explanation of how they sustain cooperative predation in the face of developmental cheats. In explaining why we have not, I draw generalizable conclusions that shed light on our use of simplified models to explain real-world behaviors in a variety of organisms.

Unravelling a diversity of cellular structures and aggregation dynamics during the early development of Myxococcus xanthus

Aggregation underlies the collective dynamics of a diversity of organisms, enabling the formation of complex structures and emergent behaviours on interaction with the environment. Cellular aggregation constitutes one of the routes to collective motility and multicellular development. Myxococcus xanthus, a social bacterium, is a valuable model for studying the aggregative path to multicellularity, a major transition in the evolutionary history of life. While the collective developmental behaviour of M. xanthus has been largely studied in high cellular densities, there is a lack of understanding at low-density conditions that can be ecologically relevant. In this work, we study the early stages of emergent collective behaviour of M. xanthus under nutrient-poor and low-density conditions, uncovering the formation of diverse cellular structures with different shapes and sizes, ranging from individual cells to networks comprising thousands of cells. We study their motility patterns and their prevalence along development and discuss their cross-scale role on the population's exploratory dynamics. This work contributes to understanding key, yet largely understudied, aspects in the early stages of multicellular development in myxobacteria, shedding light on the dynamics underlying aggregative processes in this and other taxa and study systems.

Regulation of late-acting operons by three transcription factors and a CRISPR-Cas component during Myxococcus xanthus development

Upon starvation, rod-shaped Myxococcus xanthus bacteria form mounds and then differentiate into round, stress-resistant spores. Little is known about the regulation of late-acting operons important for spore formation. C-signaling has been proposed to activate FruA, which binds DNA cooperatively with MrpC to stimulate transcription of developmental genes. We report that this model can explain regulation of the fadIJ operon involved in spore metabolism, but not that of the spore coat biogenesis operons exoA-I, exoL-P, and nfsA-H. Rather, a mutation in fruA increased the transcript levels from these operons early in development, suggesting negative regulation by FruA, and a mutation in mrpC affected transcript levels from each operon differently. FruA bound to all four promoter regions in vitro, but strikingly each promoter region was unique in terms of whether or not MrpC and/or the DNA-binding domain of Nla6 bound, and in terms of cooperative binding. Furthermore, the DevI component of a CRISPR-Cas system is a negative regulator of all four operons, based on transcript measurements. Our results demonstrate complex regulation of sporulation genes by three transcription factors and a CRISPR-Cas component, which we propose produces spores suited to withstand starvation and environmental insults.

Two reasons to kill: predation and kin discrimination in myxobacteria

Myxobacteria are social microbial predators that use cell-cell contacts to identify bacterial or fungal prey and to differentiate kin relatives to initiate cellular responses. For prey killing, they assemble Tad-like and type III-like secretion systems at contact sites. For kin discrimination (KD), they assemble outer membrane exchange complexes composed of the TraA and TraB receptors at contacts sites. A type VI secretion system and Rhs proteins also mediate KD. Following cellular recognition, these systems deliver appropriate effectors into target cells. For prey, this leads to cell death and lysis for nutrient consumption by myxobacteria. In KD, a panel of effectors are delivered, and if adjacent cells are clonal cells, resistance ensues because they express a cognate panel of immunity factors; while nonkin lack complete immunity and are intoxicated. This review compares and contrasts recent findings from these systems in myxobacteria.

Formation and emergent dynamics of spatially organized microbial systems

Spatial organization is the norm rather than the exception in the microbial world. While the study of microbial physiology has been dominated by studies in well-mixed cultures, there is now increasing interest in understanding the role of spatial organization in microbial physiology, coexistence and evolution. Where studied, spatial organization has been shown to influence all three of these aspects. In this mini review and perspective article, we emphasize that the dynamics within spatially organized microbial systems (SOMS) are governed by feedbacks between local physico-chemical conditions, cell physiology and movement, and evolution. These feedbacks can give rise to emergent dynamics, which need to be studied through a combination of spatio-temporal measurements and mathematical models. We highlight the initial formation of SOMS and their emergent dynamics as two open areas of investigation for future studies. These studies will benefit from the development of model systems that can mimic natural ones in terms of species composition and spatial structure.

Flagellar Motor Transformed: Biophysical Perspectives of the Myxococcus xanthus Gliding Mechanism

Many bacteria move on solid surfaces using gliding motility, without involvement of flagella or pili. Gliding of Myxococcus xanthus is powered by a proton channel homologous to the stators in the bacterial flagellar motor. Instead of being fixed in place and driving the rotation of a circular protein track like the flagellar basal body, the gliding machinery of M. xanthus travels the length of the cell along helical trajectories, while mechanically engaging with the substrate. Such movement entails a different molecular mechanism to generate propulsion on the cell. In this perspective, we will discuss the similarities and differences between the M. xanthus gliding machinery and bacterial flagellar motor, and use biophysical principles to generate hypotheses about the operating mechanism, efficiency, sensitivity to control, and mechanosensing of M. xanthus gliding.

Emergent Myxobacterial Behaviors Arise from Reversal Suppression Induced by Kin Contacts

A wide range of biological systems, from microbial swarms to bird flocks, display emergent behaviors driven by coordinated movement of individuals. To this end, individual organisms interact by recognizing their kin and adjusting their motility based on others around them. However, even in the best-studied systems, the mechanistic basis of the interplay between kin recognition and motility coordination is not understood. Here, using a combination of experiments and mathematical modeling, we uncover the mechanism of an emergent social behavior in Myxococcus xanthus. By overexpressing the cell surface adhesins TraA and TraB, which are involved in kin recognition, large numbers of cells adhere to one another and form organized macroscopic circular aggregates that spin clockwise or counterclockwise. Mechanistically, TraAB adhesion results in sustained cell-cell contacts that trigger cells to suppress cell reversals, and circular aggregates form as the result of cells’ ability to follow their own cellular slime trails. Furthermore, our in silico simulations demonstrate a remarkable ability to predict self-organization patterns when phenotypically distinct strains are mixed. For example, defying naive expectations, both models and experiments found that strains engineered to overexpress different and incompatible TraAB adhesins nevertheless form mixed circular aggregates. Therefore, this work provides key mechanistic insights into M. xanthus social interactions and demonstrates how local cell contacts induce emergent collective behaviors by millions of cells.

IMPORTANCE In many species, large populations exhibit emergent behaviors whereby all related individuals move in unison. For example, fish in schools can all dart in one direction simultaneously to avoid a predator. Currently, it is impossible to explain how such animals recognize kin through brain cognition and elicit such behaviors at a molecular level. However, microbes also recognize kin and exhibit emergent collective behaviors that are experimentally tractable. Here, using a model social bacterium, we engineer dispersed individuals to organize into synchronized collectives that create emergent patterns. With experimental and mathematical approaches, we explain how this occurs at both molecular and population levels. The results demonstrate how the combination of local physical interactions triggers intracellular signaling, which in turn leads to emergent behaviors on a population scale.

Cell density, alignment, and orientation correlate with C-signal-dependent gene expression during Myxococcus xanthus development

Starving Myxococcus xanthus bacteria use short-range C-signaling to coordinate their movements and construct multicellular mounds, which mature into fruiting bodies as rods differentiate into spherical spores. Differentiation requires efficient C-signaling to drive the expression of developmental genes, but how the arrangement of cells within nascent fruiting bodies (NFBs) affects C-signaling is not fully understood. Here, we used confocal microscopy and cell segmentation to visualize and quantify the arrangement, morphology, and gene expression of cells near the bottom of NFBs at much higher resolution than previously achieved. We discovered that "transitioning cells" (TCs), intermediate in morphology between rods and spores, comprised 10 to 15% of the total population. Spores appeared midway between the center and the edge of NFBs early in their development and near the center as maturation progressed. The developmental pattern, as well as C-signal-dependent gene expression in TCs and spores, were correlated with cell density, the alignment of neighboring rods, and the tangential orientation of rods early in the development of NFBs. These dynamic radial patterns support a model in which the arrangement of cells within the NFBs affects C-signaling efficiency to regulate precisely the expression of developmental genes and cellular differentiation in space and time. Developmental patterns in other bacterial biofilms may likewise rely on short-range signaling to communicate multiple aspects of cellular arrangement, analogous to juxtacrine and paracrine signaling during animal development.

Profiling Myxococcus xanthus Swarming Phenotypes through Mutation and Environmental Variation

Myxococcus xanthus is a bacterium that lives on surfaces as a predatory biofilm called a swarm. As a growing swarm feeds on prey and expands, it displays dynamic multicellular patterns such as traveling waves called ripples and branching protrusions called flares. The rate at which a swarm expands across a surface, and the emergence of the coexisting patterns, are all controlled through coordinated cell movement. M. xanthus cells move using two motility systems known as adventurous (A) and social (S). Both are involved in swarm expansion and pattern formation. In this study, we describe a set of M. xanthus swarming genotype-to-phenotype associations that include both genetic and environmental perturbations. We identified new features of the swarming phenotype, recorded and measured swarm expansion using time-lapse microscopy, and compared the impact of mutations on different surfaces. These observations and analyses have increased our ability to discriminate between swarming phenotypes and provided context that allows us to identify some phenotypes as improbable outliers within the M. xanthus swarming phenome. IMPORTANCE Myxococcus xanthus grows on surfaces as a predatory biofilm called a swarm. In nature, a feeding swarm expands by moving over and consuming prey bacteria. In the laboratory, a swarm is created by spotting cell suspension onto nutrient agar in lieu of prey. The suspended cells quickly settle on the surface as the liquid is absorbed into the agar, and the new swarm then expands radially. An assay that measures the expansion rate of a swarm of mutant cells is the first, and sometimes only, measurement used to decide whether a particular mutation impacts swarm motility. We have broadened the scope of this assay by increasing the accuracy of measurements and introducing prey, resulting in new identifiable and quantifiable features that can be used to improve genotype-to-phenotype associations.

Quantification of Myxococcus xanthus Aggregation and Rippling Behaviors: Deep-Learning Transformation of Phase-Contrast into Fluorescence Microscopy Images

Myxococcus xanthus bacteria are a model system for understanding pattern formation and collective cell behaviors. When starving, cells aggregate into fruiting bodies to form metabolically inert spores. During predation, cells self-organize into traveling cell-density waves termed ripples. Both phase-contrast and fluorescence microscopy are used to observe these patterns but each has its limitations. Phase-contrast images have higher contrast, but the resulting image intensities lose their correlation with cell density. The intensities of fluorescence microscopy images, on the other hand, are well-correlated with cell density, enabling better segmentation of aggregates and better visualization of streaming patterns in between aggregates; however, fluorescence microscopy requires the engineering of cells to express fluorescent proteins and can be phototoxic to cells. To combine the advantages of both imaging methodologies, we develop a generative adversarial network that converts phase-contrast into synthesized fluorescent images. By including an additional histogram-equalized output to the state-of-the-art pix2pixHD algorithm, our model generates accurate images of aggregates and streams, enabling the estimation of aggregate positions and sizes, but with small shifts of their boundaries. Further training on ripple patterns enables accurate estimation of the rippling wavelength. Our methods are thus applicable for many other phenotypic behaviors and pattern formation studies.

The environment topography alters the way to multicellularity in Myxococcus xanthus

The social soil-dwelling bacterium Myxococcus xanthus can form multicellular structures, known as fruiting bodies. Experiments in homogeneous environments have shown that this process is affected by the physicochemical properties of the substrate, but they have largely neglected the role of complex topographies. We experimentally demonstrate that the topography alters single-cell motility and multicellular organization in M. xanthus In topographies realized by randomly placing silica particles over agar plates, we observe that the cells' interaction with particles drastically modifies the dynamics of cellular aggregation, leading to changes in the number, size, and shape of the fruiting bodies and even to arresting their formation in certain conditions. We further explore this type of cell-particle interaction in a computational model. These results provide fundamental insights into how the environment topography influences the emergence of complex multicellular structures from single cells, which is a fundamental problem of biological, ecological, and medical relevance.

Myxococcus xanthus predation of Gram-positive or Gram-negative bacteria is mediated by different bacteriolytic mechanisms

Myxococcus xanthus kills other species to use their biomass as energy source. Its predation mechanisms allow feeding on a broad spectrum of bacteria, but the identity of predation effectors and their mode of action remains largely unknown. We initially focused on the role of hydrolytic enzymes for prey killing and compared the activity of secreted M. xanthus proteins against four prey strains. 72 secreted proteins were identified by mass spectrometry, and among them a family 19 glycoside hydrolase that displayed bacteriolytic activity in vivo and in vitro This enzyme, which we name LlpM (lectin/lysozyme-like protein of M. xanthus), was not essential for predation, indicating that additional secreted components are required to disintegrate prey. Furthermore, secreted proteins lysed only Gram-positive, but not Gram-negative species. We thus compared the killing of different preys by cell-associated mechanisms: Individual M. xanthus cells killed all four test strains in a cell-contact dependent manner, but were only able to disintegrate Gram-negative, not Gram-positive cell envelopes. Thus, our data indicate that M. xanthus uses different, multifactorial mechanisms for killing and degrading different preys. Besides secreted enzymes, cell-associated mechanisms that have not been characterized so far, appear to play a major role for prey killing.IMPORTANCEPredation is an important survival strategy of the widespread myxobacteria, but it remains poorly understood on the mechanistic level. Without a basic understanding of how prey cell killing and consumption is achieved, it also remains difficult to investigate the role of predation for the complex myxobacterial lifestyle, reciprocal predator-prey relationships or the impact of predation on complex bacterial soil communities.We study predation in the established model organism Myxococcus xanthus, aiming to dissect the molecular mechanisms of prey cell lysis. In this study, we addressed the role of secreted bacteriolytic proteins, as well as potential mechanistic differences in the predation of Gram-positive and Gram-negative bacteria. Our observation shows that secreted enzymes are sufficient for killing and degrading Gram-positive species, but that cell-associated mechanisms may play a major role for killing Gram-negative and Gram-positive prey on fast timescales.

Linking single-cell decisions to collective behaviours in social bacteria

Social bacteria display complex behaviours whereby thousands of cells collectively and dramatically change their form and function in response to nutrient availability and changing environmental conditions. In this review, we focus on Myxococcus xanthus motility, which supports spectacular transitions based on prey availability across its life cycle. A large body of work suggests that these behaviours require sensory capacity implemented at the single-cell level. Focusing on recent genetic work on a core cellular pathway required for single-cell directional decisions, we argue that signal integration, multi-modal sensing and memory are at the root of decision making leading to multicellular behaviours. Hence, Myxococcus may be a powerful biological system to elucidate how cellular building blocks cooperate to form sensory multicellular assemblages, a possible origin of cognitive mechanisms in biological systems. This article is part of the theme issue 'Basal cognition: conceptual tools and the view from the single cell'.

Interplay of mesoscale physics and agent-like behaviors in the parallel evolution of aggregative multicellularity

Myxobacteria and dictyostelids are prokaryotic and eukaryotic multicellular lineages, respectively, that after nutrient depletion aggregate and develop into structures called fruiting bodies. The developmental processes and resulting morphological outcomes resemble one another to a remarkable extent despite their independent origins, the evolutionary distance between them and the lack of traceable homology in molecular mechanisms. We hypothesize that the morphological parallelism between the two lineages arises as the consequence of the interplay within multicellular aggregates between generic processes, physical and physicochemical processes operating similarly in living and non-living matter at the mesoscale (~10^-3-10^-1 m) and agent-like behaviors, unique to living systems and characteristic of the constituent cells, considered as autonomous entities acting according to internal rules in a shared environment. Here, we analyze the contributions of generic and agent-like determinants in myxobacteria and dictyostelid development and their roles in the generation of their common traits. Consequent to aggregation, collective cell-cell contacts mediate the emergence of liquid-like properties, making nascent multicellular masses subject to novel patterning and morphogenetic processes. In both lineages, this leads to behaviors such as streaming, rippling, and rounding-up, as seen in non-living fluids. Later the aggregates solidify, leading them to exhibit additional generic properties and motifs. Computational models suggest that the morphological phenotypes of the multicellular masses deviate from the predictions of generic physics due to the contribution of agent-like behaviors of cells such as directed migration, quiescence, and oscillatory signal transduction mediated by responses to external cues. These employ signaling mechanisms that reflect the evolutionary histories of the respective organisms. We propose that the similar developmental trajectories of myxobacteria and dictyostelids are more due to shared generic physical processes in coordination with analogous agent-type behaviors than to convergent evolution under parallel selection regimes. Insights from the biology of these aggregative forms may enable a unified understanding of developmental evolution, including that of animals and plants.

The cell organization underlying structural colour is involved in Flavobacterium IR1 predation

Flavobacterium IR1 is a gliding bacterium with a high degree of colonial organization as a 2D photonic crystal, resulting in vivid structural coloration when illuminated. Enterobacter cloacae B12, an unrelated bacterium, was isolated from the brown macroalga Fucus vesiculosus from the same location as IR1. IR1 was found to be a predator of B12. A process of surrounding, infiltration, undercutting and killing of B12 supported improved growth of IR1. A combination of motility and capillarity facilitated the engulfment of B12 colonies by IR1. Predation was independent of illumination. Mutants of IR1 that formed photonic crystals less effectively than the wild type were reduced in predation. Conversely, formation of a photonic crystal was not advantageous in resisting predation by Rhodococcus spp. PIR4. These observations suggest that the organization required to create structural colour has a biological function (facilitating predation) but one that is not directly related to the photonic properties of the colony. This work is the first experimental evidence supporting a role for this widespread type of cell organization in the Flavobacteriia.

Conditional requirement of SglT for type IV pili function and S-motility in Myxococcus xanthus

Myxobacteria exhibit complex social behaviors such as predation, outer membrane exchange and fruiting body formation. These behaviors depend on coordinated movements of cells on solid surfaces that involve social (S) motility. S-motility is powered by extension-retraction cycles of type 4 pili (Tfp) and exopolysaccharides (EPS) that provide a matrix for group cellular movement. Here, we characterized a new class of S-motility mutants in Myxococcus xanthus. These mutants have a distinctive phenotype: they lack S-motility even though they produce pili and EPS and the phenotype is temperature-sensitive. The point mutations were mapped to a single locus, MXAN_3284, named sglT. Similar to pilT mutants, sglT mutants are hyperpiliated and, strikingly, the temperature-sensitive phenotype is caused by null mutations. Our results indicate that SglT plays a critical role in Tfp function associated with pilus retraction and that the block in pili retraction is caused by a Tfp assembly defect in the absence of SglT at high-temperature growth.

The Predation Strategy of Myxococcus xanthus

Myxobacteria are ubiquitous in soil environments. They display a complex life cycle: vegetatively growing cells coordinate their motility to form multicellular swarms, which upon starvation aggregate into large fruiting bodies where cells differentiate into spores. In addition to growing as saprophytes, Myxobacteria are predators that actively kill bacteria of other species to consume their biomass. In this review, we summarize research on the predation behavior of the model myxobacterium Myxococcus xanthus, which can access nutrients from a broad spectrum of microorganisms. M. xanthus displays an epibiotic predation strategy, i.e., it induces prey lysis from the outside and feeds on the released biomass. This predatory behavior encompasses various processes: Gliding motility and induced cell reversals allow M. xanthus to encounter prey and to remain within the area to sweep up its biomass, which causes the characteristic “rippling” of preying populations. Antibiotics and secreted bacteriolytic enzymes appear to be important predation factors, which are possibly targeted to prey cells with the aid of outer membrane vesicles. However, certain bacteria protect themselves from M. xanthus predation by forming mechanical barriers, such as biofilms and mucoid colonies, or by secreting antibiotics. Further understanding the molecular mechanisms that mediate myxobacterial predation will offer fascinating insight into the reciprocal relationships of bacteria in complex communities, and might spur application-oriented research on the development of novel antibacterial strategies.

Dynamic polarity control by a tunable protein oscillator in bacteria

In bacteria, cell polarization involves the controlled targeting of specific proteins to the poles, defining polar identity and function. How a specific protein is targeted to one pole and what are the processes that facilitate its dynamic relocalization to the opposite pole is still unclear. The Myxococcus xanthus polarization example illustrates how the dynamic and asymmetric localization of polar proteins enable a controlled and fast switch of polarity. In M. xanthus, the opposing polar distribution of the small GTPase MglA and its cognate activating protein MglB defines the direction of movement of the cell. During a reversal event, the switch of direction is triggered by the Frz chemosensory system, which controls polarity reversals through a so-called gated relaxation oscillator. In this review, we discuss how this genetic architecture can provoke sharp behavioral transitions depending on Frz activation levels, which is central to multicellular behaviors in this bacterium.

Biophysics at the coffee shop: lessons learned working with George Oster

Over the past 50 years, the use of mathematical models, derived from physical reasoning, to describe molecular and cellular systems has evolved from an art of the few to a cornerstone of biological inquiry. George Oster stood out as a pioneer of this paradigm shift from descriptive to quantitative biology not only through his numerous research accomplishments, but also through the many students and postdocs he mentored over his long career. Those of us fortunate enough to have worked with George agree that his sharp intellect, physical intuition, and passion for scientific inquiry not only inspired us as scientists but also greatly influenced the way we conduct research. We would like to share a few important lessons we learned from George in honor of his memory and with the hope that they may inspire future generations of scientists.

Agent-Based Modeling Reveals Possible Mechanisms for Observed Aggregation Cell Behaviors

Myxococcus xanthus is a soil bacterium that serves as a model system for biological self-organization. Cells form distinct, dynamic patterns depending on environmental conditions. An agent-based model was used to understand how M. xanthus cells aggregate into multicellular mounds in response to starvation. In this model, each cell is modeled as an agent represented by a point particle and characterized by its position and moving direction. At low agent density, the model recapitulates the dynamic patterns observed by experiments and a previous biophysical model. To study aggregation at high cell density, we extended the model based on the recent experimental observation that cells exhibit biased movement toward aggregates. We tested two possible mechanisms for this biased movement and demonstrate that a chemotaxis model with adaptation can reproduce the observed experimental results leading to the formation of stable aggregates. Furthermore, our model reproduces the experimentally observed patterns of cell alignment around aggregates.

A gated relaxation oscillator mediated by FrzX controls morphogenetic movements in Myxococcus xanthus

Dynamic control of cell polarity is of critical importance for many aspects of cellular development and motility. In Myxococcus xanthus, MglA, a G protein, and MglB, its cognate GTPase-activating protein, establish a polarity axis that defines the direction of movement of the cell and that can be rapidly inverted by the Frz chemosensory system. Although vital for collective cell behaviours, how Frz triggers this switch has remained unknown. Here, we use genetics, imaging and mathematical modelling to show that Frz controls polarity reversals via a gated relaxation oscillator. FrzX, which we identify as a target of the Frz kinase, provides the gating and thus acts as the trigger for reversals. Slow relocalization of the polarity protein RomR then creates a refractory period during which another switch cannot be triggered. A secondary Frz output, FrzZ, decreases this delay, allowing rapid reversals when required. Thus, this architecture results in a highly tuneable switch that allows a wide range of reversal frequencies.

Reversals and collisions optimize protein exchange in bacterial swarms

Swarming groups of bacteria coordinate their behavior by self-organizing as a population to move over surfaces in search of nutrients and optimal niches for colonization. Many open questions remain about the cues used by swarming bacteria to achieve this self-organization. While chemical cue signaling known as quorum sensing is well-described, swarming bacteria often act and coordinate on time scales that could not be achieved via these extracellular quorum sensing cues. Here, cell-cell contact-dependent protein exchange is explored as a mechanism of intercellular signaling for the bacterium Myxococcus xanthus. A detailed biologically calibrated computational model is used to study how M. xanthus optimizes the connection rate between cells and maximizes the spread of an extracellular protein within the population. The maximum rate of protein spreading is observed for cells that reverse direction optimally for swarming. Cells that reverse too slowly or too fast fail to spread extracellular protein efficiently. In particular, a specific range of cell reversal frequencies was observed to maximize the cell-cell connection rate and minimize the time of protein spreading. Furthermore, our findings suggest that predesigned motion reversal can be employed to enhance the collective behavior of biological synthetic active systems.

Mesoscale pattern formation of self-propelled rods with velocity reversal

We study self-propelled particles with velocity reversal interacting by uniaxial (nematic) alignment within a coarse-grained hydrodynamic theory. Combining analytical and numerical continuation techniques, we show that the physics of this active system is essentially controlled by the reversal frequency. In particular, we find that elongated, high-density, ordered patterns, called bands, emerge via subcritical bifurcations from spatially homogeneous states. Our analysis reveals further that the interaction of bands is weakly attractive and, consequently, bands fuse upon collision in analogy with nonequilibrium nucleation processes. Moreover, we demonstrate that a renormalized positive line tension can be assigned to stable bands below a critical reversal rate, beyond which they are transversally unstable. In addition, we discuss the kinetic roughening of bands as well as their nonlinear dynamics close to the threshold of transversal instability. Altogether, the reduction of the multiparticle system onto the dynamics of bands provides a unified framework to understand the emergence and stability of nonequilibrium patterns in this self-propelled particle system. In this regard, our results constitute a proof of principle in favor of the hypothesis in microbiology that velocity reversal of gliding rod-shaped bacteria regulates the transitions between various self-organized patterns observed during the bacterial life cycle.

The Chemical Ecology of Predatory Soil Bacteria

The study of natural products is entering a renaissance, driven by the discovery that the majority of bacterial secondary metabolites are not produced under standard laboratory conditions. Understanding the ecological role of natural products is key to efficiently directing our screening efforts, and to ensuring that each screen efficiently captures the full biosynthetic repertoire of the producing organisms. Myxobacteria represent one of the most common and diverse groups of bacteria, with roughly 2500 strains publically available. Fed largely through predation, the myxobacteria have developed a large repertoire of natural products that target other microorganisms, including bacteria and fungi. Many of these interactions can be observed in predation assays, providing direct evidence for environmental interactions. With a focus on Myxococcus xanthus, this review will highlight how recent advances in myxobacteria are revealing the chemical ecology of bacterial natural products.

Myxobacteria: Moving, Killing, Feeding, and Surviving Together

Myxococcus xanthus, like other myxobacteria, is a social bacterium that moves and feeds cooperatively in predatory groups. On surfaces, rod-shaped vegetative cells move in search of the prey in a coordinated manner, forming dynamic multicellular groups referred to as swarms. Within the swarms, cells interact with one another and use two separate locomotion systems. Adventurous motility, which drives the movement of individual cells, is associated with the secretion of slime that forms trails at the leading edge of the swarms. It has been proposed that cellular traffic along these trails contributes to M. xanthus social behavior via stigmergic regulation. However, most of the cells travel in groups by using social motility, which is cell contact-dependent and requires a large number of individuals. Exopolysaccharides and the retraction of type IV pili at alternate poles of the cells are the engines associated with social motility. When the swarms encounter prey, the population of M. xanthus lyses and takes up nutrients from nearby cells. This cooperative and highly density-dependent feeding behavior has the advantage that the pool of hydrolytic enzymes and other secondary metabolites secreted by the entire group is shared by the community to optimize the use of the degradation products. This multicellular behavior is especially observed in the absence of nutrients. In this condition, M. xanthus swarms have the ability to organize the gliding movements of 1000s of rods, synchronizing rippling waves of oscillating cells, to form macroscopic fruiting bodies, with three subpopulations of cells showing division of labor. A small fraction of cells either develop into resistant myxospores or remain as peripheral rods, while the majority of cells die, probably to provide nutrients to allow aggregation and spore differentiation. Sporulation within multicellular fruiting bodies has the benefit of enabling survival in hostile environments, and increases germination and growth rates when cells encounter favorable conditions. Herein, we review how these social bacteria cooperate and review the main cell–cell signaling systems used for communication to maintain multicellularity.

Superdiffusion, large-scale synchronization, and topological defects

We study an ensemble of random walkers carrying internal noisy phase oscillators which are synchronized among the walkers by local interactions. Due to individual mobility, the interaction partners of every walker change randomly, hereby introducing an additional, independent source of fluctuations, thus constituting the intrinsic nonequilibrium nature of the temporal dynamics. We employ this paradigmatic model system to discuss how the emergence of order is affected by the motion of individual entities. In particular, we consider both normal diffusive motion and superdiffusion. A non-Hamiltonian field theory including multiplicative noise terms is derived which describes the nonequilibrium dynamics at the macroscale. This theory reveals a defect-mediated transition from incoherence to quasi-long-range order for normal diffusion of oscillators in two dimensions, implying a power-law dependence of all synchronization properties on system size. In contrast, superdiffusive transport suppresses the emergence of topological defects, thereby inducing a continuous synchronization transition to long-range order in two dimensions. These results are consistent with particle-based simulations.

Wavelength selection of rippling patterns in myxobacteria

Rippling patterns of myxobacteria appear in starving colonies before they aggregate to form fruiting bodies. These periodic traveling cell density waves arise from the coordination of individual cell reversals, resulting from an internal clock regulating them and from contact signaling during bacterial collisions. Here we revisit a mathematical model of rippling in myxobacteria due to Igoshin et al. [Proc. Natl. Acad. Sci. USA 98, 14913 (2001)PNASA60027-842410.1073/pnas.221579598 and Phys. Rev. E 70, 041911 (2004)PLEEE81539-375510.1103/PhysRevE.70.041911]. Bacteria in this model are phase oscillators with an extra internal phase through which they are coupled to a mean field of oppositely moving bacteria. Previously, patterns for this model were obtained only by numerical methods, and it was not possible to find their wave number analytically. We derive an evolution equation for the reversal point density that selects the pattern wave number in the weak signaling limit, shows the validity of the selection rule by solving numerically the model equations, and describes other stable patterns in the strong signaling limit. The nonlocal mean-field coupling tends to decohere and confine patterns. Under appropriate circumstances, it can annihilate the patterns leaving a constant density state via a nonequilibrium phase transition reminiscent of destruction of synchronization in the Kuramoto model.

Mechanism for Collective Cell Alignment in Myxococcus xanthus Bacteria

Myxococcus xanthus cells self-organize into aligned groups, clusters, at various stages of their lifecycle. Formation of these clusters is crucial for the complex dynamic multi-cellular behavior of these bacteria. However, the mechanism underlying the cell alignment and clustering is not fully understood. Motivated by studies of clustering in self-propelled rods, we hypothesized that M. xanthus cells can align and form clusters through pure mechanical interactions among cells and between cells and substrate. We test this hypothesis using an agent-based simulation framework in which each agent is based on the biophysical model of an individual M. xanthus cell. We show that model agents, under realistic cell flexibility values, can align and form cell clusters but only when periodic reversals of cell directions are suppressed. However, by extending our model to introduce the observed ability of cells to deposit and follow slime trails, we show that effective trail-following leads to clusters in reversing cells. Furthermore, we conclude that mechanical cell alignment combined with slime-trail-following is sufficient to explain the distinct clustering behaviors observed for wild-type and non-reversing M. xanthus mutants in recent experiments. Our results are robust to variation in model parameters, match the experimentally observed trends and can be applied to understand surface motility patterns of other bacterial species.

How Myxobacteria Cooperate

Prokaryotes often reside in groups where a high degree of relatedness has allowed the evolution of cooperative behaviors. However, very few bacteria or archaea have made the successful transition from unicellular to obligate multicellular life. A notable exception is the myxobacteria, in which cells cooperate to perform group functions highlighted by fruiting body development, an obligate multicellular function. Like all multicellular organisms, myxobacteria face challenges in how to organize and maintain multicellularity. These challenges include maintaining population homeostasis, carrying out tissue repair and regulating the behavior of non-cooperators. Here, we describe the major cooperative behaviors that myxobacteria use: motility, predation and development. In addition, this review emphasizes recent discoveries in the social behavior of outer membrane exchange, wherein kin share outer membrane contents. Finally, we review evidence that outer membrane exchange may be involved in regulating population homeostasis, thus serving as a social tool for myxobacteria to make the cyclic transitions from unicellular to multicellular states.

Rhizobial galactoglucan determines the predatory pattern of Myxococcus xanthus and protects Sinorhizobium meliloti from predation

Myxococcus xanthus is a social bacterium that preys on prokaryotic and eukaryotic microorganisms. Co-culture of M. xanthus with reference laboratory strains and field isolates of the legume symbiont Sinorhizobium meliloti revealed two different predatory patterns that resemble frontal and wolf-pack attacks. Use of mutants impaired in the two types of M. xanthus surface motility (A or adventurous and S or social motility) and a csgA mutant, which is unable to form macroscopic travelling waves known as ripples, has demonstrated that both motility systems but not rippling are required for efficient predation. To avoid frontal attack and reduce killing rates, rhizobial cells require a functional expR gene. ExpR regulates expression of genes involved in a variety of functions. The use of S. meliloti mutants impaired in several of these functions revealed that the exopolysaccharide galactoglucan (EPS II) is the major determinant of the M. xanthus predatory pattern. The data also suggest that this biopolymer confers an ecological advantage to rhizobial survival in soil, which may have broad environmental implications.

Myxococcus xanthus gliding motors are elastically coupled to the substrate as predicted by the focal adhesion model of gliding motility

Myxococcus xanthus is a model organism for studying bacterial social behaviors due to its ability to form complex multi-cellular structures. Knowledge of M. xanthus surface gliding motility and the mechanisms that coordinated it are critically important to our understanding of collective cell behaviors. Although the mechanism of gliding motility is still under investigation, recent experiments suggest that there are two possible mechanisms underlying force production for cell motility: the focal adhesion mechanism and the helical rotor mechanism, which differ in the biophysics of the cell–substrate interactions. Whereas the focal adhesion model predicts an elastic coupling, the helical rotor model predicts a viscous coupling. Using a combination of computational modeling, imaging, and force microscopy, we find evidence for elastic coupling in support of the focal adhesion model. Using a biophysical model of the M. xanthus cell, we investigated how the mechanical interactions between cells are affected by interactions with the substrate. Comparison of modeling results with experimental data for cell-cell collision events pointed to a strong, elastic attachment between the cell and substrate. These results are robust to variations in the mechanical and geometrical parameters of the model. We then directly measured the motor-substrate coupling by monitoring the motion of optically trapped beads and find that motor velocity decreases exponentially with opposing load. At high loads, motor velocity approaches zero velocity asymptotically and motors remain bound to beads indicating a strong, elastic attachment.

Studies of collective bacterial motility on solid surfaces are essential for understanding self-organization of biofilms. The Gram-negative bacterium Myxococcus xanthus has long been used as a model organism for studying surface motility but its mechanism of gliding is still under investigation. Recent experiments point to two potential mechanisms for gliding motility that differ qualitatively in the details of their cell-substrate interactions. To investigate the biophysical nature of this interaction (viscous vs. elastic coupling), we developed a synergistically multidisciplinary approach combining computational modeling, time-lapse microscopy, and biophysical optical trap experiments. First we studied the mechanical cell interaction behavior in isolated cell pair collisions in a computational model and compared the results with experimental cell behavior. The results indicated a strong adhesive attachment between cell and substrate which is further confirmed by applying opposing loads on beads attached to cell surface in an optical trap. Thus our results conclusively showed strong adhesive attachments between cell and substrate, providing support for an elastic rather than viscous coupling between cell and substrate similar to phenomena observed in focal adhesions from eukaryotic cells.

Agent-based modeling: a systematic assessment of use cases and requirements for enhancing pharmaceutical research and development productivity

A crisis continues to brew within the pharmaceutical research and development (R&D) enterprise: productivity continues declining as costs rise, despite ongoing, often dramatic scientific and technical advances. To reverse this trend, we offer various suggestions for both the expansion and broader adoption of modeling and simulation (M&S) methods. We suggest strategies and scenarios intended to enable new M&S use cases that directly engage R&D knowledge generation and build actionable mechanistic insight, thereby opening the door to enhanced productivity. What M&S requirements must be satisfied to access and open the door, and begin reversing the productivity decline? Can current methods and tools fulfill the requirements, or are new methods necessary? We draw on the relevant, recent literature to provide and explore answers. In so doing, we identify essential, key roles for agent-based and other methods. We assemble a list of requirements necessary for M&S to meet the diverse needs distilled from a collection of research, review, and opinion articles. We argue that to realize its full potential, M&S should be actualized within a larger information technology framework—a dynamic knowledge repository—wherein models of various types execute, evolve, and increase in accuracy over time. We offer some details of the issues that must be addressed for such a repository to accrue the capabilities needed to reverse the productivity decline. © 2013 Wiley Periodicals, Inc.