Session T14: Biological Active Matter I

TBD

TBD   

Substrate stiffness-dependent bacterial growth dynamics in 3D

Complex microenvironments inside our body—such as the gut mucosal layer—host diverse microbial communities that symbiotically regulate our metabolism and health. Our daily diet, immune response, and physical activities dynamically alter the mechanical properties of the gut mucosal layer. Interestingly, in 2D culture, the variation in mechanical stiffness of soft agar substrates significantly affects bacterial growth, morphology, and pathogenicity. However, despite extensive metagenomic profiling of gut microbiota, bacterial growth dynamics in 3D and its dependence on the stiffness of their natural habitat remain poorly understood. Here, we employ a porous growth medium made from jammed polyelectrolyte microgels, which replicates the viscoelastic properties of mucus. We use different microbial strains isolated from red flour beetles and directly quantify their population scale growth dynamics within 3D medium of varying stiffness. The optically translucent 3D growth medium supports direct visualization of bacterial proliferation through live-cell imaging and absorbance-based growth curves. By combining our experimental results with an agent-based simulation, we will present how increase in stiffness differentially affect the growth of various bacterial strains.   

Morphodynamics of growing bacterial communities in polymeric environments

Many bacteria live in polymeric environments, such as mucus in the body, exopolymers in the ocean, and cell-secreted extracellular polymeric substances (EPS) that encapsulate biofilms. However, most studies of bacteria focus on cells in polymer-free fluids. How do interactions with polymers influence the behavior of bacterial communities? To address this question, we experimentally probe the growth of non-motile Escherichia coli in solutions of inert polymers. We find that, when the polymer is sufficiently concentrated, the cells grow in striking “cable-like” morphologies—in stark contrast to the compact morphologies that arise in the conventionally-studied polymer-free case. Experiments and agent-based simulations show that these unusual community morphologies arise from a combination of polymer-induced entropic attraction between cells and their hindered ability to diffusely separate from each other in a viscous solution. These results suggest a pivotal role of polymers in regulating microbe-host interactions, e.g. by promoting bacterial exposure to external biochemicals that protect the host against pathogens. More broadly, this work helps to uncover quantitative principles governing the morphogenesis of diverse forms of growing active matter in polymeric environments   

Cooperation of motility- and growth-driven activity in biofilm dynamics

Bacterial communities have often been investigated as active nematic systems in which activity is driven either by cell motility or cell growth. Although it is known that both mechanisms are present in a single community, it remains unclear what roles these coexisting sources of activity play in cellular interactions and collective behaviors. We have explored this at the single cell level using experimental and computational approaches.

We used confocal fluorescence microscopy to capture the spatiotemporal behavior and patterning of Bacillus subtilis biofilms, focusing on the specific contributions of flagella-propelled motile cells and growing chains of matrix-producing cells. These experiments showed that cell type proportion and spatial distribution are maintained during biofilm expansion. The contributions of the two cell types on dominant loop motifs, topological defects, local velocity and order were also explored. We probed these dynamics further using a finite element modeling framework in which cells are represented as elastic spherocylinders with the ability to self-propel or chain. By varying key parameters, such as activity level, adhesion, and cell type proportion, we saw that both sources of activity are important for pattern formation, although their heterogeneous interactions are more influential than their activity levels.   

Instantaneous polar order enhances cell aggregation in thin Myxococcus xanthus layers - experiment

Colonies of the social bacterium Myxococcus xanthus transition from a thin layer of cells to three-dimensional droplet-like fruiting bodies in a nutrient-poor environment. This morphological transition happens as the cells reduce their reversal frequency, but mechanically why this change in motility leads to the formation of 3D layering is not understood. As a system composed of self-propelled rods [1], many features of the densely packed cell layer are well captured when modeled as an active nematic [2]. However, the role of local polar order has not been explored. Using a mutant with fluorescently labeled MglB proteins, we directly measured the polarity of individual cells and revealed a transient local polar order in thin M. xanthus colonies controlled by cell reversal frequency. We find that polar order leads to large fluctuations in surface stress and drives out-of-plane cell motion. Positive defects in the nematic director field that develop high polarity then ultimately drive layering and fruiting body formation. By controlling their reversal frequency, M. xanthus cells control local polarity and regulate the behavior of the population.

[1] Bar, et al. Annual Review of Condensed Matter Physics, 11(1):441–466, 2020.

[2] Copenhagen, et al. Nature Physics, 17(2):211–215, 2021.   

Instantaneous polar order enhances cell aggregation in thin Myxococcus xanthus layers - theory

Populations of self-propelled rods, such as bacteria, are active materials with both polar and nematic characteristics. The motion of cells is polar, while the interactions between cells is nematic. We study the social bacterium Myxococcus xanthus, a gliding species that utilizes its properties as an active material to drive layer formation as part of a developmental cycle [1]. M. xanthus cells reverse direction every few minutes. Reversal frequency drops during starvation, leading to increased layer formation. The directed motion of non-reversing cells results in regions with high polar order, while also displaying half-integer charge defects characteristic of nematics. We aim to understand the interplay of polar order and nematic defects within M. xanthus layers. We track cells and study their motion within monolayers, but cell tracking is nearly impossible during layer formation events. We introduced the essential properties of M. xanthus populations into a customized version of the molecular dynamics simulation program LAMMPS [2], and simulate monolayers and layer formation events to study the role of polarity in active materials with nematic interactions.

[1] Copenhagen, et al. Nature Physics, 17(2):211–215, 2021

[2] A. P. Thompson, et al, Comp Phys Comm, 271 (2022) 10817   

Self-buckling and self-writhing of semi-flexible swimmers

Multi-flagellated microorganisms can buckle and writhe under their own activity as they swim through a viscous fluid. New equilibrium configurations and steady-state dynamics emerge which depend both on the organism's mechanical properties and the oriented distribution of flagella along its surface. Modeling the cell body as a semi-flexible Kirchhoff rod driven from equilibrium by a dynamically evolving flagellar orientation field, we derive the Euler-Poincaré equations governing the evolution of the system, and rationalize experimental observations of buckling and writhing of elongated P. mirabilis cells. We identify, through numerical simulation, a sequence of pitchfork and Hopf bifurcations as the body is made more compliant. The results suggest a maximum speed that can be achieved by swimming microorganisms for a given body stiffness.   

Spiral waves in a bacterial population

Spiral waves are discovered in various chemical, biological and physical systems, such as chemical excitable medium, cardiac tissue, and neural networks. The onset of spiral waves in living systems is often associated with essential living functions. For example, spiral waves of electrochemical activities in neural tissues may serve as a rhythmic organizer in cortex neurons, while those in cardiac tissues may cause ventricular arrhythmia. Here, we discovered a unique type of spiral waves in a bacterial population resulting from cell density variation. The waves are highly stable in space and time and are resilient to perturbations. Our findings provide new insight to the synchronization phenomena and pattern formation in living matter.   

Author not Attending

Photosynthetic microorganisms are fundamental to the global ecosystem. They form a large portion of the base of major food webs, including oceanic, and contribute about half of all global oxygen production. These organisms also present possible exciting solutions to many of the most pressing global issues, from the production of fuel alternatives to sustainable agriculture. Light management is essential to the function of such organisms. Specifically, spatio-temporal variations provide information critical to biological regulation and impart energy to fuel intracellular processes. Crucially, these organisms must avoid excess light, as even small deviations can cause serious photooxidative cellular damage and death. Motile organisms deploy two strategies to mitigate intense exposure. Firstly, by using light as information, phototaxis (PT) mechanisms redirect organisms towards/away from light. Secondly, by using light as energy, photosynthesis (PS) systems regulate or dissipate excesses, non-photochemical quenching (NPQ). Observations suggest a fundamental link between PS, PT and NPQ, which has not been studied in quantitative detail. However, the links between these strategies is poorly understood. In this work we aim to bridge this gap, combining experimental measurements of the model microswimmer Chlamydomonas reinhardtii and a modelling approach. This is aimed at linking the intracellular level (SP, NPQ) and the extracellular level (PT) to understand how light is managed by motile photosynthetic microorganisms, and further to enable predictions of the responses at the individual and collective levels.   

Nematode motility in granular media

Caenorhabditis elegans—an optically transparent nematode—are extensively used as a model organism to explore questions in genetics, developmental biology, and neurobiology. Many of these studies identify the behavioral traits of worms by observing their locomotory patterns. While in their natural settings these worms navigate complex three-dimensional, disordered environments such as soft soil, rotten fruit, and plant stem, most of our understanding of their locomotion comes from studying them on soft two-dimensional surfaces or inside homogeneous liquid media. In this study, we aim to address how worms navigate through a three-dimensional, granular medium—much similar to their natural habitat. We have designed a transparent, self-healing granular material by packing micron-scale hydrogel particles to mimic the natural habitat of nematodes. Through direct visualization of nematode locomotion inside these granular microenvironments, we are exploring how the stiffness of these 3D media affects worm motility. We will present how worms smoothly alter their motility pattern in different granular environments.   

Trying so hard but going nowhere: Swimming of drugged Daphnia magna

Daphnia or water fleas are millimeter sized microcrustaceans commonly studied as model organism in ecology, ecotoxicology and evolutionary biology. They propel themselves through water using powerstroke motion, by periodically beating their antennae. These antennae movements change dynamically to achieve particular swimming gaits whose descriptions in the literature have been qualitative and vaguely quantitative. Our study creates a granular level quantitative classification of baseline motion parameters of these swimming gaits. To further study the impact of these gaits on the dynamics, speed and efficiency of swimming, we treated these organisms with a dopamine receptor agonist. This drug is known to decrease the average swimming speed of the daphnids, however the exact physical mechanism by which that happens remains unclear. We image the beat patterns of the Daphnia antennae using high-speed video microscopy. By tracking the position and shape of the antennae during the beating cycle, we identify the features of the swimming gait that lead to emergence of distinct mobility patterns that decreases their overall speed.

 

    

Tracking Bacillus subtilis in 2D and Study of its Heterogeneous Motility with Run-and-Tumble Model

Bacteria swim in the medium by consuming energy, and they can be considered as a living active matter. Swimming of a flagellated bacterium is often described by run-and-tumble (RT) dynamics, which models the trajectory of particle as a combination of run and tumble states. The motility of bacteria in the real world is affected by various natural stochasticities and heterogeneities. In this work, we study the motility of bacteria by comparing the trajectory of swimming B. subtilis with that of RT simulation. For the data collection, we adopt instance embedding, which is a deep learning (DL) based instance segmentation method, to detect the positions of bacteria from experimental video. Training data required for DL is prepared by generating synthetic images and trajectories of bacteria based on experimental data. In RT simulation, we introduce heterogeneity by dispersing the internal speed of particles while stochasticity is reflected through diffusion parameters. As a result, our heterogeneity model successfully reproduces the probability distribution of relative displacement of the experimental trajectory, whereas the simulation with homogeneous model results in much less variance in the x directional distribution of the relative displacement.