Biology subjects

Larkin, J. W.

Publications and source records attributed to Larkin, J. W..

7 recordsLinked to original sources

bioRxiv2026

Bacteria hyperpolarize in response to oxygen drop

Aerobic microbes use oxygen as a terminal electron acceptor to establish an electrochemical gradient across their cell membranes. While this membrane potential ({triangleup}{Psi}) is essential for multiple cellular processes, it is unknown if and how it is maintained in bacteria during shifts in oxygen availability. We find that bacteria hyperpolarize in response to drops in oxygen. Focusing on Bacillus subtilis and guided by modeling, we report that hyperpolarization magnitude scales with the degree of electron acceptor deprivation. We find that potassium efflux contributes to the response. Surveying mutants, we uncover genes involved in potassium homeostasis and oxygen stress that contribute to hyperpolarization. We show that hyperpolarization scales with faster growth rates resulting from nutrient type and colony spatial heterogeneity. Finally, we demonstrate that oxygen shift increases susceptibility to antibiotics. Our results demonstrate a conserved link between {triangleup}{Psi} and oxygen stress, suggesting a common mechanism for responding to shifting oxygen availability.

microbiology↗

bioRxiv2026

Motile and matrix-producing cells drive distinct modes of cell-scale motion in Bacillus subtilis colonies

The physics of cell motion and growth drives the expansion of groups of cells including bacterial colonies. Under different conditions, many species of bacteria grow with strikingly different dynamics, which can arise from the physics of constituent cells. For example, on low-percentage agar substrates, colonies often expand rapidly via motility as swarms, while on higher percentage substrates, biofilms expand slowly due to growth and pressure. However, in bacterial species Bacillus subtilis, both swarm and biofilm phenotypes contain differentiated cells in both the motile state and the matrix-producing state, provoking the question: how does phenotypic heterogeneity influence the cell-level motions that drive development? To answer this question, we used a bead-tracking assay in which we follow the motion of cell-sized fluorescent beads embedded in growing B. subtilis colonies. By being pushed due to their interactions with cells, beads passively report on local cell motion. We found that, in rapidly expanding swarms, bead motion was bimodal: some beads moved rapidly and diffusively, while others appeared to be slow or stationary. However, after following the seemingly trapped beads over many hours, we found that the beads in fact moved slowly and ballistically. In biofilms grown on higher percentage agar, we found that some beads were trapped, moving sub-diffusively over the course of biofilm growth, while others moved ballistically. We hypothesized that slow, ballistic bead motion in both swarms and biofilms was driven by groups of radially expanding matrix-producing cells. To test this hypothesis, we performed bead tracking experiments in colonies formed by regulatory mutant strains that were locked into motility or matrix production. In swarms of motile-only cells, we observed fast, diffusive bead motion with no population of slow, ballistic beads. In matrix-only biofilms, we observed that ballistic motion was heavily favored compared to wild type. These results support the hypothesis that expanding clusters of matrix cells drive slow, ballistic motion at the cellular scale during colony growth. Our results demonstrate that heterogeneous cell phenotypes contribute to heterogeneous local physics in bacterial colonies, influencing the distributions of cellular phenotypes.

biophysics↗

bioRxiv2026

Formation of a swelling gel underlies a morphological transition in Bacillus subtilis biofilms

Microbes across species and environments form biofilms, living materials composed of cells and extracellular polymers. Biofilm-dwelling cells benefit from emergent soft matter physics that sculpts three-dimensional morphologies and osmotically absorbs nutrients. Although biofilms are modeled as viscoelastic gels, the physical origins of the phase transition underlying their conversion from groups of cells to living gels have not been systematically investigated. Here, we show that Bacillus subtilis biofilms use polymer composition to tune their physical properties and drive gel formation. Using imaging and water immersion experiments with matrix knockout strains, we demonstrate the complementary roles of two polymers in this developmental transition: hydrophilic poly-{gamma}-glutamate swells colonies by absorbing water and exopolysaccharides serve as effective cross-linkers, causing a sol-gel-like phase transition that imparts structural integrity. With matrix knockout co-culture biofilms, we independently modulate the production of each polymer and reveal a phase space of biofilm morphologies. Colonies that produce both polymers develop macroscopic wrinkles. A thin-film model predicts biofilm wrinkling from swelling-generated internal strain coupled to elasticity. The model reproduces the shape of our observed morphological phase diagram. Our results demonstrate that bacteria leverage gelation to vary their material properties and morphologies, with implications for microbial ecology and engineering living matter.

biophysics↗

bioRxiv2026

Colony morphogenesis regulates sporulation dynamics in bacterial biofilms

In multicellular systems, organized phenotypic heterogeneity emerges from the interplay of processes spanning scales from molecular to population-level. Using Bacillus subtilis, we investigated feedback between the collective process of colony expansion and the distribution of spore development among individual cells, a process triggered by starvation. Biofilms are commonly studied using a strain with inhibited sporulation. Intact regulation yielded high-frequency sporulation early in biofilm growth. Biofilm composition was organized by a wave of sporulation driving biofilms toward dormancy from within. However, expansion was also maintained by non-sporulating cells in a narrow front at the external edge. Along with mathematical modeling, we also used mutants with altered biofilm morphogenesis to probe the relationship between colony expansion and sporulation. Sporulation dynamics were patterned by radial expansion, but the faster biofilms spread, the greater the separation of growth and sporulation distributions. We demonstrate essential interplay between cell behavior and the physics of collective expansion that organizes differentiation among cells.

microbiology↗

bioRxiv2024

An Agent-Based Model of Metabolic Signaling Oscillations in Bacillus subtilis Biofilms

Microbes of nearly every species can form biofilms, communities of cells bound together by a self-produced matrix. It is not understood how variation at the cellular level impacts putatively beneficial, colony-level behaviors, such as cell-to-cell signaling. Here we investigate this problem with an agent-based computational model of metabolically driven electrochemical signaling in Bacillus subtilis biofilms. In this process, glutamate-starved interior cells release potassium, triggering a depolarizing wave that spreads to exterior cells and limits their glutamate uptake. More nutrients diffuse to the interior, temporarily reducing glutamate stress and leading to oscillations. In our model, each cell has a membrane potential coupled to metabolism. As a simulated biofilm grows, collective membrane potential oscillations arise spontaneously as cells deplete nutrients and trigger potassium release, reproducing experimental observations. We further validate our model by comparing spatial signaling patterns and cellular signaling rates with those observed experimentally. By oscillating external glutamate and potassium, we find that biofilms synchronize to external potassium more strongly than to glutamate, providing a potential mechanism for previously observed biofilm synchronization. By tracking cellular glutamate concentrations, we find that oscillations evenly distribute nutrients in space: non-oscillating biofilms have an external layer of well-fed cells surrounding a starved core, whereas oscillating biofilms exhibit a relatively uniform distribution of glutamate. Our work shows the potential of agent-based models to connect cellular properties to collective phenomena and facilitates studies of how inheritance of cellular traits can affect the evolution of group behaviors.

microbiology↗

bioRxiv2024

Non-Optical, Label-free Electrical Capacitance Imaging of Microorganisms

Many fundamental insights into microbiology have come from imaging, which is typically synonymous with optical techniques. However, the sample preparation needed for many optical microscopy methods such as labeling, fixing, or genetic modification, limits the range of species and environments we can investigate. Here we demonstrate the use of electrical capacitance measurements as a non-optical method for imaging live microbial samples. In electrical capacitance imaging (ECI), samples are positioned in contact with a semiconductor sensor array, and localized capacitance measurements are made across the array. From these measurements, we generate textured images of a variety of microbial colonies. We determine that capacitance is correlated with local sample thickness by comparing ECI data to 3D confocal scans. We further illustrate with ECI that a difference in capacitance signal allows microbial species to be spatially distinguished in co-culture conditions. In order to highlight the versatility of our system, we capture the cross-sectional development of floating pellicle biofilms in a liquid culture at millimeter length scales during weeks-long time-lapse experiments. These novel results establish a new low-cost and portable platform which can be used for spatially and temporally resolved experiments in diverse environments with a wide variety of microbial species. IMPORTANCEMicrobes live in diverse environments, and occupy biological roles across many timescales. Investigating the full scope of microbial activity requires imaging systems appropriate to each context. Though optical microscopy is powerful, the use of light, lenses, and other hardware limits where it can be applied. At the same time, existing non-optical imaging methods are frequently destructive to samples and require extensive equipment. In this paper we present a non-optical imaging system that is small, cheap, requires no sample labeling, and is compatible with a variety of microbial species. Our system uses semiconductor chips to measure the inherent material properties of a sample with spatial sensitivity, producing images of microbes contrasted against their environment and each other. Our technique captures label-free, micrometer-resolution images with a pocket-sized device, enabling microbiological imaging experiments in new environments with new species.

microbiology↗

bioRxiv2022

Computational model of fractal interface formation in bacterial biofilms

Bacteria benefit from cellular heterogeneity: cells differentiate into diverse gene expression states. As colonies grow, cellular phenotypes arrange into spatial patterns. To uncover the functional role of these emergent patterns, we must understand how they arise from cellular growth and mechanical interactions. Here we present a simple, agent-based model to predict patterns of motile and extracellular matrix-producing cells in biofilms of Bacillus subtilis. By incorporating phenotypic inheritance, mechanical interactions, and peripheral motile cell dispersal, our model predicts the emergence of a pattern: matrix cells surround a fractal-like interior motile population. We find that, while some properties of the motile-matrix interface depend on initial conditions, the motile distribution at large radii depends solely on the models growth mechanism. The phenotypic interface exhibits a fractal dimension that increases as biofilms grow but reaches a maximum as the peripheral layer of matrix cells exceeds the capacity of the inner cells to push it out of the way. By varying parameters, we find correlations between the interface fractal dimension and expansion of motile cells. We validate findings using experiments on B. subtilis biofilms in microfluidics. Our model demonstrates the emergence of colony-level phenotypes from single cell-level interactions and cells modifying their own environment.

biophysics↗