Biofilms as self-shaping growing nematics

The yoga of droplets: coalescence in complex fluids

Coalescence of liquid drops is a widely observed phenomenon across a diverse range of natural and industrial processes, ranging from the formation of raindrops and the growth of tumor cells to inkjet printing. The physics involved in this seemingly simple process of coalescence is far from simple, and the rheological complexity of the fluid under investigation makes the problem even more challenging. The present article provides a brief overview of existing knowledge on this topic and discusses the potential avenues for future research. Special attention is given to non-Newtonian fluids and soft materials, which exhibit distinct behaviors compared to Newtonian liquids, revealing fascinating deviations that demand deeper investigation.

Smectic-like bundle formation of planktonic bacteria upon nutrient starvation

Bacteria aggregate through various intercellular interactions to build biofilms, but the effect of environmental changes on them remains largely unexplored. Here, by using an experimental device that overcomes past difficulties, we observed the collective response of Escherichia coli aggregates to dynamic changes in the growth conditions. We discovered that nutrient starvation caused bacterial cells to arrange themselves into bundle-shaped clusters, developing a structure akin to that of smectic liquid crystals. The degree of the smectic-like bundle order was evaluated by a deep learning approach. Our experiments suggest that both the depletion attraction by extracellular polymeric substances and the growth arrest are essential for the bundle formation. Since these effects of nutrient starvation at the single-cell level are common to many bacterial species, bundle formation might also be a common collective behavior that bacterial cells may exhibit under harsh environments.

Confined Mechanical Microenvironment Regulated Antibiotic Resistance in 3D Biofilm Aggregates Probed by Scanning Electrochemical Microscopy

Antibiotic resistance is a significant global concern. Clinical trials have highlighted discrepancies in antibiotic doses between in vivo three-dimensional (3D) biofilms and in vitro two-dimensional biofilm models. A critical factor often overlooked is the confined mechanical microenvironment (e.g., host extracellular matrix (ECM) stiffness) surrounding the in vivo biofilms, leading to inaccurate diagnosis and increased antibiotic resistance. Herein, we designed a 3D agarose-gel-based in vitro biofilm model and applied scanning electrochemical microscopy (SECM) to monitor the metabolic dynamics in situ, including cellular respiration and reactive oxygen species of an embedded single biofilm aggregate. We discovered distinct respiration patterns for biofilm aggregates embedded in stiff and soft gels at the single aggregate level, which was corroborated by transcriptional analysis. Our findings indicate that mechanical cues mediate antibiotic tolerance by reducing metabolic activity and increasing the production of extracellular polymeric substances (EPS). Additionally, we identified that metabolite glycine enhances the tricarboxylic acid cycle, suggesting its potential as an adjuvant to improve antibiotic efficacy. Knocking out the upregulated EPS-related gene (ΔyjbE) results in significantly reduced survival rates of ΔyjbE mutants in stiff agarose gels compared to the wild type, thereby enhancing antibiotic efficacy. Overall, our study demonstrates the versatility of the SECM-based strategy for investigating both metabolic dynamics and antibiotic resistance in biofilms and uncovers the role of ECM stiffness in mediating antibiotic resistance in 3D biofilms, paving the way for improved clinical strategies in antibiotic treatment.

Morphogenesis of confined biofilms: how mechanical interactions determine cellular patterning and global geometry

Biofilms are surface-attached bacterial communities encased within extracellular matrices that play significant roles in health and society and serve as prototypical examples of proliferating active nematics. Recent advances in fluorescence microscopy have facilitated an unprecedented view of biofilm development at the single-cell level, thus providing the opportunity to develop a mechanistic understanding of how biofilm development is influenced by mechanical interactions with the environment. Here, we review recent studies that examined the morphogenesis of Vibrio cholerae biofilms under confinement at both single-cell and continuum levels. We describe how biofilms under different confinement modes-embedded and interstitial-can acquire various global geometries and forms of cell orientational ordering different from those in unconfined biofilms, and we demonstrate how these properties arise from the mechanical interplay between the biofilm and its confining medium. We also discuss how this interplay is fundamentally governed by the extracellular matrix, which facilitates the transmission of mechanical stress from the medium into the biofilm via adhesion and friction, and serves as the key feature that distinguishes biofilms from classical bacterial colonies. These studies lay the groundwork for many potential future directions, all of which will contribute to the establishment of a new "developmental biology" of biofilms.

Surface remodeling and inversion of cell-matrix interactions underlie community recognition and dispersal in Vibrio cholerae biofilms

Biofilms are ubiquitous surface-associated bacterial communities embedded in an extracellular matrix. It is commonly assumed that biofilm cells are glued together by the matrix; however, how the specific biochemistry of matrix components affects the cell-matrix interactions and how these interactions vary during biofilm growth remain unclear. Here, we investigate cell-matrix interactions in Vibrio cholerae, the causative agent of cholera. We combine genetics, microscopy, simulations, and biochemical analyses to show that V. cholerae cells are not attracted to the main matrix component (Vibrio polysaccharide, VPS), but can be attached to each other and to the VPS network through surface-associated VPS and crosslinks formed by the protein Bap1. Downregulation of VPS production and surface trimming by the polysaccharide lyase RbmB cause surface remodeling as biofilms age, shifting the nature of cell-matrix interactions from attractive to repulsive and facilitating cell dispersal as aggregated groups. Our results shed light on the dynamics of diverse cell-matrix interactions as drivers of biofilm development.

Analytical interaction potential for Lennard-Jones rods

An analytical form has been derived using Ostrogradsky's integration method for the interaction between two thin rods of finite lengths in arbitrary relative configurations in a three-dimensional space, each treated as a line of point particles interacting through the Lennard-Jones 12-6 potential. Simplified analytical forms for coplanar, parallel, and collinear rods are also derived. Exact expressions for the force and torque between the rods are obtained. Similar results for a point particle interacting with a thin rod are provided. These interaction potentials can be widely used for analytical descriptions and computational modeling of systems involving rodlike objects such as liquid crystals, colloids, polymers, elongated viruses and bacteria, and filamentous materials including carbon nanotubes, nanowires, biological filaments, and their bundles.

Engineering Programmable Electroactive Living Materials for Highly Efficient Uranium Capture and Accumulation

Uranium is the primary fuel for nuclear energy, critical for sustainable, carbon-neutral energy transitions. However, limited terrestrial resources and environmental risks from uranium contamination require innovative immobilization and recovery solutions. In this work, we present a novel uranium recovery method using programmable electroactive living materials (ELMs). Utilizing Shewanella oneidensis, this approach leverages the intrinsic extracellular electron transfer capability of exoelectrogenic species, combining their adaptability and programmability with the robustness of engineered multicellular systems. These exoelectrogenic cells were endowed to selectively capture and enhance U(VI) reduction by expressing uranyl-binding proteins, coupled with a reconfigured transmembrane Mtr electron nanoconduit. By incorporating biofilm-promoting circuits, we improved cell-to-cell interactions and biofilm formation, enabling the stable assembly of ELMs with robust structural integrity. The ELMs demonstrated superior electrogenic activity, achieving a 3.30-fold increase in current density and a 3.15-fold increase in voltage output compared to controls in microbial electrochemical and fuel cells. When applied for uranium recovery, the ELMs exhibited robust U(VI) capture, reduction, and accumulation capabilities, with a maximum capacity of 808.42 μmol/g. This work not only provides a versatile and environmentally friendly solution for uranium recovery, but also highlights the potential of ELMs in sustainable environmental and energy technologies.

Surface remodeling and inversion of cell-matrix interactions underlies community recognition and dispersal in Vibrio cholerae biofilms

Biofilms are ubiquitous surface-associated bacterial communities embedded in an extracellular matrix. While it is commonly assumed that biofilm-dwelling cells are glued together by the matrix, how the cell-matrix interaction depends on the specific biochemistry of the matrix components and how this interaction varies during biofilm growth remains unclear. Here, we investigated cell-matrix interactions in Vibrio cholerae ( Vc ), the causative agent of cholera. We combine genetics, microscopy, simulation, and biochemical tools to show that Vc cells are not attractive to V ibrio p oly s accharide (VPS), the main matrix component, but they can be bridged with each other and to the VPS network through crosslinking by Bap1. Downregulation of VPS and surface trimming by the polysaccharide lyase RbmB cause surface remodeling as biofilms age, shifting the nature of cell-matrix interactions from attractive to repulsive and facilitating cell dispersal as aggregated groups. Our results suggest a new conceptual model in understanding the intricate cell-matrix interaction as the major driver for biofilm development, which is potentially generalizable to certain other biofilm-forming species and exopolysaccharides.

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 strongly coupled to vertical expansion via 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. Finally, we show that a simple biophysical model connecting vertical and horizontal growth dynamics can reproduce the above phenomena, suggesting that the spherical cap and spherical cap napkin ring shapes emerge due to the biophysical consequences of diffusion-limited growth. Thus, to understand the fitness of a growing biofilm, one must account for its shape, not just its cellular doubling time.

Agent-based modeling of stress anisotropy driven nematic ordering in growing biofilms

Living active collectives have evolved with remarkable self-patterning capabilities to adapt to the physical and biological constraints crucial for their growth and survival. However, the intricate process by which complex multicellular patterns emerge from a single founder cell remains elusive. In this study, we utilize an agent-based model, validated through single-cell microscopy imaging, to track the three-dimensional (3D) morphodynamics of cells within growing bacterial biofilms encased by agarose gels. The confined growth conditions give rise to a spatiotemporally heterogeneous stress landscape within the biofilm. In the core of the biofilm, where high hydrostatic and low shear stresses prevail, cell packing appears disordered. In contrast, near the gel-cell interface, a state of high shear stress and low hydrostatic stress emerges, driving nematic ordering, albeit with a time delay inherent to shear stress relaxation. Strikingly, we observe a robust spatiotemporal correlation between stress anisotropy and nematic ordering within these confined biofilms. This correlation suggests a mechanism whereby stress anisotropy plays a pivotal role in governing the spatial organization of cells. The reciprocity between stress anisotropy and cell ordering in confined biofilms opens new avenues for innovative 3D mechanically guided patterning techniques for living active collectives, which hold significant promise for a wide array of environmental and biomedical applications.

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.