Session B13: Physics of Biofilms I

Live

Biofilms are complex self-assembling structures formed by bacteria and extracellular polymeric substances (EPS). Biofilm structure not only provides mechanical advantages, but increased resistance to antibiotics, protection to predation and starvation. Biofilms adhere to a solid interface and grow unconstrained towards a fluid medium. The evolution of this free surface is set by a complex array of mechanical interactions on multiple scales, and is limited by nutrient and spatial availability. Using high-resolution interferometry we study the evolution of surface growth and fluctuations of Vibrio cholerae strains with different rates of EPS production. The interface is then characterized according to its fractal dimension and roughness to account for its local and global features. We compare our experimental data with PDE models, such as the Kardar-Parisi-Zhang equation and a simple biomass transfer model. These results provide evidence that optical profiling of biofilm surfaces can be used as an alternative for the analysis of developing biofilms without the need of genetic engineering and fluorescence microscopy.   

Live

Bacterial biofilms represent a major form of microbial life on Earth and serve as a model active nematic system, in which activity results from growth of the rod-shaped bacterial cells. In their natural environments, ranging from human organs to industrial pipelines, biofilms have evolved to grow robustly under significant fluid shear. Despite intense practical and theoretical interest, it is unclear how strong fluid flow alters the local and global architectures of biofilms. Here, we combine highly time-resolved single-cell live imaging with 3D multi-scale modeling to investigate the mechanisms by which flow affects the dynamics of all individual cells in growing biofilms. Our experiments and cell-based simulations reveal three quantitatively different growth phases in strong external flow, and the transitions between them. In the initial stages of biofilm development, flow induces a downstream gradient in cell orientation, causing asymmetrical droplet-like biofilm shapes. In the later developmental stages, when the majority of cells are sheltered from the flow by the surrounding extracellular matrix, buckling-induced cell verticalization in the biofilm core restores radially symmetric biofilm growth, in agreement with predictions of a 3D continuum model.   

Live

All living creatures interact with their external environment and bacterial cells are no exception. In nature, bacterial cells exist in the surface-attached community lifestyle embedded in an extracellular matrix, known as biofilms. In many conditions, biofilms grow inside a structured, confined environment. However, despite the importance of the bacteria-environment interaction, little is known as to how mechanical confinement interferes with the biofilm developmental program and how the proliferation of biofilm cells, in turn, deforms or even damages the surrounding environments as feedback to control the biofilm growth. In this presentation, we will integrate single-cell live imaging, finite element modeling, mechanics theories, and mutagenesis to investigate how Vibrio cholerae biofilms grow inside agarose gels. With single-cell resolution imaging, we found that overall biofilm morphology is susceptible to growth-induced mechanical stress and different degree of confinement. And biofilms behave as active soft matter with highly cell ordering. By using mutants lacking single or a combination of the vibrio polysaccharide (VPS) and accessory proteins, we investigated how cell ordering changes as a function of extracellular matrix components.   

Live

Bacterial biofilms are considered to be one of the most abundant forms of microbial life on earth. Their shape and architecture strongly depends on the environmental conditions in which they are grown as well as the specific properties of the species and strain used. In this study we set out to determine which distinct properties of a bacterial species or strains account for the differences between the structure of biofilm microcolonies. In order to achieve this, we introduce a metric to distinguish biofilms based on architectural measurements at single cell resolution. We use this metric to perform quantitative analysis of biofilms grown from the four different bacterial species E. coli, S. enterica, V. cholerae, and P. aeruginosa, revealing that multicellular structural parameters as well as the cell shape are highly correlated with the differences in architecture between these biofilms. Further experiments based on mutants of V. cholerae that exhibit key differences in biofilm architecture confirm our initial findings and can be matched by simulations based on physical interactions between cells.   

Live

Many bacterial species develop surface-dwelling multi-cellular colonies known as biofilms. Biofilm growth is widely regarded to depend on physical properties of the underlying substrate, such as substrate stiffness and porosity. Biofilm studies are however largely restricted to agar substrates, which have complex mechanical properties and in which stiffness and porosity cannot be independently tuned. Here, we report the use of synthetic polyacrylamide hydrogels with tunable stiffness and controllable pore size to assess the effects of substrate mechanics on biofilm development. We use time lapse microscopy to track the growth and form of expanding Serratia marcescens colonies and traction force microscopy to measure forces the bacteria exert on the surface. We find that biofilm colony growth can increase on purely elastic substrates with increasing substrate stiffness, unlike what is found on traditional agar substrates. Our results suggest that the transport and spread of bacteria can be independently modified and controlled by substrate stiffness.   

Live

A common cause of medical infections and failures is the formation of bacterial biofilms, which are produced by bacteria when attached to a surface. To study the characteristic growth patterns of catheter-infecting bacteria, we observed common pathogen Pseudomonas Aeruginosa at attachment periods of 2 hours and 24 hours after inoculation on gel surfaces of different concentrations. We saw significantly higher amounts of bacteria after two hours than after twenty-four hours, suggesting that bacteria die or detach over time. In a current study, we make use of data left from previous researches to observe bacterial attachment to a different kind of gel, the poly(ethylene glycol) diacrylate (PEGDA) hydrogels, to compare to the agar-based gel experiments. By analyzing the trends of bacteria attachment over different periods of time, and in different stiffness of gels, we hope to further analyze the growth characteristics of common infection-causing bacteria.   

Live

During chronic infections and in microbiota, bacteria predominantly colonize their hosts as multicellular structures called biofilms. A common assumption is that biofilms exclusively interact with their hosts biochemically. However, the contributions of mechanics, while being central to the process of biofilm formation, have been overlooked as a factor influencing host physiology. Specifically, how biofilms form on soft, tissue-like materials remains unknown. Here, we show that biofilms of the pathogens Vibrio cholerae and Pseudomonas aeruginosa can induce large deformations of soft synthetic hydrogels. Biofilms buildup internal mechanical stress as single cells grow within the elastic matrix. By combining mechanical measurements and mutations in matrix components, we found that biofilms deform by buckling, and that adhesion transmits these forces to their substrates. Finally, we demonstrate that V. cholerae biofilms can generate sufficient mechanical stress to deform and even disrupt soft epithelial cell monolayers, suggesting a mechanical mode of infection.   

Live

Biological pattern formation has been extensively studied using reaction-diffusion models. These models are inherently local, however many biological systems are known to exhibit nonlocality. In this talk we will discuss nonlocal pattern forming mechanisms in the context of bacterial colony formation with an emphasis on arrested fronts. This will lead to a nonlocal framework to understand the interfacial motion in biological systems. We will apply our approach to model the evolution of bacterial colonies that inhibit the growth of genetically identical colonies.   

Live

Bacteria often live in surface attached communities called biofilms. Most interactions in biofilms affect physically nearby cells, so the outcome of bacterial interactions depends on the population’s spatial structure. Biofilm structure is reminiscent of the structure of glasses; both are densely packed and structurally disordered. Glasses are non-equilibrium solids, whose properties depend on how they are formed, as well as how long they have been aging. However, little is known about how biofilm structure is impacted by details about how the biofilm was formed. Here we develop a three dimensional agent based model of biofilm formation to investigate the role of physical and biological interactions in biofilm formation.   

Live

Biofilms are ubiquitous bacterial communities embedded in an extracellular matrix. Biofilm is the predominant lifestyle of bacteria in nature, and it can cause clogging and fouling in industry and chronic infections in medicine. Many natural and industrially or clinically relevant biofilms grow inside a structured, confined environment, such as biofilms formed in food industry and in eukaryotic hosts. However, little is known as to how biofilms grow in these mechanically confined environments. In this talk, I will discuss about our recent progress in single-cell imaging and characterization tools to study the morphological evolution of biofilms grown under confinement in the model organism Vibrio cholerae, the agent causing the cholera pandemic. Using a combination of state-of-the-art imaging, image analysis, mutagenesis, computer simulations, and soft-matter theories, I will show how the mechanical environment and the biofilm growth reciprocally interact with each other, leading to the morphogenesis of confined biofilms. The fundamental understanding from our work will potentially enhance the use of beneficial biofilms in our society and mitigate biofilm-related problems in industrial and medical settings.   

Live

Bacteria are ubiquitous in our daily life, frequently as surface-attached biofilm communities. In some cases, biofilms serve a positive purpose, such as improving health or remediating polluted water; in other cases, they negatively impact our lives, such as by causing infection or fouling equipment. For both positive and negative purposes, understanding the factors that regulate the onset of biofilm formation is crucial in determining how to control or treat them. However, how bacteria transition between the free-swimming planktonic state to the sedentary biofilm state in these heterogeneous environments is poorly understood. Here, we use computational modeling to investigate how biofilm formation depends on bacterial properties as well as the properties of their environment. Specifically, by analyzing the competition between chemotactic dispersal and quorum sensing, we establish universal rules predicting how the onset and extent of biofilm formation depend on cell concentration and motility, nutrient diffusion and consumption, chemotactic sensing, and autoinducer secretion. The findings from this study therefore yield quantitative principles to predict biofilm formation.