Spatiotemporal establishment of dense bacterial colonies growing on hard agar

Capillary interactions drive the self-organization of bacterial colonies

Many bacteria inhabit thin layers of water on solid surfaces both naturally in soils or on hosts or textiles and in the lab on agar hydrogels. In these environments, cells experience capillary forces, yet an understanding of how these forces shape bacterial collective behaviors remains elusive. Here, we show that the water menisci formed around bacteria lead to capillary attraction between cells while still allowing them to slide past one another. We develop an experimental apparatus that allows us to control bacterial collective behaviors by varying the strength and range of capillary forces. Combining 3D imaging and cell tracking with agent-based modeling, we demonstrate that capillary attraction organizes rod-shaped bacteria into densely packed, nematic groups, and profoundly influences their collective dynamics and morphologies. Our results suggest that capillary forces may be a ubiquitous physical ingredient in shaping microbial communities in partially hydrated environments.

Comprehensive Characterization of fucAO Operon Activation in Escherichia coli

Wildtype Escherichia coli cells cannot grow on L-1,2-propanediol, as the fucAO operon within the fucose (fuc) regulon is thought to be silent in the absence of L-fucose. Little information is available concerning the transcriptional regulation of this operon. Here, we first confirm that fucAO operon expression is highly inducible by fucose and is primarily attributable to the upstream operon promoter, while the fucO promoter within the 3'-end of fucA is weak and uninducible. Using 5'RACE, we identify the actual transcriptional start site (TSS) of the main fucAO operon promoter, refuting the originally proposed TSS. Several lines of evidence are provided showing that the fucAO locus is within a transcriptionally repressed region on the chromosome. Operon activation is dependent on FucR and Crp but not SrsR. Two Crp-cAMP binding sites previously found in the regulatory region are validated, where the upstream site plays a more critical role than the downstream site in operon activation. Furthermore, two FucR binding sites are identified, where the downstream site near the first Crp site is more important than the upstream site. Operon transcription relies on Crp-cAMP to a greater degree than on FucR. Our data strongly suggest that FucR mainly functions to facilitate the binding of Crp to its upstream site, which in turn activates the fucAO promoter by efficiently recruiting RNA polymerase.

Phenotypic Patterning through Copy Number Adaptation to Environmental Gradients

We recently described a paradigm for engineering bacterial adaptation using plasmids coupled to the same origin of replication. In this study, we use plasmid coupling to generate spatially separated and phenotypically distinct populations in response to heterogeneous environments. Using a custom microfluidic device, we continuously tracked engineered populations along induced gradients, enabling an in-depth analysis of the spatiotemporal dynamics of plasmid coupling. Our observations reveal a pronounced phenotypic separation within 4 h exposure to an opposing gradient of AHL and arabinose. Additionally, by modulating the burden strength balance between coupled plasmids, we demonstrate the inherent limitations and tunability of this system. Intriguingly, phenotypic separation persists for an extended time, hinting at a biophysical spatial retention mechanism reminiscent of natural speciation processes. Complementing our experimental data, mathematical models provide invaluable insights into the underlying mechanisms and guide optimization of plasmid coupling for prospective applications of environmental copy number adaptation engineering across separated domains.

The biophysical basis of bacterial colony growth

Bacteria often attach to surfaces and grow densely-packed communities called biofilms. As biofilms grow, they expand across the surface, increasing their surface area and access to nutrients. Thus, the overall growth rate of a biofilm is directly dependent on its "range expansion" rate. One factor that limits the range expansion rate is vertical growth; at the biofilm edge there is a direct trade-off between horizontal and vertical growth-the more a biofilm grows up, the less it can grow out. Thus, the balance of horizontal and vertical growth impacts the range expansion rate and, crucially, the overall biofilm growth rate. However, the biophysical connection between horizontal and vertical growth remains poorly understood, due in large part to difficulty in resolving biofilm shape with sufficient spatial and temporal resolution from small length scales to macroscopic sizes. Here, we experimentally show that the horizontal expansion rate of bacterial colonies is controlled by the contact angle at the biofilm edge. Using white light interferometry, we measure the three-dimensional surface morphology of growing colonies, and find that small colonies are surprisingly well-described as spherical caps. At later times, nutrient diffusion and uptake prevent the tall colony center from growing exponentially. However, the colony edge always has a region short enough to grow exponentially; the size and shape of this region, characterized by its contact angle, along with cellular doubling time, determines the range expansion rate. We found that the geometry of the exponentially growing biofilm edge is well-described as a spherical-cap-napkin-ring, i.e., a spherical cap with a cylindrical hole in its center (where the biofilm is too tall to grow exponentially). We derive an exact expression for the spherical-cap-napkin-ring-based range expansion rate; further, to first order, the expansion rate only depends on the colony contact angle, the thickness of the exponentially growing region, and the cellular doubling time. We experimentally validate both of these expressions. In line with our theoretical predictions, we find that biofilms with long cellular doubling times and small contact angles do in fact grow faster than biofilms with short cellular doubling times and large contact angles. Accordingly, sensitivity analysis shows that biofilm growth rates are more sensitive to their contact angles than to their cellular growth rates. Thus, to understand the fitness of a growing biofilm, one must account for its shape, not just its cellular doubling time.

BMX: Biological modelling and interface exchange

High performance computing has a great potential to provide a range of significant benefits for investigating biological systems. These systems often present large modelling problems with many coupled subsystems, such as when studying colonies of bacteria cells. The aim to understand cell colonies has generated substantial interest as they can have strong economic and societal impacts through their roles in in industrial bioreactors and complex community structures, called biofilms, found in clinical settings. Investigating these communities through realistic models can rapidly exceed the capabilities of current serial software. Here, we introduce BMX, a software system developed for the high performance modelling of large cell communities by utilising GPU acceleration. BMX builds upon the AMRex adaptive mesh refinement package to efficiently model cell colony formation under realistic laboratory conditions. Using simple test scenarios with varying nutrient availability, we show that BMX is capable of correctly reproducing observed behavior of bacterial colonies on realistic time scales demonstrating a potential application of high performance computing to colony modelling. The open source software is available from the zenodo repository https://doi.org/10.5281/zenodo.8084270 under the BSD-2-Clause licence.

Quantitative approaches to study phenotypic effects of large-scale genetic perturbations

How microbes interact with their environment and how the complex interplay of their genes enables them to survive and thrive under stress is a fundamental question in microbial system biology, which is also important from a public health perspective. Large-scale studies of gene-gene, gene-drug, and drug-drug interactions have proven to be powerful tools for elucidating gene function and functional modules in the cell. Approaches that systematically quantify phenotypes in libraries of microbial strains with genome-wide genetic perturbations are crucial for progress in this area. Here, we review recent advances in this field, and point out applications to the study of gene-drug interactions. We highlight newly developed techniques for the rapid generation of genome-wide mutant libraries and the high-throughput measurement of more complex phenotypes and other observables, such as cell morphology or thermal stability of the proteome.

Microbial models of development: Inspiration for engineering self-assembled synthetic multicellularity

While the field of synthetic developmental biology has traditionally focused on the study of the rich developmental processes seen in metazoan systems, an attractive alternate source of inspiration comes from microbial developmental models. Microbes face unique lifestyle challenges when forming emergent multicellular collectives. As a result, the solutions they employ can inspire the design of novel multicellular systems. In this review, we dissect the strategies employed in multicellular development by two model microbial systems: the cellular slime mold Dictyostelium discoideum and the biofilm-forming bacterium Bacillus subtilis. Both microbes face similar challenges but often have different solutions, both from metazoan systems and from each other, to create emergent multicellularity. These challenges include assembling and sustaining a critical mass of participating individuals to support development, regulating entry into development, and assigning cell fates. The mechanisms these microbial systems exploit to robustly coordinate development under a wide range of conditions offer inspiration for a new toolbox of solutions to the synthetic development community. Additionally, recreating these phenomena synthetically offers a pathway to understanding the key principles underlying how these behaviors are coordinated naturally.

Capture ELISA for KPC Detection in Gram-Negative Bacilli: Development and Standardisation

The detection of KPC-type carbapenemases is necessary for guiding appropriate antibiotic therapy and the implementation of antimicrobial stewardship and infection control measures. Currently, few tests are capable of differentiating carbapenemase types, restricting the lab reports to their presence or not. The aim of this work was to raise antibodies and develop an ELISA test to detect KPC-2 and its D179 mutants. The ELISA-KPC test was designed using rabbit and mouse polyclonal antibodies. Four different protocols were tested to select the bacterial inoculum with the highest sensitivity and specificity rates. The standardisation procedure was performed using 109 previously characterised clinical isolates, showing 100% of sensitivity and 89% of specificity. The ELISA-KPC detected all isolates producing carbapenemases, including KPC variants displaying the ESBL phenotype such as KPC-33 and -66.

Vertical growth dynamics of biofilms

During the biofilm life cycle, bacteria attach to a surface and then reproduce, forming crowded, growing communities. Many theoretical models of biofilm growth dynamics have been proposed; however, difficulties in accurately measuring biofilm height across relevant time and length scales have prevented testing these models, or their biophysical underpinnings, empirically. Using white light interferometry, we measure the heights of microbial colonies with nanometer precision from inoculation to their final equilibrium height, producing a detailed empirical characterization of vertical growth dynamics. We propose a heuristic model for vertical growth dynamics based on basic biophysical processes inside a biofilm: diffusion and consumption of nutrients and growth and decay of the colony. This model captures the vertical growth dynamics from short to long time scales (10 min to 14 d) of diverse microorganisms, including bacteria and fungi.

Use of the speckle imaging sub-pixel correlation analysis in revealing a mechanism of microbial colony growth

The microbial colony growth is driven by the activity of the cells located on the edges of the colony. However, this process is not visible unless specific staining or cross-sectioning of the colony is done. Speckle imaging technology is a non-invasive method that allows visualization of the zones of increased microbial activity within the colony. In this study, the laser speckle imaging technique was used to record the growth of the microbial colonies. This method was tested on three different microorganisms: Vibrio natriegens, Escherichia coli, and Staphylococcus aureus. The results showed that the speckle analysis system is not only able to record the growth of the microbial colony but also to visualize the microbial growth activity in different parts of the colony. The developed speckle imaging technique visualizes the zone of "the highest microbial activity" migrating from the center to the periphery of the colony. The results confirm the accuracy of the previous models of colony growth and provide algorithms for analysis of microbial activity within the colony.

Tilt-induced polar order and topological defects in growing bacterial populations

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 nonmotile cases is largely unknown. Here, we investigate the relevance of topological defects in colony formation processes of nonmotile E. coli populations, and found that both ±1/2 topological defects contribute to the three-dimensional growth. Analyzing the cell flow in the bottom layer of the colony, we observe that +1/2 defects attract cells and -1/2 defects repel cells, in agreement with previous studies on motile cells, in the initial stage of the colony growth. However, later, cells gradually flow toward -1/2 defects as well, exhibiting a sharp contrast to the existing knowledge. By investigating three-dimensional cell orientations by confocal microscopy, we find that vertical tilting of cells is promoted near the defects. Crucially, this leads to the emergence of a polar order in the otherwise nematic two-dimensional cell orientation. We extend the theory of active nematics by incorporating this polar order and the vertical tilting, which successfully explains the influx toward -1/2 defects in terms of a polarity-induced force. Our work reveals that three-dimensional cell orientations may result in qualitative changes in properties of active nematics, especially those of topological defects, which may be generically relevant in active matter systems driven by cellular growth instead of self-propulsion.

Spatial scales of competition and a growth-motility trade-off interact to determine bacterial coexistence

The coexistence of competing species is a long-lasting puzzle in evolutionary ecology research. Despite abundant experimental evidence showing that the opportunity for coexistence decreases as niche overlap increases between species, bacterial species and strains competing for the same resources are commonly found across diverse spatially heterogeneous habitats. We thus hypothesized that the spatial scale of competition may play a key role in determining bacterial coexistence, and interact with other mechanisms that promote coexistence, including a growth-motility trade-off. To test this hypothesis, we let two Pseudomonas putida strains compete at local and regional scales by inoculating them either in a mixed droplet or in separate droplets in the same Petri dish, respectively. We also created conditions that allow the bacterial strains to disperse across abiotic or fungal hyphae networks. We found that competition at the local scale led to competitive exclusion while regional competition promoted coexistence. When competing in the presence of dispersal networks, the growth-motility trade-off promoted coexistence only when the strains were inoculated in separate droplets. Our results provide a mechanism by which existing laboratory data suggesting competitive exclusion at a local scale is reconciled with the widespread coexistence of competing bacterial strains in complex natural environments with dispersal.

Mechanisms driving spatial distribution of residents in colony biofilms: an interdisciplinary perspective

Biofilms are consortia of microorganisms that form collectives through the excretion of extracellular matrix compounds. The importance of biofilms in biological, industrial and medical settings has long been recognized due to their emergent properties and impact on surrounding environments. In laboratory situations, one commonly used approach to study biofilm formation mechanisms is the colony biofilm assay, in which cell communities grow on solid-gas interfaces on agar plates after the deposition of a population of founder cells. The residents of a colony biofilm can self-organize to form intricate spatial distributions. The assay is ideally suited to coupling with mathematical modelling due to the ability to extract a wide range of metrics. In this review, we highlight how interdisciplinary approaches have provided deep insights into mechanisms causing the emergence of these spatial distributions from well-mixed inocula.

Scattering angle resolved optical coherence tomography measures morphological changes in Bacillus subtilis colonies

SIGNIFICANCE

An unmet need is recognized for early detection and diagnosis of neurological diseases. Many psychological markers emerge years after disease onset. Mitochondrial dysfunction and corresponding neurodegeneration occur before onset of large-scale cell and tissue pathology. Early detection of subcellular morphology changes could serve as a beacon for early detection of neurological diseases. This study is on bacterial colonies, Bacillus subtilis, which are similar in size to mitochondria.

AIM

This study investigates whether morphological changes can be detected in Bacillus subtilis using scattering angle resolved optical coherence tomography (SAR-OCT).

APPROACH

The SAR-OCT was applied to detect scattering angle distribution changes in Bacillus subtilis. The rod-to-coccus shape transition of the bacteria was imaged, and the backscattering angle was analyzed by recording the distribution of the ratio of low- to medium angle scattering (L/M ratio). Bacillus orientation at different locations in colonies was analytically modeled and compared with SAR-OCT results.

RESULTS

Significant differences in the distribution of backscattering angle were observed in Bacillus subtilis transitioning from rod-to-coccus shapes. In Bacillus subtilis, the C -parameter of the Burr distribution of the SAR-OCT-derived L/M ratio was significantly smaller in coccus compared with rod-shaped bacteria. SAR-OCT-derived L/M ratio varied with bacterial position in the colony and is consistent with predicted orientations from previous studies.

CONCLUSIONS

Study results support the potential of utilizing SAR-OCT to detect bacterial morphological changes.

The effect of production parameters on the spatial distribution of bacterial cells in the sausage meat matrix

In this work, the effect of processing conditions created with common meat technology equipment, on the spatial distribution of a green fluorescent protein producing -Escherichia coli in sausage meat was evaluated using confocal fluorescence microscopy and expressed with the help of the dispersion index. The results indicated that the reduction in mean particle size by prolonged comminution improved the distribution of cells in the sausage meat. Furthermore, higher fat content seemed to favor a random distribution, although not significantly. Independent of the any variation of the sausage meat production parameters, Listeria monocytogenes was effectively controlled in fermented sausages, although a theoretically less homogenous distribution of the starter culture in the sausage meat, tended to improve the effect, however, insignificantly. An early onset of the quorum-sensing-driven bacteriocin production in poorly distributed larger colonies may have been the reason for this. No differences in the composition of the microbiome between sausages with poor and good distribution of the starter culture were observed.

Agent-Based Modeling of Microbial Communities

Microbial communities are complex living systems that populate the planet with diverse functions and are increasingly harnessed for practical human needs. To deepen the fundamental understanding of their organization and functioning as well as to facilitate their engineering for applications, mathematical modeling has played an increasingly important role. Agent-based models represent a class of powerful quantitative frameworks for investigating microbial communities because of their individualistic nature in describing cells, mechanistic characterization of molecular and cellular processes, and intrinsic ability to produce emergent system properties. This review presents a comprehensive overview of recent advances in agent-based modeling of microbial communities. It surveys the state-of-the-art algorithms employed to simulate intracellular biomolecular events, single-cell behaviors, intercellular interactions, and interactions between cells and their environments that collectively serve as the driving forces of community behaviors. It also highlights three lines of applications of agent-based modeling, namely, the elucidation of microbial range expansion and colony ecology, the design of synthetic gene circuits and microbial populations for desired behaviors, and the characterization of biofilm formation and dispersal. The review concludes with a discussion of existing challenges, including the computational cost of the modeling, and potential mitigation strategies.

Morphological instability and roughening of growing 3D bacterial colonies

The morphogenesis of two-dimensional bacterial colonies has been well studied. However, little is known about the colony morphologies of bacteria growing in three dimensions, despite the prevalence of three-dimensional environments (e.g., soil, inside hosts) as natural bacterial habitats. Using experiments on bacteria in granular hydrogel matrices, we find that dense multicellular colonies growing in three dimensions undergo a common morphological instability and roughen, adopting a characteristic broccoli-like morphology when they exceed a critical size. Analysis of a continuum “active fluid” model of the expanding colony reveals that this behavior originates from an interplay of competition for nutrients with growth-driven colony expansion, both of which vary spatially. These results shed light on the fundamental biophysical principles underlying growth in three dimensions.

How do growing bacterial colonies get their shapes? While colony morphogenesis is well studied in two dimensions, many bacteria grow as large colonies in three-dimensional (3D) environments, such as gels and tissues in the body or subsurface soils and sediments. Here, we describe the morphodynamics of large colonies of bacteria growing in three dimensions. Using experiments in transparent 3D granular hydrogel matrices, we show that dense colonies of four different species of bacteria generically become morphologically unstable and roughen as they consume nutrients and grow beyond a critical size—eventually adopting a characteristic branched, broccoli-like morphology independent of variations in the cell type and environmental conditions. This behavior reflects a key difference between two-dimensional (2D) and 3D colonies; while a 2D colony may access the nutrients needed for growth from the third dimension, a 3D colony inevitably becomes nutrient limited in its interior, driving a transition to unstable growth at its surface. We elucidate the onset of the instability using linear stability analysis and numerical simulations of a continuum model that treats the colony as an “active fluid” whose dynamics are driven by nutrient-dependent cellular growth. We find that when all dimensions of the colony substantially exceed the nutrient penetration length, nutrient-limited growth drives a 3D morphological instability that recapitulates essential features of the experimental observations. Our work thus provides a framework to predict and control the organization of growing colonies—as well as other forms of growing active matter, such as tumors and engineered living materials—in 3D environments.

Emergence of sector and spiral patterns from a two-species mutualistic cross-feeding model

The ubiquitous existence of microbial communities marks the importance of understanding how species interact within the community to coexist and their spatial organization. We study a two-species mutualistic cross-feeding model through a stochastic cellular automaton on a square lattice using kinetic Monte Carlo simulation. Our model encapsulates the essential dynamic processes such as cell growth, and nutrient excretion, diffusion and uptake. Focusing on the interplay among nutrient diffusion and individual cell division, we discover three general classes of colony morphology: co-existing sectors, co-existing spirals, and engulfment. When the cross-feeding nutrient is widely available, either through high excretion or fast diffusion, a stable circular colony with alternating species sector emerges. When the consumer cells rely on being spatially close to the producers, we observe a stable spiral. We also see one species being engulfed by the other when species interfaces merge due to stochastic fluctuation. By tuning the diffusion rate and the growth rate, we are able to gain quantitative insights into the structures of the sectors and the spirals.

Intra-colony channel morphology in Escherichia coli biofilms is governed by nutrient availability and substrate stiffness

Nutrient-transporting channels have been recently discovered in mature Escherichia coli biofilms, however the relationship between intra-colony channel structure and the surrounding environmental conditions is poorly understood. Using a combination of fluorescence mesoscopy and a purpose-designed open-source quantitative image analysis pipeline, we show that growth substrate composition and nutrient availability have a profound effect on the morphology of intra-colony channels in mature E. coli biofilms. Under all nutrient conditions, intra-colony channel width was observed to increase non-linearly with radial distance from the centre of the biofilm. Notably, the channels were around 25% wider at the centre of carbon-limited biofilms compared to nitrogen-limited biofilms. Channel density also differed in colonies grown on rich and minimal media, with the former creating a network of tightly packed channels and the latter leading to well-separated, wider channels with defined edges. Our approach paves the way for measurement of internal patterns in a wide range of biofilms, offering the potential for new insights into infection and pathogenicity.

Contribution of the genomic and nutritional differentiation to the spatial distribution of bacterial colonies

Colony growth is a common phenomenon of structured populations dispersed in nature; nevertheless, studies on the spatial distribution of colonies are largely insufficient. Here, we performed a systematic survey to address the questions of whether and how the spatial distribution of colonies was influenced by the genome and environment. Six Escherichia coli strains carrying either the wild-type or reduced genomes and eight media of varied nutritional richness were used to evaluate the genomic and environmental impacts, respectively. The genome size and nutritional variation contributed to the mean size and total area but not the variation and shape of size distribution of the colonies formed within the identical space and of equivalent spatial density. The spatial analysis by means of the Voronoi diagram found that the Voronoi correlation remained nearly constant in common, in comparison to the Voronoi response decreasing in correlation to genome reduction and nutritional enrichment. Growth analysis at the single colony level revealed positive correlations of the relative growth rate to both the maximal colony size and the Voronoi area, regardless of the genomic and nutritional variety. This result indicated fast growth for the large space assigned and supported homeostasis in the Voronoi correlation. Taken together, the spatial distribution of colonies might benefit efficient clonal growth. Although the mechanisms remain unclear, the findings provide quantitative insights into the genomic and environmental contributions to the growth and distribution of spatially or geographically isolated populations.

Growth instabilities shape morphology and genetic diversity of microbial colonies

Cellular populations assume an incredible variety of shapes ranging from circular molds to irregular tumors. While we understand many of the mechanisms responsible for these spatial patterns, little is known about how the shape of a population influences its ecology and evolution. Here, we investigate this relationship in the context of microbial colonies grown on hard agar plates. This a well-studied system that exhibits a transition from smooth circular disks to more irregular and rugged shapes as either the nutrient concentration or cellular motility is decreased. Starting from a mechanistic model of colony growth, we identify two dimensionless quantities that determine how morphology and genetic diversity of the population depend on the model parameters. Our simulations further reveal that population dynamics cannot be accurately described by the commonly-used surface growth models. Instead, one has to explicitly account for the emergent growth instabilities and demographic fluctuations. Overall, our work links together environmental conditions, colony morphology, and evolution. This link is essential for a rational design of concrete, biophysical perturbations to steer evolution in the desired direction.

Systematic microscopical analysis reveals obligate synergy between extracellular matrix components during Bacillus subtilis colony biofilm development

Single-species bacterial colony biofilms often present recurring morphologies that are thought to be of benefit to the population of cells within and are known to be dependent on the self-produced extracellular matrix. However, much remains unknown in terms of the developmental process at the single cell level. Here, we design and implement systematic time-lapse imaging and quantitative analyses of the growth of Bacillus subtilis colony biofilms. We follow the development from the initial deposition of founding cells through to the formation of large-scale complex structures. Using the model biofilm strain NCIB 3610, we examine the movement dynamics of the growing biomass and compare them with those displayed by a suite of otherwise isogenic matrix-mutant strains. Correspondingly, we assess the impact of an incomplete matrix on biofilm morphologies and sessile growth rate. Our results indicate that radial expansion of colony biofilms results from the division of bacteria at the biofilm periphery rather than being driven by swelling due to fluid intake. Moreover, we show that lack of exopolysaccharide production has a negative impact on cell division rate, and the extracellular matrix components act synergistically to give the biomass the structural strength to produce aerial protrusions and agar substrate-deforming ability.

Formation of unique T-shape budding and differential impacts of low surface water on Bacillus mycoides rhizoidal colony

Bacillus mycoides Ko01 strain grows rapidly and forms extensive rhizoidal colonies on hard agar despite limited surface water availability. The agar concentrations affect the handedness of the colonies as well as other colony architectures. In this study, we found that the local curvature of cell chains in the developing colonies did not vary based on the agar concentration, while concentration does affect the handedness of chirality at the macroscale. This result suggests independence between the microscale filament curvature and macroscale colony chirality. In addition, we discovered a novel microscopic property of cells that has not been observed before: T-shaped budding under extremely low surface water availability conditions. We propose that this feature gives rise to chaotic colony morphology. Together with bundling of chains, cells form a unique set of spatial arrangements under different surface water availability. These properties appear to impact the structural features of thick tendrils, and thereby the overall morphology of colonies. Our study provides additional insights as to how bacteria proliferate, spread, and develop macroscale colony architecture under water-limited conditions.

Founder cell configuration drives competitive outcome within colony biofilms

Bacteria can form dense communities called biofilms, where cells are embedded in a self-produced extracellular matrix. Exploiting competitive interactions between strains within the biofilm context can have potential applications in biological, medical, and industrial systems. By combining mathematical modelling with experimental assays, we reveal that spatial structure and competitive dynamics within biofilms are significantly affected by the location and density of the founder cells used to inoculate the biofilm. Using a species-independent theoretical framework describing colony biofilm formation, we show that the observed spatial structure and relative strain biomass in a mature biofilm comprising two isogenic strains can be mapped directly to the geographical distributions of founder cells. Moreover, we define a predictor of competitive outcome that accurately forecasts relative abundance of strains based solely on the founder cells’ potential for radial expansion. Consequently, we reveal that variability of competitive outcome in biofilms inoculated at low founder density is a natural consequence of the random positioning of founding cells in the inoculum. Extension of our study to non-isogenic strains that interact through local antagonisms, shows that even for strains with different competition strengths, a race for space remains the dominant mode of competition in low founder density biofilms. Our results, verified by experimental assays using Bacillus subtilis, highlight the importance of spatial dynamics on competitive interactions within biofilms and hence to related applications.

Mechanical limitation of bacterial motility mediated by growing cell chains

Contrasting most known bacterial motility mechanisms, a bacterial sliding motility discovered in at least two Gram-positive bacterial families does not depend on designated motors. Instead, the cells maintain end-to-end connections following cell divisions to form long chains and exploit cell growth and division to push the cells forward. To investigate the dynamics of this motility mechanism, we constructed a mechanical model that depicts the interplay of the forces acting on and between the cells comprising the chain. Due to the exponential growth of individual cells, the tips of the chains can, in principle, accelerate to speeds faster than any known single-cell motility mechanism can achieve. However, analysis of the mechanical model shows that the exponential acceleration comes at the cost of an exponential buildup in mechanical stress in the chain, making overly long chains prone to breakage. Additionally, the mechanical model reveals that the dynamics of the chain expansion hinges on a single non-dimensional parameter. Perturbation analysis of the mechanical model further predicts the critical stress leading to chain breakage and its dependence on the non-dimensional parameter. Finally, we developed a simplistic population expansion model that uses the predicted breaking behavior to estimate the physical limit of chain-mediated population expansion. Predictions from the models provide critical insights into how this motility depends on key physical properties of the cell and the substrate. Overall, our models present a generically applicable theoretical framework for cell chain-mediated bacterial sliding motility and provide guidance for future experimental studies on such motility.

Spatiotemporal bio-shielding of bacteria through consolidated geometrical structuring

The probiotic bacterium Lactobacillus plantarum is often reckoned as a ‘generalist’ for its ability to adapt and survive in diverse ecological niches. The genomic signatures of L. plantarum have shown its intricate evolutionary ancestry and dynamic lifestyles. Here, we report on a unique geometrical arrangement of the multicellular population of L. plantarum cells. Prominently, a phenomenon of the cone-shaped colony formation and V-shaped cell chaining are discovered in response to the acidic-pH environment. Moreover, subsequent cold stress response triggers an unusual cellular arrangement of consolidated bundles, which appeared to be independently governed by a small heat shock protein (HSP 1). We further report that the V-shaped L. plantarum chaining demonstrates potent antagonistic activity against Candida albicans, a pathogenic yeast, both in vitro and in a Caenorhabditis elegans co-infection model. Finally, we deduce that the multifaceted traits manifested by this probiotic bacterium is an outcome of its dynamic flexibility and cellular heterogeneity.

Spatial regulation of cell motility and its fitness effect in a surface-attached bacterial community

On a surface, microorganisms grow into a multi-cellular community. When a community becomes densely populated, cells migrate away to expand the community's territory. How microorganisms regulate surface motility to optimize expansion remains poorly understood. Here, we characterized surface motility of Proteus mirabilis. P. mirabilis is well known for its ability to expand its colony rapidly on a surface. Cursory visual inspection of an expanding colony suggests partial migration, i.e., one fraction of a population migrates while the other is sessile. Quantitative microscopic imaging shows that this migration pattern is determined by spatially inhomogeneous regulation of cell motility. Further analyses reveal that this spatial regulation is mediated by the Rcs system, which represses the expression of the motility regulator (FlhDC) in a nutrient-dependent manner. Alleviating this repression increases the colony expansion speed but results in a rapid drop in the number of viable cells, lowering population fitness. These findings collectively demonstrate how Rcs regulates cell motility dynamically to increase the fitness of an expanding bacterial population, illustrating a fundamental trade-off underlying bacterial colonization of a surface.

Large-scale orientational order in bacterial colonies during inward growth

During colony growth, complex interactions regulate the bacterial orientation, leading to the formation of large-scale ordered structures, including topological defects, microdomains, and branches. These structures may benefit bacterial strains, providing invasive advantages during colonization. Active matter dynamics of growing colonies drives the emergence of these ordered structures. However, additional biomechanical factors also play a significant role during this process. Here, we show that the velocity profile of growing colonies creates strong radial orientation during inward growth when crowded populations invade a closed area. During this process, growth geometry sets virtual confinement and dictates the velocity profile. Herein, flow-induced alignment and torque balance on the rod-shaped bacteria result in a new stable orientational equilibrium in the radial direction. Our analysis revealed that the dynamics of these radially oriented structures, also known as aster defects, depend on bacterial length and can promote the survival of the longest bacteria around localized nutritional hotspots. The present results indicate a new mechanism underlying structural order and provide mechanistic insights into the dynamics of bacterial growth on complex surfaces.

Active Extensile Stress Promotes 3D Director Orientations and Flows

We use numerical simulations and linear stability analysis to study an active nematic layer where the director is allowed to point out of the plane. Our results highlight the difference between extensile and contractile systems. Contractile stress suppresses the flows perpendicular to the layer and favors in-plane orientations of the director. By contrast extensile stress promotes instabilities that can turn the director out of the plane, leaving behind a population of distinct, in-plane regions that continually elongate and divide. This supports extensile forces as a mechanism for the initial stages of layer formation in living systems, and we show that a planar drop with extensile (contractile) activity grows into three dimensions (remains in two dimensions). The results also explain the propensity of disclination lines in three dimensional active nematics to be of twist type in extensile or wedge type in contractile materials.

Slow expanders invade by forming dented fronts in microbial colonies

Living organisms never cease to evolve, so there is a significant interest in predicting and controlling evolution in all branches of life sciences. The most basic question is whether a trait should increase or decrease in a given environment. The answer seems to be trivial for traits such as the growth rate in a bioreactor or the expansion rate of a tumor. Yet, it has been suggested that such traits can decrease, rather than increase, during evolution. Here, we report a mutant that outcompeted the ancestor despite having a slower expansion velocity when in isolation. To explain this observation, we developed and validated a theory that describes spatial competition between organisms with different expansion rates and arbitrary competitive interactions.

Most organisms grow in space, whether they are viruses spreading within a host tissue or invasive species colonizing a new continent. Evolution typically selects for higher expansion rates during spatial growth, but it has been suggested that slower expanders can take over under certain conditions. Here, we report an experimental observation of such population dynamics. We demonstrate that mutants that grow slower in isolation nevertheless win in competition, not only when the two types are intermixed, but also when they are spatially segregated into sectors. The latter was thought to be impossible because previous studies focused exclusively on the global competitions mediated by expansion velocities, but overlooked the local competitions at sector boundaries. Local competition, however, can enhance the velocity of either type at the sector boundary and thus alter expansion dynamics. We developed a theory that accounts for both local and global competitions and describes all possible sector shapes. In particular, the theory predicted that a slower on its own, but more competitive, mutant forms a dented V-shaped sector as it takes over the expansion front. Such sectors were indeed observed experimentally, and their shapes matched quantitatively with the theory. In simulations, we further explored several mechanisms that could provide slow expanders with a local competitive advantage and showed that they are all well-described by our theory. Taken together, our results shed light on previously unexplored outcomes of spatial competition and establish a universal framework to understand evolutionary and ecological dynamics in expanding populations.

Bringing cells to the edge

A network of open channels allows cells and molecular cargo to travel from the center to the periphery of lab-grown colonies of Pseudomonas aeruginosa, helping to eradicate competing species.

A Predictive Reaction-diffusion Based Model of E.coli Colony Growth Control

Bacterial colony formations exhibit diverse morphologies and dynamics. A mechanistic understanding of this process has broad implications to ecology and medicine. However, many control factors and their impacts on colony formation remain underexplored. Here we propose a reaction-diffusion based dynamic model to quantitatively describe cell division and colony expansion, where control factors of colony spreading take the form of nonlinear density-dependent function and the intercellular impacts take the form of density-dependent hill function. We validate the model using experimental E. coli colony growth data and our results show that the model is capable of predicting the whole colony expansion process in both time and space under different conditions. Furthermore, the nonlinear control factors can predict colony morphology at both center and edge of the colony.

A traveling-wave solution for bacterial chemotaxis with growth

Bacterial cells navigate their environment by directing their movement along chemical gradients. This process, known as chemotaxis, can promote the rapid expansion of bacterial populations into previously unoccupied territories. However, despite numerous experimental and theoretical studies on this classical topic, chemotaxis-driven population expansion is not understood in quantitative terms. Building on recent experimental progress, we here present a detailed analytical study that provides a quantitative understanding of how chemotaxis and cell growth lead to rapid and stable expansion of bacterial populations. We provide analytical relations that accurately describe the dependence of the expansion speed and density profile of the expanding population on important molecular, cellular, and environmental parameters. In particular, expansion speeds can be boosted by orders of magnitude when the environmental availability of chemicals relative to the cellular limits of chemical sensing is high. Analytical understanding of such complex spatiotemporal dynamic processes is rare. Our analytical results and the methods employed to attain them provide a mathematical framework for investigations of the roles of taxis in diverse ecological contexts across broad parameter regimes.

Mechanical forces drive a reorientation cascade leading to biofilm self-patterning

In growing active matter systems, a large collection of engineered or living autonomous units metabolize free energy and create order at different length scales as they proliferate and migrate collectively. One such example is bacterial biofilms, surface-attached aggregates of bacterial cells embedded in an extracellular matrix that can exhibit community-scale orientational order. However, how bacterial growth coordinates with cell-surface interactions to create distinctive, long-range order during biofilm development remains elusive. Here we report a collective cell reorientation cascade in growing Vibrio cholerae biofilms that leads to a differentially ordered, spatiotemporally coupled core-rim structure reminiscent of a blooming aster. Cell verticalization in the core leads to a pattern of differential growth that drives radial alignment of the cells in the rim, while the growing rim generates compressive stresses that expand the verticalized core. Such self-patterning disappears in nonadherent mutants but can be restored through opto-manipulation of growth. Agent-based simulations and two-phase active nematic modeling jointly reveal the strong interdependence of the driving forces underlying the differential ordering. Our findings offer insight into the developmental processes that shape bacterial communities and provide ways to engineer phenotypes and functions in living active matter.

Spatial alanine metabolism determines local growth dynamics of Escherichia coli colonies

Bacteria commonly live in spatially structured biofilm assemblages, which are encased by an extracellular matrix. Metabolic activity of the cells inside biofilms causes gradients in local environmental conditions, which leads to the emergence of physiologically differentiated subpopulations. Information about the properties and spatial arrangement of such metabolic subpopulations, as well as their interaction strength and interaction length scales are lacking, even for model systems like Escherichia coli colony biofilms grown on agar-solidified media. Here, we use an unbiased approach, based on temporal and spatial transcriptome and metabolome data acquired during E. coli colony biofilm growth, to study the spatial organization of metabolism. We discovered that alanine displays a unique pattern among amino acids and that alanine metabolism is spatially and temporally heterogeneous. At the anoxic base of the colony, where carbon and nitrogen sources are abundant, cells secrete alanine via the transporter AlaE. In contrast, cells utilize alanine as a carbon and nitrogen source in the oxic nutrient-deprived region at the colony mid-height, via the enzymes DadA and DadX. This spatially structured alanine cross-feeding influences cellular viability and growth in the cross-feeding-dependent region, which shapes the overall colony morphology. More generally, our results on this precisely controllable biofilm model system demonstrate a remarkable spatiotemporal complexity of metabolism in biofilms. A better characterization of the spatiotemporal metabolic heterogeneities and dependencies is essential for understanding the physiology, architecture, and function of biofilms.

Bacterial Filamentation Drives Colony Chirality

Chirality is ubiquitous in nature, with consequences at the cellular and tissue scales. As Escherichia coli colonies expand radially, an orthogonal component of growth creates a pinwheel-like pattern that can be revealed by fluorescent markers. To elucidate the mechanistic basis of this colony chirality, we investigated its link to left-handed, single-cell twisting during E. coli elongation. While chemical and genetic manipulation of cell width altered single-cell twisting handedness, colonies ceased to be chiral rather than switching handedness, and anaerobic growth altered colony chirality without affecting single-cell twisting. Chiral angle increased with increasing temperature even when growth rate decreased. Unifying these findings, we discovered that colony chirality was associated with the propensity for cell filamentation. Inhibition of cell division accentuated chirality under aerobic growth and generated chirality under anaerobic growth. Thus, regulation of cell division is intrinsically coupled to colony chirality, providing a mechanism for tuning macroscale spatial patterning. IMPORTANCE Chiral objects, such as amino acids, are distinguishable from their mirror image. For living systems, the fundamental mechanisms relating cellular handedness to chirality at the multicellular scale remain largely mysterious. Here, we use chemical, genetic, and environmental perturbations of Escherichia coli to investigate whether pinwheel patterns in bacterial colonies are directly linked to single-cell growth behaviors. We discover that chirality can be abolished without affecting single-cell twisting; instead, the degree of chirality was linked to the proportion of highly elongated cells at the colony edge. Inhibiting cell division boosted the degree of chirality during aerobic growth and even introduced chirality to otherwise achiral colonies during anaerobic growth. These findings reveal a fascinating connection between cell division and macroscopic colony patterning.

Role of bacterial persistence in spatial population expansion

Bacterial persistence, tolerance to antibiotics via stochastic phenotype switching, provides a survival strategy and a fitness advantage in temporally fluctuating environments. Here we study its possible benefit in spatially varying environments using a Fisher wave approach. We study the spatial expansion of a population with stochastic switching between two phenotypes in spatially homogeneous conditions and in the presence of an antibiotic barrier. Our analytical results show that the expansion speed in growth-supporting conditions depends on the fraction of persister cells at the leading edge of the population wave. The leading edge contains a small fraction of persister cells, keeping the effect on the expansion speed minimal. The fraction of persisters increases gradually in the interior of the wave. This persister pool benefits the population when it is stalled by an antibiotic environment. In that case, the presence of persister enables the population to spread deeper into the antibiotic region and to cross an antibiotic region more rapidly. Further we observe that optimal switching rates maximize the expansion speed of the population in spatially varying environments with alternating regions of growth permitting conditions and antibiotics. Overall, our results show that stochastic switching can promote population expansion in the presence of antibiotic barriers or other stressful environments.

The spatial organization of microbial communities during range expansion

Microbes in nature often live in dense and diverse communities exhibiting a variety of spatial structures. Microbial range expansion is a universal ecological process that enables populations to form spatial patterns. It can be driven by both passive and active processes, for example, mechanical forces from cell growth and bacterial motility. In this review, we provide a taste of recent creative and sophisticated efforts being made to address basic questions in spatial ecology and pattern formation during range expansion. We especially highlight the role of motility to shape community structures, and discuss the research challenges and future directions.

Spatiotemporal dynamics of growth and death within spherical bacterial colonies

Bacterial growth within colonies and biofilms is heterogeneous. Local reduction of growth rates has been associated with tolerance against various antibiotics. However, spatial gradients of growth rates are poorly characterized in three-dimensional bacterial colonies. Here, we report two spatially resolved methods for measuring growth rates in bacterial colonies. As bacteria grow and divide, they generate a velocity field that is directly related to the growth rates. We derive profiles of growth rates from the velocity field and show that they are consistent with the profiles obtained by single-cell-counting. Using these methods, we reveal that even small colonies initiated with a few thousand cells of the human pathogen Neisseria gonorrhoeae develop a steep gradient of growth rates within two generations. Furthermore, we show that stringent response decelerates growth inhibition at the colony center. Based on our results, we suggest that aggregation-related growth inhibition can protect gonococci from external stresses even at early biofilm stages.

Geometrically regulating evolutionary dynamics in biofilms

The theoretical understanding of evolutionary dynamics in spatially structured populations often relies on nonspatial models. Biofilms are among such populations where a more accurate understanding is of theoretical interest and can reveal new solutions to existing challenges. Here, we studied how the geometry of the environment affects the evolutionary dynamics of expanding populations, using the Eden model. Our results show that fluctuations of subpopulations during range expansion in two- and three-dimensional environments are not Brownian. Furthermore, we found that the substrate's geometry interferes with the evolutionary dynamics of populations that grow upon it. Inspired by these findings, we propose a periodically wedged pattern on surfaces prone to develop biofilms. On such patterned surfaces, natural selection becomes less effective and beneficial mutants would have a harder time establishing. Additionally, this modification accelerates genetic drift and leads to less diverse biofilms. Both interventions are highly desired for biofilms.

A general principle for spontaneous genetic symmetry breaking and pattern formation within cell populations

Elements within biological systems interact and frequently self-organize from initially disordered states into highly structured patterns. The local self-activation and lateral inhibition mechanism, derived from the coupling between two reacting and diffusing chemicals, has been believed to be one of the main causes for biological pattern formation. Graded positional information can be produced by the limited diffusion of one single signaling molecule through cell populations with no pre-patterns being required. We demonstrate, using multiscale computations, that spontaneous symmetry breaking can be driven within expanding and non-expanding cell populations, without local self-enhancement of activators and long-range inhibition. Instead, cells can self-organize into structured gene patterns via a combination of timing gene expression in cells and the graded positional information which has been coupled to the gene expression. We show that the genetic symmetry breaking in expanding E. coli populations occurs at a critical colony size, which is independent of the cell doubling time but scales with the diffusion speed of the signaling molecule. We also show the quasi-3D structure of gene patterns, and observe that the wave length of periodic genetic stripes is in proportion to the genetic oscillation cycle time and in inverse proportion to cell doubling time. Our results provide insights into relevant biological development processes.

Pareto optimality between growth-rate and lag-time couples metabolic noise to phenotypic heterogeneity in Escherichia coli

Despite mounting evidence that in clonal bacterial populations, phenotypic variability originates from stochasticity in gene expression, little is known about noise-shaping evolutionary forces and how expression noise translates to phenotypic differences. Here we developed a high-throughput assay that uses a redox-sensitive dye to couple growth of thousands of bacterial colonies to their respiratory activity and show that in Escherichia coli, noisy regulation of lower glycolysis and citric acid cycle is responsible for large variations in respiratory metabolism. We found that these variations are Pareto optimal to maximization of growth rate and minimization of lag time, two objectives competing between fermentative and respiratory metabolism. Metabolome-based analysis revealed the role of respiratory metabolism in preventing the accumulation of toxic intermediates of branched chain amino acid biosynthesis, thereby supporting early onset of cell growth after carbon starvation. We propose that optimal metabolic tradeoffs play a key role in shaping and preserving phenotypic heterogeneity and adaptation to fluctuating environments.

From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions

Accurate measurements of cellular protein concentrations are invaluable to quantitative studies of gene expression and physiology in living cells. Here, we developed a versatile mass spectrometric workflow based on data-independent acquisition proteomics (DIA/SWATH) together with a novel protein inference algorithm (xTop). We used this workflow to accurately quantify absolute protein abundances in Escherichia coli for > 2,000 proteins over > 60 growth conditions, including nutrient limitations, non-metabolic stresses, and non-planktonic states. The resulting high-quality dataset of protein mass fractions allowed us to characterize proteome responses from a coarse (groups of related proteins) to a fine (individual) protein level. Hereby, a plethora of novel biological findings could be elucidated, including the generic upregulation of low-abundant proteins under various metabolic limitations, the non-specificity of catabolic enzymes upregulated under carbon limitation, the lack of large-scale proteome reallocation under stress compared to nutrient limitations, as well as surprising strain-dependent effects important for biofilm formation. These results present valuable resources for the systems biology community and can be used for future multi-omics studies of gene regulation and metabolic control in E. coli.

Challenges of analysing stochastic gene expression in bacteria using single-cell time-lapse experiments

Stochastic gene expression causes phenotypic heterogeneity in a population of genetically identical bacterial cells. Such non-genetic heterogeneity can have important consequences for the population fitness, and therefore cells implement regulation strategies to either suppress or exploit such heterogeneity to adapt to their circumstances. By employing time-lapse microscopy of single cells, the fluctuation dynamics of gene expression may be analysed, and their regulatory mechanisms thus deciphered. However, a careful consideration of the experimental design and data-analysis is needed to produce useful data for deriving meaningful insights from them. In the present paper, the individual steps and challenges involved in a time-lapse experiment are discussed, and a rigorous framework for designing, performing, and extracting single-cell gene expression dynamics data from such experiments is outlined.

Correlation between the spatial distribution and colony size was common for monogenetic bacteria in laboratory conditions

Background

Geographically separated population growth of microbes is a common phenomenon in microbial ecology. Colonies are representative of the morphological characteristics of this structured population growth. Pattern formation by single colonies has been intensively studied, whereas the spatial distribution of colonies is poorly investigated.

Results

The present study describes a first trial to address the questions of whether and how the spatial distribution of colonies determines the final colony size using the model microorganism Escherichia coli, colonies of which can be grown under well-controlled laboratory conditions. A computational tool for image processing was developed to evaluate colony density, colony size and size variation, and the Voronoi diagram was applied for spatial analysis of colonies with identical space resources. A positive correlation between the final colony size and the Voronoi area was commonly identified, independent of genomic and nutritional differences, which disturbed the colony size and size variation.

Conclusions

This novel finding of a universal correlation between the spatial distribution and colony size not only indicated the fair distribution of spatial resources for monogenetic colonies growing with identical space resources but also indicated that the initial localization of the microbial colonies decided by chance determined the fate of the subsequent population growth. This study provides a valuable example for quantitative analysis of the complex microbial ecosystems by means of experimental ecology.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02180-8.

Repulsive expansion dynamics in colony growth and gene expression

Spatial expansion of a population of cells can arise from growth of microorganisms, plant cells, and mammalian cells. It underlies normal or dysfunctional tissue development, and it can be exploited as the foundation for programming spatial patterns. This expansion is often driven by continuous growth and division of cells within a colony, which in turn pushes the peripheral cells outward. This process generates a repulsion velocity field at each location within the colony. Here we show that this process can be approximated as coarse-grained repulsive-expansion kinetics. This framework enables accurate and efficient simulation of growth and gene expression dynamics in radially symmetric colonies with homogenous z-directional distribution. It is robust even if cells are not spherical and vary in size. The simplicity of the resulting mathematical framework also greatly facilitates generation of mechanistic insights.

Spatiotemporal dynamics are ubiquitous in biology. To understand these phenomena in nature or to program them using synthetic gene circuits, it is critical to resort to mathematical modeling to deduce mechanistic insights or to explore plausible outcomes. Historically, modeling of spatiotemporal dynamics depends on the use of agent-based models or their continuum counterparts consisting of partial differential equations. Here, we show that a class of colony expansion can be treated as being driven by the steric force generated by growing and diving cells. This approximation leads to a drastically simplified framework consisting of only ordinary differential equations. This framework greatly improves the computational efficiency and facilitates development of mechanistic insights into the dynamics of colony growth and pattern formation.

How Physical Interactions Shape Bacterial Biofilms

Biofilms are structured communities formed by a single or multiple microbial species. Within biofilms, bacteria are embedded into extracellular matrix, allowing them to build macroscopic objects. Biofilm structure can respond to environmental changes such as the presence of antibiotics or predators. By adjusting expression levels of surface and extracellular matrix components, bacteria tune cell-to-cell interactions. One major challenge in the field is the fact that these components are very diverse among different species. Deciphering how physical interactions within biofilms are affected by changes in gene expression is a promising approach to obtaining a more unified picture of how bacteria modulate biofilms. This review focuses on recent advances in characterizing attractive and repulsive forces between bacteria in correlation with biofilm structure, dynamics, and spreading. How bacteria control physical interactions to maximize their fitness is an emerging theme.

Mechanics of biofilms formed of bacteria with fimbriae appendages

Gram-negative bacteria, as well as some Gram-positive bacteria, possess hair-like appendages known as fimbriae, which play an important role in adhesion of the bacteria to surfaces or to other bacteria. Unlike the sex pili or flagellum, the fimbriae are quite numerous, with of order 1000 fimbriae appendages per bacterial cell. In this paper, a recently developed hybrid model for bacterial biofilms is used to examine the role of fimbriae tension force on the mechanics of bacterial biofilms. Each bacterial cell is represented in this model by a spherocylindrical particle, which interact with each other through collision, adhesion, lubrication force, and fimbrial force. The bacterial cells absorb water and nutrients and produce extracellular polymeric substance (EPS). The flow of water and EPS, and nutrient diffusion within these substances, is computed using a continuum model that accounts for important effects such as osmotic pressure gradient, drag force on the bacterial cells, and viscous shear. The fimbrial force is modeled using an outer spherocylinder capsule around each cell, which can transmit tensile forces to neighboring cells with which the fimbriae capsule collides. We find that the biofilm structure during the growth process is dominated by a balance between outward drag force on the cells due to the EPS flow away from the bacterial colony and the inward tensile fimbrial force acting on chains of cells connected by adhesive fimbriae appendages. The fimbrial force also introduces a large rotational motion of the cells and disrupts cell alignment caused by viscous torque imposed by the EPS flow. The current paper characterizes the competing effects of EPS drag and fimbrial force using a series of computations with different values of the ratio of EPS to bacterial cell production rate and different numbers of fimbriae per cell.

Gas production reveals the metabolism of immobilized Chlorella vulgaris during different trophic modes

The metabolism of heterotrophic and mixotrophic cultivation modes of Chlorella vulgaris, a potential source of biofuel and CO₂ mitigation, was studied in immobilized cultures. The gas concentration (O₂ and CO₂) was measured thanks to an original device manufactured using 3D printing. The biomass was monitored by 3D imaging and image processing. Net O₂ and CO₂ sources were obtained by a balance equation considering a calibrated leakage and the dissolved gas. Combined experimental and theoretical gas yields (mass of gas per mass of biomass), the photosynthesis proportion of mixotrophic colony was determined. Its increase with light intensity is not linear. Therefore, the highest light intensity (104μmol∙m^-2∙s^-1) revealed the limit of photosynthesis potential in the growth of mixotrophic colony. In the presence of light, the colony adopts a cylindrical shape instead of a spherical cap. This study proposed mechanisms of synergy inside the colony for heterotrophic and mixotrophic modes.