The spreading of bacterial colonies at solid-air interfaces is determined by the physico-chemical properties of the involved interfaces. The production of surfactant molecules by bacteria is a widespread strategy that allows the colony to efficiently expand over the substrate. On the one hand, surfactant molecules lower the surface tension of the colony, effectively increasing the wettability of the substrate, which facilitates spreading. On the other hand, gradients in the surface concentration of surfactant molecules result in Marangoni flows that drive spreading. These flows may cause an instability of the circular colony shape and the subsequent formation of fingers. In this work, we study the effect of bacterial surfactant production and substrate wettability on colony growth and shape within the framework of a hydrodynamic thin film model. We show that variations in the wettability and surfactant production are sufficient to reproduce four different types of colony growth, which have been described in the literature, namely, arrested and continuous spreading of circular colonies, slightly modulated front lines and the formation of pronounced fingers.
Bacteria can adjust the structure of colonies and biofilms to enhance their survival rate under external stress. Here, we explore the link between bacterial interaction forces and colony structure. We show that the activity of extracellular pilus motors enhances local ordering and accelerates fusion dynamics of bacterial colonies. The radial distribution function of mature colonies shows local fluid-like order. The degree and dynamics of ordering are dependent on motor activity. At a larger scale, the fusion dynamics of two colonies shows liquid-like behavior whereby motor activity strongly af…
We investigate the emergence of global alignment in colonies of dividing rod-shaped cells under confinement. Using molecular dynamics simulations and continuous modeling, we demonstrate that geometrical anisotropies in the confining environment give rise to imbalance in the normal stresses, which, in turn, drives a collective rearrangement of the cells. This behavior crucially relies on the colony's solid-like mechanical response at short time scales and can be recovered within the framework of active hydrodynamics upon modeling bacterial colonies as growing viscoelastic gels characterized by …
Colonies of bacteria endowed with a pili-based self-propulsion machinery are ideal models for investigating the structure and dynamics of active many-particle systems. We study Neisseria gonorrhoeae colonies with a molecular-dynamics-based approach. A generic, adaptable simulation method for particle systems with fluctuating bond-like interactions is devised. The simulations are employed to investigate growth of bacterial colonies and the dependence of the colony structure on cell-cell interactions. In colonies, pilus retraction enhances local ordering. For colonies consisting of different typ…
Engineering spatially organized biofilms for creating adaptive and sustainable biomaterials is a forthcoming mission of synthetic biology. Existing technologies of patterning biofilm materials suffer limitations associated with the high technical barrier and the requirements of special equipment. Here we present controlled meniscus-driven fluidics, MeniFluidics; an easily implementable technique for patterning living bacterial populations. We demonstrate multiscale patterning of living-colony and biofilm formation with submillimetre resolution. Relying on fast bacterial spreading in liquid cha…
Bacterial colonies are abundant on living and nonliving surfaces and are known to mediate a broad range of processes in ecology, medicine, and industry. Although extensively researched, from single cells to demographic scales, a comprehensive biomechanical picture, highlighting the cell-to-colony dynamics, is still lacking. Here, using molecular dynamics simulations and continuous modeling, we investigate the geometrical and mechanical properties of a bacterial colony growing on a substrate with a free boundary and demonstrate that such an expanding colony self-organizes into a "mosaic" of mic…
The transition from monolayers to multilayered structures in bacterial colonies is a fundamental step in biofilm development. Observed across different morphotypes and species, this transition is triggered within freely growing bacterial microcolonies comprising a few hundred cells. Using a combination of numerical simulations and analytical modeling, here we demonstrate that this transition originates from the competition between growth-induced in-plane active stresses and vertical restoring forces, due to the cell-substrate interactions. Using a simple chainlike colony of laterally confined …
Bacteria commonly live in structured communities that affect human health and influence ecological systems. Heterogeneous populations, such as motile and non-motile populations, often coexist in bacteria communities. Motile subpopulations in microbial communities are believed to be important to dispersal, quest for food, and material transport. However, except in circumstances where motile cells drive colony expansion (e.g. bacterial swarming), the physiological functions of motile subpopulations in bacterial communities are largely unclear. Here we discovered that motile cells in routinely cu…
Commenting on the paper "Swarming Ring Patterns in Bacterial Colonies Exposed to Ultraviolet Radiation" of A.M. Delprato et al., Phys. Rev. Lett 87, 158102 (2001) we point out that their observed ring pattern formation by colonies of soil bacteria Bacillus subtilis exposed to ultra violet (UV) radiation might be caused by the artificial confinement of motile bacteria evolved to live in a 3-dimensional environment to a 2-dimensional geometry. We propose that to investigate the reaction of Bacillus subtilis to UV radiation coming from above, a seminal experiment should have a 3-dimensional setup…
Colonies of rod-shaped bacteria constitute a system of colloidal active matter with nematic properties. As a single initial bacterium multiplies through repeated divisions, the resulting colony quickly loses long-range orientational order, but retains locally ordered domains. At the boundaries of these domains, topological defects emerge, which move around randomly as the colony grows. In both experiments and simulations, we find that these defects are created at a rate that corresponds to the exponential growth of the colony, resulting in a stable defect density. Both this defect density and …
Segregation of populations is a key question in evolution theory. One important aspect is the relation between spatial organization and the population's composition. Here we study a specific example -- sectors in expanding bacterial colonies. Such sectors are spatially segregated sub-populations of mutants. The sectors can be seen both in disk-shaped colonies and in branching colonies. We study the sectors using two models we have used in the past to study bacterial colonies -- a continuous reaction-diffusion model with non-linear diffusion and a discrete ``Communicating Walkers'' model. We fi…
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 {\sl Bacillus subtilis} and {\sl Serratia marcescens}, two model swarm species th…
Many mature bacterial colonies and biofilms are complex three-dimensional (3D) structures. One key step in their developmental program is a transition from a two-dimensional (2D) monolayer into a 3D architecture. Despite the importance of controlling the growth of microbial colonies and biofilms in a variety of medical and industrial settings, the underlying physical mechanisms behind single-cell dynamics, collective behaviors of densely-packed cells, and 3D complex colony expansion remain largely unknown. In this work, we explore the mechanisms behind the 2D-to-3D transition of motile Pseudom…
We discuss the structure of the equilibrium states of a regularized Keller-Segel model describing the chemotaxis of bacterial populations. We consider the limit of high degradation of the secreted chemical where analytical results can be obtained. Below a critical effective temperature, the system experiences a second order phase transition from a homogeneous phase to an inhomogeneous phase formed by two domains with uniform concentration separated by a thin interface (domain wall). We study the properties of the interface and determine the bifurcation between a circular shape (spot) and a str…
The emergent spatial patterns generated by growing bacterial colonies have been the focus of intense study in physics during the last twenty years. Both experimental and theoretical investigations have made possible a clear qualitative picture of the different structures that such colonies can exhibit, depending on the medium on which they are growing. However, there are relatively few quantitative descriptions of these patterns. In this paper, we use a mechanistically detailed simulation framework to measure the scaling exponents associated with the advancing fronts of bacterial colonies on h…
We present a new reaction-diffusion model for chiral branching growth of colonies of the bacteria Paenibacillus dendritiformis. In our model the bacteria are represented by a density field with non-linear diffusion and a complex scalar field which represents bacterial orientation. The orientation field introduces anisotropy into the flux of bacteria, representing self-propulsion along their long axes. The model can also reproduce tip-splitting growth of other strains (shorter bacteria) of the same species. The model can capture changes of small number of bacteria, thus it can be used to study …
Models based on surfactant driven instabilities have been employed to describe pattern formation by swarming bacteria. However, by definition, such models cannot account for the effect of bacterial sensing and decision making. Here we present a more complete model for bacterial pattern formation which accounts for these effects by coupling active bacterial motility to the passive fluid dynamics. We experimentally identify behaviours which cannot be captured by previous models based on passive population dispersal and show that a more accurate description is provided by our model. It is seen th…
Anaerobic processes (e.g., methanogenesis and fermentation) largely contribute to element cycling and natural contaminant attenuation/mobilization, even in well-oxygenated porous environments, such as shallow aquifers. This paradox is commonly explained by the occurrence of small-scale anoxic microenvironments generated by the coupling of bacterial respiration and the heterogeneous oxygen (O2) transport by porewater. Such microenvironments allow facultatively and obligately anaerobic bacteria to proliferate in oxic environments. Microenvironment dynamics are still poorly understood due to the …
Bacterial conglomerates such as biofilms and microcolonies are ubiquitous in nature and play an important role in industry and medicine. In contrast to well-mixed, diluted cultures routinely used in microbial research, bacteria in a microcolony interact mechanically with one another and with the substrate to which they are attached. Despite their ubiquity, little is known about the role of such mechanical interactions on growth and biological evolution of microbial populations. Here we use a computer model of a microbial colony of rod-shaped cells to investigate how physical interactions betwe…
Many bacteria rely on active cell appendages, such as type IV pili, to move over substrates and interact with neighboring cells. Here, we study the motion of individual cells and bacterial colonies, mediated by the collective interactions of multiple pili. It was shown experimentally that the substrate motility of Neisseria gonorrhoeae cells can be described as a persistent random walk with a persistence length that exceeds the mean pili length. Moreover, the persistence length increases for a higher number of pili per cell. With the help of a simple, tractable stochastic model, we test whethe…
Microbial colonies cultured on agar Petri dishes have become a model system to study biological evolution in populations expanding in space. Processes such as clonal segregation and gene surfing have been shown to be affected by interactions between microbial cells and their environment. In this work we investigate the role of mechanical interactions such as cell-surface adhesion. We compare two strains of the bacterium E. coli: a wild-type strain and a "shaved" strain that adheres less to agar. We show that the shaved strain has a selective advantage over the wild type: although both strains …
Colonies of bacteria grown on thin agar plate exhibit fractal patterns as a result of adaptation to their environments. The bacterial colony pattern formation is regulated crucially by chemotaxis, the movement of cells along a chemical concentration gradient. Here, the dynamics of pattern formation in bacterial colony is investigated theoretically through a continuum model that considers chemotaxis. In the case of the gradient sensed by the bacterium is nearly uniform, the bacterial colony patterns are self-similar, which they look the same at every scale. The scaling law of the bacterial colo…
Various bacterial strains (e.g. strains belonging to the genera Bacillus, Paenibacillus, Serratia and Salmonella) exhibit colonial branching patterns during growth on poor semi-solid substrates. These patterns reflect the bacterial cooperative self-organization. Central part of the cooperation is the collective formation of lubricant on top of the agar which enables the bacteria to swim. Hence it provides the colony means to advance towards the food. One method of modeling the colonial development is via coupled reaction-diffusion equations which describe the time evolution of the bacterial de…
In the growth of bacterial colonies, a great variety of complex patterns are observed in experiments, depending on external conditions and the bacterial species. Typically, existing models employ systems of reaction-diffusion equations or consist of growth processes based on rules, and are limited to a discrete lattice. In contrast, the two-dimensional model proposed here is an off-lattice simulation, where bacteria are modelled as rigid circles and nutrients are point-like, Brownian particles. Varying the nutrient diffusion and concentration, we simulate a wide range of morphologies compatibl…
It is widely accepted that population genetics theory is the cornerstone of evolutionary analyses. Empirical tests of the theory, however, are challenging because of the complex relationships between space, dispersal, and evolution. Critically, we lack quantitative validation of the spatial models of population genetics. Here we combine analytics, on and off-lattice simulations, and experiments with bacteria to perform quantitative tests of the theory. We study two bacterial species, the gut microbe Escherichia coli and the opportunistic pathogen Pseudomonas aeruginosa, and show that spatio-ge…
University of Luxembourg（卢森堡大学）；Indian Institute of Technology Delhi（德里印度理工学院）；Heinrich-Heine-Universität Düsseldorf（杜塞尔多夫海因里希·海涅大学）；Max Rubner-Institut（马克斯·鲁布纳研究所）
We study the spreading of a bacterial colony undergoing turbulent like collective motion. We present two minimalistic models to investigate the interplay between population growth and coherent structures arising from turbulence. Using Direct Numerical Simulation (DNS) of the proposed models we find that turbulence has two prominent effects on the spatial growth of the colony: (a) the front speed is enhanced, and (b) the front gets crumpled. Both these effects, which we highlight by using statistical tools, are markedly different in our two models. We also show that the crumpled front structure…
Growing tissue and bacterial colonies are active matter systems where cell divisions and cellular motion generate active stress. Although they operate in the non-equilibrium regime, these biological systems can form large-scale ordered structures such as nematically aligned cells, topological defects, and fingerings. Mechanical instabilities also play an essential role during growth by generating large structural folding. How active matter dynamics and mechanical instabilities together develop large-scale order in growing tissue is not well understood. Here, we use chain forming Bacillus subti…
Many bacterial species exchange signaling molecules to coordinate population-wide responses. For this process known as quorum sensing the concentration of the respective molecules is crucial. Here we consider the interaction between spatially distributed bacterial colonies so that the spreading of the signaling molecules in space becomes important. The exponential growth of the signal-producing populations and the corresponding increase in signaling molecule production result in an exponential concentration profile that spreads with uniform speed. The theoretical predictions are supported by e…
The front of a compact bacterial colony growing on a Petri dish is a paradigmatic instance of non-equilibrium fluctuations in the celebrated Eden, or Kardar-Parisi-Zhang (KPZ), universality class. While in many experiments the scaling exponents crucially differ from the expected KPZ values, the source of this disagreement has remained poorly understood. We have performed growth experiments with B. subtilis 168 and E. coli ATCC 25922 under conditions leading to compact colonies in the classically-alleged Eden regime, where individual motility is suppressed. Non-KPZ scaling is indeed observed fo…
It has been argued that there is biological and modeling evidence that a non-linear diffusion coefficient of the type D(b) = D_0 b^{k} underlies the formation of a number of growth patterns of bacterial colonies. We study a reaction-diffusion system with a non-linear diffusion coefficient introduced by Ben-Jacob et al. Due to the fact that the bacterial diffusion coefficient vanishes when the bacterial density b -> 0, the standard linear stability analysis for fronts cannot be used. We introduce an extension of the stability analysis which can be applied to such singular fronts, map out the re…
Rod-shaped bacteria, such as Escherichia coli, commonly live forming mounded colonies. They initially grow two-dimensionally on a surface and finally achieve three-dimensional growth. While it was recently reported that three-dimensional growth is promoted by topological defects of winding number $+1/2$ in populations of motile bacteria, how cellular alignment plays a role in non-motile cases is largely unknown. Here, we investigate the relevance of topological defects in colony formation processes of non-motile E. coli populations, and found that both $\pm 1/2$ topological defects contribute …
We study the migration of chemotactic wild-type Escherichia coli populations in semisolid (soft) agar in the concentration range C = 0.15-0.5% (w/v). For C < 0.35%, expanding bacterial colonies display characteristic chemotactic rings. At C = 0.35%, however, bacteria migrate as broad circular bands rather than sharp rings. These are growth/diffusion waves arising because of suppression of chemotaxis by the agar and have not been previously reported experimentally to our knowledge. For C = 0.4-0.5%, expanding colonies do not span the depth of the agar and develop pronounced front instabilities.…
