Paenibacillus dendritiformis bacterial colony growth depends on surfactant but not on bacterial motion

Simulation of head-tail biofilm streamer growth based on immersed boundary method

Biofilms are subjected to various forces in the fluid field, as a result, the biofilm forms a head-tail structure known as a streamer to reduce pressure differential resistance. To characterize biofilm growth in fluid, we establish a head-tail biofilm streamer growth model based on the immersed boundary method using MATLAB software, and simulate streamer growth in various environmental conditions to explore the factors affecting its growth. Firstly, we found that a higher flow velocity makes the streamer grow faster and thereby produce more biomass. Secondly, we explored the effect of the position of nutrient source on the streamer growth, found that when the nutrient source overlaps with the streamer, its length is longer than when the nutrient source and the streamer are mismatched. Further we found that the Young's modulus of the streamer also influences its growth length. Streamers with small Young's modulus were more likely to deform, making them grow longer than the streamers with large Young's modulus. Finally, we determined the relationship between the tail length and the head diameter of the streamer through mechanical analysis, and found that there is an optimal ratio of the tail length to the head diameter which exposes the streamer to the minimum drag in the fluid field.

Immobility of isolated swarmer cells due to local liquid depletion

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

VirB11, a traffic ATPase, mediated flagella assembly and type IV pilus morphogenesis to control the motility and virulence of Xanthomonas albilineans

Xanthomonas albilineans (Xal) is a gram-negative bacterial pathogen responsible for developing sugarcane leaf scald disease, which engenders significant economic losses within the sugarcane industry. In the current study, homologous recombination exchange was carried out to induce mutations within the virB/D4-like type IV secretion system (T4SS) genes of Xal. The results revealed that the virB11-deletion mutant (ΔvirB11) exhibited a loss in swimming and twitching motility. Application of transmission electron microscopy analysis further demonstrated that the ΔvirB11 failed to develop flagella formation and type IV pilus morphology and exhibited reduced swarming behaviour and virulence. However, these alterations had no discernible impact on bacterial growth. Comparative transcriptome analysis between the wild-type Xal JG43 and the deletion-mutant ΔvirB11 revealed 123 differentially expressed genes (DEGs), of which 28 and 10 DEGs were notably associated with flagellar assembly and chemotaxis, respectively. In light of these findings, we postulate that virB11 plays an indispensable role in regulating the processes related to motility and chemotaxis in Xal.

Unique behavioral patterns of wandering colonies of Brevibacillus thermoruber on agar plates

Brevibacillus thermoruber strain Nabari cells grow as widely spreading dendritic colonies on reasoner's 2A-agar (1.5%) plates at around 55°C but as small motile colonies at 37°C. Motile colonies can be divided into colonies that move in straight or curved lines over long distances (wandering colonies), and colonies that rotate at a fixed location (rotating colonies). The addition of surfactant to the agar medium greatly increased the frequency of wandering colonies and facilitated the study of such colonies. The morphology of the wandering colonies varied: circular at the tip and pointed at the back, lemon-shaped with pointed ends, crescent-shaped, bullet-shaped, fish-like, and so on. A single colony may split into multiple colonies as it moves, or multiple colonies may merge into a single colony. The most surprising aspect of the movement of wandering colonies was that when a moving colony collides with another colony, it sometimes does not make a U-turn, but instead retreats straight back, as if bouncing back. The migration mechanisms of wandering colonies are discussed based on optical microscopic observations of swimming patterns of single cells in water and scanning electron microscopy of the arrangement of bacterial cells in wandering colonies.

Involvement of Flagellin in Kin Recognition between Bacillus velezensis Strains

Kin discrimination in nature is an effective way for bacteria to stabilize population cooperation and maintain progeny benefits. However, so far, the research on kin discrimination for Bacillus still has concentrated on "attack and defense" between cells and diffusion-dependent molecular signals of quorum sensing, kin recognition in Bacillus, however, has not been reported. To determine whether flagellar is involve in the kin recognition of Bacillus, we constructed Bacillus velezensis SQR9 assembled with flagellin of its kin and non-kin strains, and performed a swarm boundary assay with SQR9, then analyzed sequence variation of flagellin and other flagellar structural proteins in B. velezensis genus. Our results showed that SQR9 assembled with flagellin of non-kin strains was more likely to form a border phenotype with wild-type strain SQR9 in swarm assay than that of kin strains, and that non-kin strains had greater variation in flagellin than kin strains. In B. velezensis, these variations in flagellin were prevalent and had evolved significantly faster than other flagellar structural proteins. Therefore, we proposed that flagellin is an effective tool partly involved in the kin recognition of B. velezensis strains. IMPORTANCE Kin selection plays an important role in stabilizing population cooperation and maintaining the progeny benefits for bacteria in nature. However, to date, the role of flagellin in kin recognition in Bacillus has not been reported. By using rhizospheric Bacillus velezensis SQR9, we accomplished flagellin region interchange among its related strains, and show that flagellin acts as a mediator to distinguish kin from non-kin in B. velezensis. We demonstrated the polymorphism of flagellin in B. velezensis through alignment analysis of flagellin protein sequences. Therefore, it was proposed that flagellin was likely to be an effective tool for mediating kin recognition in B. velezensis.

The role of biofilm matrix composition in controlling colony expansion and morphology

Biofilms are biological viscoelastic gels composed of bacterial cells embedded in a self-secreted polymeric extracellular matrix (ECM). In environmental settings, such as in the rhizosphere and phyllosphere, biofilm colonization occurs at the solid-air interface. The biofilms' ability to colonize and expand over these surfaces depends on the formation of osmotic gradients and ECM viscoelastic properties. In this work, we study the influence of biofilm ECM components on its viscoelasticity and expansion, using the model organism Bacillus subtilis and deletion mutants of its three major ECM components, TasA, EPS and BslA. Using a multi-scale approach, we quantified macro-scale viscoelasticity and expansion dynamics. Furthermore, we used a microsphere assay to visualize the micro-scale expansion patterns. We find that the viscoelastic phase angle Φ is likely the best viscoelastic parameter correlating to biofilm expansion dynamics. Moreover, we quantify the sensitivity of the biofilm to changes in substrate water potential as a function of ECM composition. Finally, we find that the deletion of ECM components significantly increases the coherence of micro-scale colony expansion patterns. These results demonstrate the influence of ECM viscoelasticity and substrate water potential on the expansion of biofilm colonies on wet surfaces at the air-solid interface, commonly found in natural environments.

Swarming behavior of a novel strain of Brevibacillus thermoruber

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

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

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

Physical characteristics of mixed-species swarming colonies

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

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

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

Bacterial motility: machinery and mechanisms

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

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.

An expanding bacterial colony forms a depletion zone with growing droplets

Many species of bacteria have developed effective means to spread on solid surfaces. This study focuses on the expansion of Pseudomonas aeruginosa on an agar gel surface under conditions of minimal evaporation. We report the occurrence and spread of a depletion zone within an expanded colony, where the bacteria laden film becomes thinner. The depletion zone is colocalized with a higher concentration of rhamnolipids, the biosurfactants that are produced by the bacteria and accumulate in the older region of the colony. With continued growth in population, dense bacterial droplets occur and coalesce in the depletion zone, displaying remarkable fluid dynamic behavior. Whereas expansion of a central depletion zone requires activities of live bacteria, new zones can be seeded elsewhere by adding rhamnolipids. These depletion zones due to the added surfactants expand quickly, even on plates covered by bacteria that have been killed by ultraviolet light. We explain the observed properties based on considerations of bacterial growth and secretion, osmotic swelling, fluid volume expansion, interfacial fluid dynamics involving Marangoni and capillary flows, and cell-cell cohesion.

THE EVOLVING WRINKLE PATTERN OF THE BACILLUS SUBTILIS BIOFILM PROVIDING MORE LIVING SPACE FOR CELLS

The biofilm wrinkle evolution is the growth mechanism by which bacteria regulate their physiological state in response to the environmental change. We use the parameter of surface complexity to describe different wrinkle patterns. The surface complexity is defined that the biofilm surface area contact with the air is divided by the projected area of the biofilm. We find that the biofilm surface complexity variation is positively proportional to the number of spores. Although each wrinkle pattern has various wrinkle thickness and width, surface complexities of some patterns are almost same, which guarantees cells have enough living space. Through the observation of the growth of the damaged biofilm, we further find that the biofilm expansion along the circumferential direction is faster than that along radial direction, which means that the internal stress along the circumferential direction contributes the wrinkle formation. Our work provides a new perspective to study biofilm morphologies, and relates the morphology evolution with phenotypes in the Bacillus subtilis biofilm.

Electroactivity of the Gram-positive bacterium Paenibacillus dendritiformis MA-72

Whilst most of the microorganisms recognized as exoelectrogens are Gram-negative bacteria, the electrogenicity of Gram-positive bacteria has not been sufficiently explored. In this study, the putative electroactivity of the Gram-positive Paenibacillus dendritiformis MA-72 strain, isolated from the anodic biofilm of long-term operated Sediment Microbial Fuel Cell (SMFC), has been investigated. SEM observations show that under polarization conditions P. dendritiformis forms a dense biofilm on carbon felt electrodes. A current density, reaching 5 mA m^-2, has been obtained at a prolonged applied potential of -0.195 V (vs. SHE), which represents 35% of the value achieved with the SMFC. The voltammetric studies confirm that the observed Faradaic current is associated with the electrochemical activity of the bacterial biofilm and not with a soluble redox mediator. The results suggest that a direct electron transfer takes place through the conductive extracellular polymer matrix via pili/nanowires and multiple cytochromes. All these findings demonstrate for the first time that the Gram-positive Paenibacillus dendritiformis MA-72 is a new exoelectrogenic bacterial strain.

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

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

Rivalry in Bacillus subtilis colonies: enemy or family?

Two colonies of Bacillus subtilis of identical strains growing adjacent to each other on an agar plate exhibit two distinct types of interactions: they either merge as they grow or demarcation occurs leading to formation of a line of demarcation at the colony fronts. The nature of this interaction depends on the agar concentration in the growth medium and the initial separation between the colonies. When the agar concentration was 0.67% or lower, the two sibling colonies were found to always merge. At 1% or higher concentrations, the colonies formed a demarcation line only when their initial separation was 20 mm or higher. Interactions of a colony with solid structures and liquid drops have indicated that biochemical factors rather than the presence of physical obstacles are responsible for the demarcation line formation. A reaction diffusion model has been formulated to predict if two sibling colonies will form a demarcation line under given agar concentration and initial separation. The model prediction agrees well with experimental findings and generates a dimensionless phase diagram containing merging and demarcation regimes. The phase diagram is in terms of a dimensionless initial separation, d[combining macron], and a dimensionless diffusion coefficient, D[combining macron], of the colonies. The phase boundary between the two interaction regimes can be described by a power law relation between d[combining macron] and D[combining macron].

Increasing access to microfluidics for studying fungi and other branched biological structures

BACKGROUND

Microfluidic systems are well-suited for studying mixed biological communities for improving industrial processes of fermentation, biofuel production, and pharmaceutical production. The results of which have the potential to resolve the underlying mechanisms of growth and transport in these complex branched living systems. Microfluidics provide controlled environments and improved optical access for real-time and high-resolution imaging studies that allow high-content and quantitative analyses. Studying growing branched structures and the dynamics of cellular interactions with both biotic and abiotic cues provides context for molecule production and genetic manipulations. To make progress in this arena, technical and logistical barriers must be overcome to more effectively deploy microfluidics in biological disciplines. A principle technical barrier is the process of assembling, sterilizing, and hydrating the microfluidic system; the lack of the necessary equipment for the preparatory process is a contributing factor to this barrier. To improve access to microfluidic systems, we present the development, characterization, and implementation of a microfluidics assembly and packaging process that builds on self-priming point-of-care principles to achieve "ready-to-use microfluidics."

RESULTS

We present results from domestic and international collaborations using novel microfluidic architectures prepared with a unique packaging protocol. We implement this approach by focusing primarily on filamentous fungi; we also demonstrate the utility of this approach for collaborations on plants and neurons. In this work we (1) determine the shelf-life of ready-to-use microfluidics, (2) demonstrate biofilm-like colonization on fungi, (3) describe bacterial motility on fungal hyphae (fungal highway), (4) report material-dependent bacterial-fungal colonization, (5) demonstrate germination of vacuum-sealed Arabidopsis seeds in microfluidics stored for up to 2 weeks, and (6) observe bidirectional cytoplasmic streaming in fungi.

CONCLUSIONS

This pre-packaging approach provides a simple, one step process to initiate microfluidics in any setting for fungal studies, bacteria-fungal interactions, and other biological inquiries. This process improves access to microfluidics for controlling biological microenvironments, and further enabling visual and quantitative analysis of fungal cultures.

Mass Spectrometry Uncovers the Role of Surfactin as an Interspecies Recruitment Factor

Microbes use metabolic exchange to sense and respond to their changing environment. Surfactins, produced by Bacillus subtilis, have been extensively studied for their role in biofilm formation, biosurfactant properties, and antimicrobial activity, affecting the surrounding microbial consortia. Using mass spectrometry, we reveal that Paenibacillus dendritiformis, originally isolated with B. subtilis, is not antagonized by the presence of surfactins and is actually attracted to them. We demonstrate here for the first time that P. dendritiformis is also actively degrading surfactins produced by B. subtilis and accumulating the degradation products that serve as territorial markers. This new attribute as an attractant of selected microbes and the conversion into a deterrent highlight the diverse role natural products have in shaping the environment and establishing mixed communities.

Plastic multicellular development of Myxococcus xanthus: genotype-environment interactions in a physical gradient

In order to investigate the contribution of the physical environment to variation in multicellular development of Myxococcus xanthus, phenotypes developed by different genotypes in a gradient of substrate stiffness conditions were quantitatively characterized. Statistical analysis showed that plastic phenotypes result from the genotype, the substrate conditions and the interaction between them. Also, phenotypes were expressed in two distinguishable scales, the individual and the population levels, and the interaction with the environment showed scale and trait specificity. Overall, our results highlight the constructive role of the physical context in the development of microbial multicellularity, with both ecological and evolutionary implications.

A statistical physics view of swarming bacteria

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

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

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

Modelling the microbial dynamics and antimicrobial resistance development of Listeria in viscoelastic food model systems of various structural complexities

Minimal processing for microbial decontamination, such as the use of natural antimicrobials, is gaining interest in the food industry as these methods are generally milder than conventional processing, therefore better maintaining the nutritional content and sensory characteristics of food products. The aim of this study was to quantify the impact of (i) structural composition and complexity, (ii) growth location and morphology, and (iii) the natural antimicrobial nisin, on the microbial dynamics of Listeria innocua. More specifically, viscoelastic food model systems of various compositions and internal structure were developed and characterised, i.e. monophasic Xanthan gum-based and biphasic Xanthan gum/Whey protein-based viscoelastic systems. The microbial dynamics of L. innocua at 10 °C, 30 °C and 37 °C were monitored and compared for planktonic growth in liquid, or in/on (immersed or surface colony growth) the developed viscoelastic systems, with or without a sublethal concentration of nisin. Microscopy imaging was used to determine the bacterial colony size and spatial organisation in/on the viscoelastic systems. Selective growth of L. innocua on the protein phase of the developed biphasic system was observed for the first time. Additionally, significant differences were observed in the colony size and distribution in the monophasic Xanthan gum-based systems depending on (i) the type of growth (surface/immersed) and (ii) the Xanthan gum concentration. Furthermore, the system viscosity in monophasic Xanthan gum-based systems had a protective role against the effects of nisin for immersed growth, and a further inhibitory effect for surface growth at a suboptimal temperature (10 °C). These findings give a systematic quantitative insight on the impact of nisin as an environmental challenge on the growth and spatial organisation of L. innocua, in viscoelastic food model systems of various structural compositions/complexities. This study highlights the importance of accounting for system structural composition/complexity when designing minimal food processing methods with natural antimicrobials.

Swarming motility and biofilm formation of Paenibacillus larvae, the etiological agent of American Foulbrood of honey bees (Apis mellifera)

American Foulbrood is a worldwide distributed, fatal disease of the brood of the Western honey bee (Apis mellifera). The causative agent of this fatal brood disease is the Gram-positive, spore-forming bacterium Paenibacillus larvae, which can be classified into four different genotypes (ERIC I-IV), with ERIC I and II being the ones isolated from contemporary AFB outbreaks. P. larvae is a peritrichously flagellated bacterium and, hence, we hypothesized that P. larvae is capable of coordinated and cooperative multicellular behaviors like swarming motility and biofilm formation. In order to analyze these behaviors of P. larvae, we firstly established appropriate functional assays. Using these assays we demonstrated that P. larvae ERIC II, but not P. larvae ERIC I, was capable of swarming. Swarming motility was hampered in a P. larvae ERIC II-mutant lacking production of paenilarvin, an iturin-like lipopeptide exclusively expressed by this genotype. Both genotypes were able to form free floating biofilm aggregates loosely attached to the walls of the culture wells. Visualizing the biofilms by Congo red and thioflavin S staining suggested structural differences between the biofilms formed. Biofilm formation was shown to be independent from paenilarvin production because the paenilarvin deficient mutant was comparably able to form a biofilm.

Microbial multicellular development: mechanical forces in action

Multicellular development occurs in diverse microbial lineages and involves the complex interaction among biochemical, physical and ecological factors. We focus on the mechanical forces that appear to be relevant for the scale and material qualities of individual cells and small cellular conglomerates. We review the effects of such forces on the development of some paradigmatic microorganisms, as well as their overall consequences in multicellular structures. Microbes exhibiting multicellular development have been considered models for the evolutionary transition to multicellularity. Therefore, we discuss how comparative, integrative and dynamic approaches to the mechanical effects involved in microbial development can provide valuable insights into some of the principles behind the evolutionary transition to multicellularity.

Modelling of surfactant-driven front instabilities in spreading bacterial colonies

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.

Assessing Travel Conditions: Environmental and Host Influences On Bacterial Surface Motility

The degree to which surface motile bacteria explore their surroundings is influenced by aspects of their local environment. Accordingly, regulation of surface motility is controlled by numerous chemical, physical, and biological stimuli. Discernment of such regulation due to these multiple cues is a formidable challenge. Additionally inherent ambiguity and variability from the assays used to assess surface motility can be an obstacle to clear delineation of regulated surface motility behavior. Numerous studies have reported single environmental determinants of microbial motility and lifestyle behavior but the translation of these data to understand surface motility and bacterial colonization of human host or environmental surfaces is unclear. Here, we describe the current state of the field and our understanding of exogenous factors that influence bacterial surface motility.

Capillary flow and mechanical buckling in a growing annular bacterial colony

A growing bacterial colony is a dense suspension of an increasing number of cells capable of individual as well as collective motion. After inoculating Pseudomonas aeruginosa over an annular area on an agar plate, we observe the growth and spread of the bacterial population, and model the process by considering the physical effects that account for the features observed. Over a course of 10-12 hours, the majority of bacteria migrate to and accumulate at the edges. We model the capillary flow induced by imbalanced evaporation flux as the cause for the accumulation, much like the well-known coffee stain phenomenon. Simultaneously, periodic buckles or protrusions occur at the inner edge. These buckles indicate that the crowding bacteria produce a jam, transforming the densely packed population at the inner edge to a solid state. The continued bacterial growth produces buckles. Subsequently, a ring of packed bacteria behind the inner edge detach from it and break into pieces, forming bacterial droplets. These droplets slowly coalesce while they continually grow and collectively surf on the agar surface in the region where the colony had previously spread over. Our study shows a clear example of how fluid dynamics and elasto-mechanics together govern the bacterial colony pattern evolution.

Continuous versus Arrested Spreading of Biofilms at Solid-Gas Interfaces: The Role of Surface Forces

We introduce and analyze a model for osmotically spreading bacterial colonies at solid-air interfaces that includes wetting phenomena, i.e., surface forces. The model is based on a hydrodynamic description for liquid suspensions which is supplemented by bioactive processes. We show that surface forces determine whether a biofilm can expand laterally over a substrate and provide experimental evidence for the existence of a transition between continuous and arrested spreading for Bacillus subtilis biofilms. In the case of arrested spreading, the lateral expansion of the biofilm is confined, albeit the colony is biologically active. However, a small reduction in the surface tension of the biofilm is sufficient to induce spreading. The incorporation of surface forces into our hydrodynamic model allows us to capture this transition in biofilm spreading behavior.

Role of tumbling in bacterial swarming

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

Pseudomonas lactis sp. nov. and Pseudomonas paralactis sp. nov., isolated from bovine raw milk

Five strains, designated WS 4672T, WS 4998, WS 4992T, WS 4997 and WS 5000, isolated from bovine raw milk formed two individual groups in a phylogenetic analysis. The most similar species on the basis of 16S rRNA gene sequences were Pseudomonas azotoformans IAM 1603T, Pseudomonas gessardii CIP 105469T and Pseudomonas libanensis CIP 105460T showing 99.7-99.6 % similarity. Using rpoD gene sequences Pseudomonas veronii LMG 17761T (93.3 %) was most closely related to strain WS 4672T and Pseudomonas libanensis CIP 105460T to strain WS 4992T (93.3 %). The five strains could be differentiated from their closest relatives and from each other by phenotypic and chemotaxonomic characterization and ANIb values calculated from draft genome assemblies. ANIb values of strains WS 4992T and WS4671T to the closest relatives are lower than 90 %. The major cellular polar lipids of both strains are phosphatidylethanolamine, phosphatidylglycerol, a phospholipid and diphosphatidylglycerol, and their major quinone is Q-9. The DNA G+C content of strains WS 4992T and WS 4672T were 60.0  and 59.7  mol%, respectively. Based on these genotypic and phenotypic traits two novel species of the genus Pseudomonas are proposed: Pseudomonas lactis sp. nov. [with type strain WS 4992T (=DSM 29167T=LMG 28435T) and the additional strains WS 4997 and WS 5000], and Pseudomonasparalactis sp. nov. [with type strain WS 4672T (=DSM 29164T=LMG 28439T) and additional strain WS 4998].

Anomalous Fluctuations in the Orientation and Velocity of Swarming Bacteria

Simultaneous acquisition of phase-contrast light microscopy and fluorescently labeled bacteria, moving within a dense swarm, reveals the intricate interactions between cells and the collective flow around them. By comparing wild-type and immotile cells embedded in a dense wild-type swarm, the effect of the active thrust generated by the flagella can be singled out. It is shown that while the distribution of angles among cell velocity, cell orientation, and the local flow around it is Gaussian-like for immotile bacteria, wild-type cells exhibit anomalous non-Gaussian deviations and are able to move in trajectories perpendicular to the collective flow. Thus, cells can maneuver or switch between local streams and jets. A minimal model describing bacteria as hydrodynamic force dipoles shows that steric effects, hydrodynamics interactions, and local alignments all have to be taken into account to explain the observed dynamics. These findings shed light on the physical mechanisms underlying bacterial swarming and the balance between individual and collective dynamics.

Active depinning of bacterial droplets: The collective surfing of Bacillus subtilis

How systems are endowed with migration capacity is a fascinating question with implications ranging from the design of novel active systems to the control of microbial populations. Bacteria, which can be found in a variety of environments, have developed among the richest set of locomotion mechanisms both at the microscopic and collective levels. Here, we uncover, experimentally, a mode of collective bacterial motility in humid environment through the depinning of bacterial droplets. Although capillary forces are notoriously enormous at the bacterial scale, even capable of pinning water droplets of millimetric size on inclined surfaces, we show that bacteria are able to harness a variety of mechanisms to unpin contact lines, hence inducing a collective slipping of the colony across the surface. Contrary to flagella-dependent migration modes like swarming, we show that this much faster "colony surfing" still occurs in mutant strains of Bacillus subtilis lacking flagella. The active unpinning seen in our experiments relies on a variety of microscopic mechanisms, which could each play an important role in the migration of microorganisms in humid environment.

Influence of Physical Effects on the Swarming Motility of Pseudomonas aeruginosa

Many species of bacteria can spread over a moist surface via a particular form of collective motion known as "surface swarming". This form of motility is typically studied by inoculating bacteria on a gel formed by 0.4-1.5% agar, which contains essential nutrients for their growth and proliferation. Using Pseudomonas aeruginosa and its pili-less mutant, ΔPilA, we investigate physical factors that either facilitate or restrict the swarming motility, measured by the rate of increase in area covered by a spreading bacterial colony, i.e., a swarm. The wild-type colony spreads over the agar surface in highly branched structures. The pili-less mutant fills up the area more fully as it spreads, but it also produces numerous and fragmented branches, or tendrils, at the swarm front. Whereas additional surfactants enhance swarming, increasing the agar percentage, adding extra salt or sugar or incorporating viscous agents in the agar matrix all decrease swarming, supporting the conclusion that swarming motility is restricted by the surface tension at the swarm front and swarm growth is limited by the rate of water supply from within the agar gel. The physical basis elaborated through this study provides a useful framework for understanding the swarming behavior of numerous species of bacteria.

Effect of Cell Aspect Ratio on Swarming Bacteria

Swarming bacteria collectively migrate on surfaces using flagella, forming dynamic whirls and jets that consist of millions of individuals. Because some swarming bacteria elongate prior to actual motion, cell aspect ratio may play a significant role in the collective dynamics. Extensive research on self-propelled rodlike particles confirms that elongation promotes alignment, strongly affecting the dynamics. Here, we study experimentally the collective dynamics of variants of swarming Bacillus subtilis that differ in length. We show that the swarming statistics depends on the aspect ratio in a critical, fundamental fashion not predicted by theory. The fastest motion was obtained for the wild-type and variants that are similar in length. However, shorter and longer cells exhibit anomalous, non-Gaussian statistics and nonexponential decay of the autocorrelation function, indicating lower collective motility. These results suggest that the robust mechanisms to maintain aspect ratios may be important for efficient swarming motility. Wild-type cells are optimal in this sense.

Dynamics of Snake-like Swarming Behavior of Vibrio alginolyticus

Swarming represents a special case of bacterial behavior where motile bacteria migrate rapidly and collectively on surfaces. Swarming and swimming motility of bacteria has been studied well for rigid, self-propelled rods. In this study we report a strain of Vibrio alginolyticus, a species that exhibits similar collective motility but a fundamentally different cell morphology with highly flexible snake-like swarming cells. Investigating swarming dynamics requires high-resolution imaging of single cells with coverage over a large area: thousands of square microns. Researchers previously have employed various methods of motion analysis but largely for rod-like bacteria. We employ temporal variance analysis of a short time-lapse microscopic image series to capture the motion dynamics of swarming Vibrio alginolyticus at cellular resolution over hundreds of microns. Temporal variance is a simple and broadly applicable method for analyzing bacterial swarming behavior in two and three dimensions with both high-resolution and wide-spatial coverage. This study provides detailed insights into the swarming architecture and dynamics of Vibrio alginolyticus isolate B522 on carrageenan agar that may lay the foundation for swarming studies of snake-like, nonrod-shaped motile cell types.

Swarming bacteria migrate by Lévy Walk

Individual swimming bacteria are known to bias their random trajectories in search of food and to optimize survival. The motion of bacteria within a swarm, wherein they migrate as a collective group over a solid surface, is fundamentally different as typical bacterial swarms show large-scale swirling and streaming motions involving millions to billions of cells. Here by tracking trajectories of fluorescently labelled individuals within such dense swarms, we find that the bacteria are performing super-diffusion, consistent with Lévy walks. Lévy walks are characterized by trajectories that have straight stretches for extended lengths whose variance is infinite. The evidence of super-diffusion consistent with Lévy walks in bacteria suggests that this strategy may have evolved considerably earlier than previously thought.

Antibiotic-induced anomalous statistics of collective bacterial swarming

Under sublethal antibiotics concentrations, the statistics of collectively swarming Bacillus subtilis transitions from normal to anomalous, with a heavy-tailed speed distribution and a two-step temporal correlation of velocities. The transition is due to changes in the properties of the bacterial motion and the formation of a motility-defective subpopulation that self-segregates into regions. As a result, both the colonial expansion and the growth rate are not affected by antibiotics. This phenomenon suggests a new strategy bacteria employ to fight antibiotic stress.

Collective motion of spherical bacteria

A large variety of motile bacterial species exhibit collective motions while inhabiting liquids or colonizing surfaces. These collective motions are often characterized by coherent dynamic clusters, where hundreds of cells move in correlated whirls and jets. Previously, all species that were known to form such motion had a rod-shaped structure, which enhances the order through steric and hydrodynamic interactions. Here we show that the spherical motile bacteria Serratia marcescens exhibit robust collective dynamics and correlated coherent motion while grown in suspensions. As cells migrate to the upper surface of a drop, they form a monolayer, and move collectively in whirls and jets. At all concentrations, the distribution of the bacterial speed was approximately Rayleigh with an average that depends on concentration in a non-monotonic way. Other dynamical parameters such as vorticity and correlation functions are also analyzed and compared to rod-shaped bacteria from the same strain. Our results demonstrate that self-propelled spherical objects do form complex ordered collective motion. This opens a door for a new perspective on the role of cell aspect ratio and alignment of cells with regards to collective motion in nature.

Upstream contamination by floating particles

It has been known at least since the work of Reynolds and Marangoni in the 1880s that floating particulates strongly affect water surface behaviour, and research involving particle–fluid interactions continues in modern applications ranging from microfluidics and cellular morphogenesis to colloidal dynamics and self-assembly. Here, we report and analyse an unexpected result from a simple experiment: clean water is discharged along an inclined channel into a lower container contaminated with floating particles. Surprisingly, the floating particles are transported both up a waterfall as long as 1 cm, and upstream in channels to lengths of at least several metres. We confirm through experiments and simulations that this upstream contamination is paradoxically driven by the downstream flow of clean water, which establishes a surface tension gradient that sustains the particulate motion. We also show that contamination may occur in practical applications, such as the discharge of a standard pipette or simulated release of waste into larger scale channels.

Genetically diverse Clostridium difficile strains harboring abundant prophages in an estuarine environment

Clostridium difficile is the leading cause of antibiotic-associated diarrheal disease in health care settings across the world. Despite its pathogenic capacity, it can be carried asymptomatically and has been found in terrestrial and marine ecosystems outside hospital environments. Little is known about these environmental strains, and few studies have been conducted on estuarine systems. Although prophage abundance and diversity are known to occur within clinical strains, prophage carriage within environmental strains of C. difficile has not previously been explored. In this study, we isolated C. difficile from sites sampled in two consecutive years in an English estuarine system. Isolates were characterized by PCR ribotype, antibiotic resistance, and motility. The prevalence and diversity of prophages were detected by transmission electron microscopy (TEM) and a phage-specific PCR assay. We show that a dynamic and diverse population of C. difficile exists within these sediments and that it includes isolates of ribotypes which are associated with severe clinical infections and those which are more frequently isolated from outside the hospital environment. Prophage carriage was found to be high (75%), demonstrating that phages play a role in the biology of these strains.

Periodic reversals in Paenibacillus dendritiformis swarming

Bacterial swarming is a type of motility characterized by a rapid and collective migration of bacteria on surfaces. Most swarming species form densely packed dynamic clusters in the form of whirls and jets, in which hundreds of rod-shaped rigid cells move in circular and straight patterns, respectively. Recent studies have suggested that short-range steric interactions may dominate hydrodynamic interactions and that geometrical factors, such as a cell's aspect ratio, play an important role in bacterial swarming. Typically, the aspect ratio for most swarming species is only up to 5, and a detailed understanding of the role of much larger aspect ratios remains an open challenge. Here we study the dynamics of Paenibacillus dendritiformis C morphotype, a very long, hyperflagellated, straight (rigid), rod-shaped bacterium with an aspect ratio of ~20. We find that instead of swarming in whirls and jets as observed in most species, including the shorter T morphotype of P. dendritiformis, the C morphotype moves in densely packed straight but thin long lines. Within these lines, all bacteria show periodic reversals, with a typical reversal time of 20 s, which is independent of their neighbors, the initial nutrient level, agar rigidity, surfactant addition, humidity level, temperature, nutrient chemotaxis, oxygen level, illumination intensity or gradient, and cell length. The evolutionary advantage of this unique back-and-forth surface translocation remains unclear.

High density waves of the bacterium Pseudomonas aeruginosa in propagating swarms result in efficient colonization of surfaces

This work describes a new, to our knowledge, strategy of efficient colonization and community development where bacteria substantially alter their physical environment. Many bacteria move in groups, in a mode described as swarming, to colonize surfaces and form biofilms to survive external stresses, including exposure to antibiotics. One such bacterium is Pseudomonas aeruginosa, which is an opportunistic pathogen responsible for both acute and persistent infections in susceptible individuals, as exampled by those for burn victims and people with cystic fibrosis. Pseudomonas aeruginosa often, but not always, forms branched tendril patterns during swarming; this phenomena occurs only when bacteria produce rhamnolipid, which is regulated by population-dependent signaling called quorum sensing. The experimental results of this work show that P. aeruginosa cells propagate as high density waves that move symmetrically as rings within swarms toward the extending tendrils. Biologically justified cell-based multiscale model simulations suggest a mechanism of wave propagation as well as a branched tendril formation at the edge of the population that depends upon competition between the changing viscosity of the bacterial liquid suspension and the liquid film boundary expansion caused by Marangoni forces. Therefore, P. aeruginosa efficiently colonizes surfaces by controlling the physical forces responsible for expansion of thin liquid film and by propagating toward the tendril tips. The model predictions of wave speed and swarm expansion rate as well as cell alignment in tendrils were confirmed experimentally. The study results suggest that P. aeruginosa responds to environmental cues on a very short timescale by actively exploiting local physical phenomena to develop communities and efficiently colonize new surfaces.

Flagella and pili-mediated near-surface single-cell motility mechanisms in P. aeruginosa

Bacterial biofilms are structured multicellular communities that are responsible for a broad range of infections. Knowing how free-swimming bacteria adapt their motility mechanisms near a surface is crucial for understanding the transition from the planktonic to the biofilm phenotype. By translating microscopy movies into searchable databases of bacterial behavior and developing image-based search engines, we were able to identify fundamental appendage-specific mechanisms for the surface motility of Pseudomonas aeruginosa. Type IV pili mediate two surface motility mechanisms: horizontally oriented crawling, by which the bacterium moves lengthwise with high directional persistence, and vertically oriented walking, by which the bacterium moves with low directional persistence and high instantaneous velocity, allowing it to rapidly explore microenvironments. The flagellum mediates two additional motility mechanisms: near-surface swimming and surface-anchored spinning, which often precedes detachment from a surface. Flagella and pili interact cooperatively in a launch sequence whereby bacteria change orientation from horizontal to vertical and then detach. Vertical orientation facilitates detachment from surfaces and thereby influences biofilm morphology.

Surviving bacterial sibling rivalry: inducible and reversible phenotypic switching in Paenibacillus dendritiformis

Natural habitats vary in available nutrients and room for bacteria to grow, but successful colonization can lead to overcrowding and stress. Here we show that competing sibling colonies of Paenibacillus dendritiformis bacteria survive overcrowding by switching between two distinct vegetative phenotypes, motile rods and immotile cocci. Growing colonies of the rod-shaped bacteria produce a toxic protein, Slf, which kills cells of encroaching sibling colonies. However, sublethal concentrations of Slf induce some of the rods to switch to Slf-resistant cocci, which have distinct metabolic and resistance profiles, including resistance to cell wall antibiotics. Unlike dormant spores of P. dendritiformis, the cocci replicate. If cocci encounter conditions that favor rods, they secrete a signaling molecule that induces a switch to rods. Thus, in contrast to persister cells, P. dendritiformis bacteria adapt to changing environmental conditions by inducible and reversible phenotypic switching.

In favorable environments, species may face space and nutrient limits due to overcrowding. Bacteria provide an excellent model for analyzing principles underlying overcrowding and regulation of density in nature, since their population dynamics can be easily and accurately assessed under controlled conditions. We describe a newly discovered mechanism for survival of a bacterial population during overcrowding. When competing with sibling colonies, Paenibacillus dendritiformis produces a lethal protein (Slf) that kills cells at the interface of encroaching colonies. Slf also induces a small proportion of the cells to switch from motile, rod-shaped cells to nonmotile, Slf-resistant, vegetative cocci. When crowding is reduced and nutrients are no longer limiting, the bacteria produce a signal that induces cocci to switch back to motile rods, allowing the population to spread. Genes encoding components of this phenotypic switching pathway are widespread among bacterial species, suggesting that this survival mechanism is not unique to P. dendritiformis.

Bacterial biofilm shows persistent resistance to liquid wetting and gas penetration

Most of the world's bacteria exist in robust, sessile communities known as biofilms, ubiquitously adherent to environmental surfaces from ocean floors to human teeth and notoriously resistant to antimicrobial agents. We report the surprising observation that Bacillus subtilis biofilm colonies and pellicles are extremely nonwetting, greatly surpassing the repellency of Teflon toward water and lower surface tension liquids. The biofilm surface remains nonwetting against up to 80% ethanol as well as other organic solvents and commercial biocides across a large and clinically important concentration range. We show that this property limits the penetration of antimicrobial liquids into the biofilm, severely compromising their efficacy. To highlight the mechanisms of this phenomenon, we performed experiments with mutant biofilms lacking ECM components and with functionalized polymeric replicas of biofilm microstructure. We show that the nonwetting properties are a synergistic result of ECM composition, multiscale roughness, reentrant topography, and possibly yet other factors related to the dynamic nature of the biofilm surface. Finally, we report the impenetrability of the biofilm surface by gases, implying defense capability against vapor-phase antimicrobials as well. These remarkable properties of B. subtilis biofilm, which may have evolved as a protection mechanism against native environmental threats, provide a new direction in both antimicrobial research and bioinspired liquid-repellent surface paradigms.