A traveling-wave solution for bacterial chemotaxis with growth

Direct measurement of dynamic attractant gradients reveals breakdown of the Patlak-Keller-Segel chemotaxis model

Chemotactic bacteria not only navigate chemical gradients, but also shape their environments by consuming and secreting attractants. Investigating how these processes influence the dynamics of bacterial populations has been challenging because of a lack of experimental methods for measuring spatial profiles of chemoattractants in real time. Here, we use a fluorescent sensor for aspartate to directly measure bacterially generated chemoattractant gradients during collective migration. Our measurements show that the standard Patlak-Keller-Segel model for collective chemotactic bacterial migration breaks down at high cell densities. To address this, we propose modifications to the model that consider the impact of cell density on bacterial chemotaxis and attractant consumption. With these changes, the model explains our experimental data across all cell densities, offering insight into chemotactic dynamics. Our findings highlight the significance of considering cell density effects on bacterial behavior, and the potential for fluorescent metabolite sensors to shed light on the complex emergent dynamics of bacterial communities.

Physiological adaptation in flagellar architecture improves Vibrio alginolyticus chemotaxis in complex environments

Bacteria navigate natural habitats with a wide range of mechanical properties, from the ocean to the digestive tract and soil, by rotating helical flagella like propellers. Species differ in the number, position, and shape of their flagella, but the adaptive value of these flagellar architectures is unclear. Many species traverse multiple types of environments, such as pathogens inside and outside a host. We investigate the hypothesis that flagellar architectures mediate environment-specific benefits in the marine pathogen Vibrio alginolyticus which exhibits physiological adaptation to the mechanical environment. In addition to its single polar flagellum, the bacterium produces lateral flagella in environments that differ mechanically from water. These are known to facilitate surface motility and attachment. We use high-throughput 3D bacterial tracking to quantify chemotactic performance of both flagellar architectures in three archetypes of mechanical environments relevant to the bacterium's native habitats: water, polymer solutions, and hydrogels. We reveal that lateral flagella impede chemotaxis in water by lowering the swimming speed but improve chemotaxis in both types of complex environments. Statistical trajectory analysis reveals two distinct underlying behavioral mechanisms: In viscous solutions of the polymer PVP K90, lateral flagella increase the swimming speed. In agar hydrogels, lateral flagella improve overall chemotactic performance, despite lowering the swimming speed, by preventing trapping in pores. Our findings show that lateral flagella are multipurpose tools with a wide range of applications beyond surfaces. They implicate flagellar architecture as a mediator of environment-specific benefits and point to a rich space of bacterial navigation behaviors in complex environments.

Direct measurement of dynamic attractant gradients reveals breakdown of the Patlak-Keller-Segel chemotaxis model

Chemotactic bacteria not only navigate chemical gradients, but also shape their environments by consuming and secreting attractants. Investigating how these processes influence the dynamics of bacterial populations has been challenging because of a lack of experimental methods for measuring spatial profiles of chemoattractants in real time. Here, we use a fluorescent sensor for aspartate to directly measure bacterially generated chemoattractant gradients during collective migration. Our measurements show that the standard Patlak-Keller-Segel model for collective chemotactic bacterial migration breaks down at high cell densities. To address this, we propose modifications to the model that consider the impact of cell density on bacterial chemotaxis and attractant consumption. With these changes, the model explains our experimental data across all cell densities, offering new insight into chemotactic dynamics. Our findings highlight the significance of considering cell density effects on bacterial behavior, and the potential for fluorescent metabolite sensors to shed light on the complex emergent dynamics of bacterial communities.

Proliferating active matter

The fascinating patterns of collective motion created by autonomously driven particles have fuelled active-matter research for over two decades. So far, theoretical active-matter research has often focused on systems with a fixed number of particles. This constraint imposes strict limitations on what behaviours can and cannot emerge. However, a hallmark of life is the breaking of local cell number conservation by replication and death. Birth and death processes must be taken into account, for example, to predict the growth and evolution of a microbial biofilm, the expansion of a tumour, or the development from a fertilized egg into an embryo and beyond. In this Perspective, we argue that unique features emerge in these systems because proliferation represents a distinct form of activity: not only do the proliferating entities consume and dissipate energy, they also inject biomass and degrees of freedom capable of further self-proliferation, leading to myriad dynamic scenarios. Despite this complexity, a growing number of studies document common collective phenomena in various proliferating soft-matter systems. This generality leads us to propose proliferation as another direction of active-matter physics, worthy of a dedicated search for new dynamical universality classes. Conceptual challenges abound, from identifying control parameters and understanding large fluctuations and nonlinear feedback mechanisms to exploring the dynamics and limits of information flow in self-replicating systems. We believe that, by extending the rich conceptual framework developed for conventional active matter to proliferating active matter, researchers can have a profound impact on quantitative biology and reveal fascinating emergent physics along the way.

Metabolic activity grows in human cancers pushed by phenotypic variability

Different evolutionary processes push cancers to increasingly aggressive behaviors, energetically sustained by metabolic reprogramming. The collective signature emerging from this transition is macroscopically displayed by positron emission tomography (PET). In fact, the most readily PET measure, the maximum standardized uptake value (SUV_max), has been found to have prognostic value in different cancers. However, few works have linked the properties of this metabolic hotspot to cancer evolutionary dynamics. Here, by analyzing diagnostic PET images from 512 patients with cancer, we found that SUV_max scales superlinearly with the mean metabolic activity (SUV_mean), reflecting a dynamic preferential accumulation of activity on the hotspot. Additionally, SUV_max increased with metabolic tumor volume (MTV) following a power law. The behavior from the patients data was accurately captured by a mechanistic evolutionary dynamics model of tumor growth accounting for phenotypic transitions. This suggests that non-genetic changes may suffice to fuel the observed sustained increases in tumor metabolic activity.

Structured foraging of soil predators unveils functional responses to bacterial defenses

Predators and their foraging strategies often determine ecosystem structure and function. Yet, the role of protozoan predators in microbial soil ecosystems remains elusive despite the importance of these ecosystems to global biogeochemical cycles. In particular, amoebae-the most abundant soil protozoan predator of bacteria-remineralize soil nutrients and shape the bacterial community. However, their foraging strategies and their role as microbial ecosystem engineers remain unknown. Here, we present a multiscale approach, connecting microscopic single-cell analysis and macroscopic whole ecosystem dynamics, to expose a phylogenetically widespread foraging strategy, in which an amoeba population spontaneously partitions between cells with fast, polarized movement and cells with slow, unpolarized movement. Such differentiated motion gives rise to efficient colony expansion and consumption of the bacterial substrate. From these insights, we construct a theoretical model that predicts how disturbances to amoeba growth rate and movement disrupt their predation efficiency. These disturbances correspond to distinct classes of bacterial defenses, which allows us to experimentally validate our predictions. All considered, our characterization of amoeba foraging identifies amoeba mobility, and not amoeba growth, as the core determinant of predation efficiency and a key target for bacterial defense systems.

A one-dimensional three-state run-and-tumble model with a 'cell cycle'

We study a one-dimensional three-state run-and-tumble model motivated by the bacterium Caulobacter crescentus which displays a cell cycle between two non-proliferating mobile phases and a proliferating sedentary phase. Our model implements kinetic transitions between the two mobile and one sedentary states described in terms of their number densities, where mobility is allowed with different running speeds in forward and backward direction. We start by analyzing the stationary states of the system and compute the mean and squared-displacements for the distribution of all cells, as well as for the number density of settled cells. The latter displays a surprising super-ballistic scaling [Formula: see text] at early times. Including repulsive and attractive interactions between the mobile cell populations and the settled cells, we explore the stability of the system and employ numerical methods to study structure formation in the fully nonlinear system. We find traveling waves of bacteria, whose occurrence is quantified in a non-equilibrium state diagram.

Collective behavior and nongenetic inheritance allow bacterial populations to adapt to changing environments

Collective behaviors require coordination among a group of individuals. As a result, individuals that are too phenotypically different from the rest of the group can be left out, reducing heterogeneity, but increasing coordination. If individuals also reproduce, the offspring can have different phenotypes from their parent(s). This raises the question of how these two opposing processes-loss of diversity by collective behaviors and generation of it through growth and inheritance-dynamically shape the phenotypic composition of an isogenic population. We examine this question theoretically using collective migration of chemotactic bacteria as a model system, where cells of different swimming phenotypes are better suited to navigate in different environments. We find that the differential loss of phenotypes caused by collective migration is environment-dependent. With cell growth, this differential loss enables migrating populations to dynamically adapt their phenotype compositions to the environment, enhancing migration through multiple environments. Which phenotypes are produced upon cell division depends on the level of nongenetic inheritance, and higher inheritance leads to larger composition adaptation and faster migration at steady state. However, this comes at the cost of slower responses to new environments. Due to this trade-off, there is an optimal level of inheritance that maximizes migration speed through changing environments, which enables a diverse population to outperform a nondiverse one. Growing populations might generally leverage the selection-like effects provided by collective behaviors to dynamically shape their own phenotype compositions, without mutations.

Influence of confinement on the spreading of bacterial populations

The spreading of bacterial populations is central to processes in agriculture, the environment, and medicine. However, existing models of spreading typically focus on cells in unconfined settings—despite the fact that many bacteria inhabit complex and crowded environments, such as soils, sediments, and biological tissues/gels, in which solid obstacles confine the cells and thereby strongly regulate population spreading. Here, we develop an extended version of the classic Keller-Segel model of bacterial spreading via motility that also incorporates cellular growth and division, and explicitly considers the influence of confinement in promoting both cell-solid and cell-cell collisions. Numerical simulations of this extended model demonstrate how confinement fundamentally alters the dynamics and morphology of spreading bacterial populations, in good agreement with recent experimental results. In particular, with increasing confinement, we find that cell-cell collisions increasingly hinder the initial formation and the long-time propagation speed of chemotactic pulses. Moreover, also with increasing confinement, we find that cellular growth and division plays an increasingly dominant role in driving population spreading—eventually leading to a transition from chemotactic spreading to growth-driven spreading via a slower, jammed front. This work thus provides a theoretical foundation for further investigations of the influence of confinement on bacterial spreading. More broadly, these results help to provide a framework to predict and control the dynamics of bacterial populations in complex and crowded environments.

The spreading of bacteria through their environments critically impacts our everyday lives; it can be harmful, underlying the progression of infections and spoilage of foods, or can be beneficial, enabling the delivery of therapeutics, sustaining plant growth, and remediating polluted terrain. In all these cases, bacteria typically inhabit crowded environments, such as soils, sediments, and biological tissues/gels, in which solid obstacles confine the cells and regulate their spreading. However, existing models of spreading typically focus on cells in unconfined settings, and thus are frequently not applicable to cells in more complex environments. Here, we address this gap in knowledge by extending the classic Keller-Segel model of bacterial spreading via motility to also incorporate cellular growth and division, and explicitly consider the influence of confinement. Through numerical simulations of this extended model, we show how confinement fundamentally alters the dynamics and morphology of spreading bacterial populations—in particular, driving a transition from chemotactic spreading of motile cells to growth-driven spreading via a slower, jammed front. These results provide a foundation for further investigations of the influence of confinement on bacterial spreading, both by yielding testable predictions for future experiments, and by providing guidelines to predict and control the dynamics of bacterial populations in complex and crowded environments.

Cellular Sensing Governs the Stability of Chemotactic Fronts

In contexts ranging from embryonic development to bacterial ecology, cell populations migrate chemotactically along self-generated chemical gradients, often forming a propagating front. Here, we theoretically show that the stability of such chemotactic fronts to morphological perturbations is determined by limitations in the ability of individual cells to sense and thereby respond to the chemical gradient. Specifically, cells at bulging parts of a front are exposed to a smaller gradient, which slows them down and promotes stability, but they also respond more strongly to the gradient, which speeds them up and promotes instability. We predict that this competition leads to chemotactic fingering when sensing is limited at too low chemical concentrations. Guided by this finding and by experimental data on E. coli chemotaxis, we suggest that the cells' sensory machinery might have evolved to avoid these limitations and ensure stable front propagation. Finally, as sensing of any stimuli is necessarily limited in living and active matter in general, the principle of sensing-induced stability may operate in other types of directed migration such as durotaxis, electrotaxis, and phototaxis.

The ecological roles of bacterial chemotaxis

How bacterial chemotaxis is performed is much better understood than why. Traditionally, chemotaxis has been understood as a foraging strategy by which bacteria enhance their uptake of nutrients and energy, yet it has remained puzzling why certain less nutritious compounds are strong chemoattractants and vice versa. Recently, we have gained increased understanding of alternative ecological roles of chemotaxis, such as navigational guidance in colony expansion, localization of hosts or symbiotic partners and contribution to microbial diversity by the generation of spatial segregation in bacterial communities. Although bacterial chemotaxis has been observed in a wide range of environmental settings, insights into the phenomenon are mostly based on laboratory studies of model organisms. In this Review, we highlight how observing individual and collective migratory behaviour of bacteria in different settings informs the quantification of trade-offs, including between chemotaxis and growth. We argue that systematically mapping when and where bacteria are motile, in particular by transgenerational bacterial tracking in dynamic environments and in situ approaches from guts to oceans, will open the door to understanding the rich interplay between metabolism and growth and the contribution of chemotaxis to microbial life.

Chemotactic smoothing of collective migration

Collective migration—the directed, coordinated motion of many self-propelled agents—is a fascinating emergent behavior exhibited by active matter with functional implications for biological systems. However, how migration can persist when a population is confronted with perturbations is poorly understood. Here, we address this gap in knowledge through studies of bacteria that migrate via directed motion, or chemotaxis, in response to a self-generated nutrient gradient. We find that bacterial populations autonomously smooth out large-scale perturbations in their overall morphology, enabling the cells to continue to migrate together. This smoothing process arises from spatial variations in the ability of cells to sense and respond to the local nutrient gradient—revealing a population-scale consequence of the manner in which individual cells transduce external signals. Altogether, our work provides insights to predict, and potentially control, the collective migration and morphology of cellular populations and diverse other forms of active matter.

Flocks of birds, schools of fish and herds of animals are all good examples of collective migration, where individuals co-ordinate their behavior to improve survival. This process also happens on a cellular level; for example, when bacteria consume a nutrient in their surroundings, they will collectively move to an area with a higher concentration of food via a process known as chemotaxis.

Several studies have examined how disturbing collective migration can cause populations to fall apart. However, little is known about how groups withstand these interferences. To investigate, Bhattacharjee, Amchin, Alert et al. studied bacteria called Escherichia coli as they moved through a gel towards nutrients.

The E. coli were injected into the gel using a three-dimensional printer, which deposited the bacteria into a wiggly shape that forces the cells apart, making it harder for them to move as a collective group. However, as the bacteria migrated through the gel, they smoothed out the line and gradually made it straighter so they could continue to travel together over longer distances.

Computer simulations revealed that this smoothing process is achieved by differences in how the cells respond to local nutrient levels based on their position. Bacteria towards the front of the group are exposed to more nutrients, causing them to become oversaturated and respond less effectively to the nutrient gradient. As a result, they move more slowly, allowing the cells behind them to eventually catch-up.

These findings reveal a general mechanism in which limitations in how individuals sense and respond to an external signal (in this case local nutrient concentrations) allows them to continue migrating together. This mechanism may apply to other systems that migrate via chemotaxis, as well as groups whose movement is directed by different external factors, such as temperature and light intensity.

Eukaryotic catecholamine hormones influence the chemotactic control of Vibrio campbellii by binding to the coupling protein CheW

Host-emitted stress hormones significantly influence the growth and behavior of various bacterial species; however, their cellular targets have so far remained elusive. Here, we used customized probes and quantitative proteomics to identify the target of epinephrine and the α-adrenoceptor agonist phenylephrine in live cells of the aquatic pathogen Vibrio campbellii. Consequently, we have discovered the coupling protein CheW, which is in the center of the chemotaxis signaling network, as a target of both molecules. We not only demonstrate direct ligand binding to CheW but also elucidate how this affects chemotactic control. These findings are pivotal for further research on hormone-specific effects on bacterial behavior.

In addition to their well-known role as stress-associated catecholamine hormones in animals and humans, epinephrine (EPI) and norepinephrine (NE) act as interkingdom signals between eukaryotic hosts and bacteria. However, the molecular basis of their effects on bacteria is not well understood. In initial phenotypic studies utilizing Vibrio campbellii as a model organism, we characterized the bipartite mode of action of catecholamines, which consists of promotion of growth under iron limitation and enhanced colony expansion on soft agar. In order to identify the molecular targets of the hormones, we designed and synthesized tailored probes for chemical proteomic studies. As the catechol group in EPI and NE acts as an iron chelator and is prone to form a reactive quinone moiety, we devised a photoprobe based on the adrenergic agonist phenylephrine (PE), which solely influenced colony expansion. Using this probe, we identified CheW, located at the core of the chemotaxis signaling network, as a major target. In vitro studies confirmed that EPI, NE, PE, and labetalol, a clinically applied antagonist, bind to purified CheW with affinity constants in the submicromolar range. In line with these findings, exposure of V. campbellii to these adrenergic agonists affects the chemotactic control of the bacterium. This study highlights an effect of eukaryotic signaling molecules on bacterial motility.