Bulletin of the American Physical Society
APS March Meeting 2021
Volume 66, Number 1
Monday–Friday, March 15–19, 2021; Virtual; Time Zone: Central Daylight Time, USA
Session E13: Physics of Biological Active Matter II: Cell ColoniesFocus Live
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Sponsoring Units: DBIO DPOLY DSOFT Chair: Joshua Shaevitz, Princeton University; Ricard Alert, Princeton University |
Tuesday, March 16, 2021 8:00AM - 8:36AM Live |
E13.00001: Motility-induced buckling and glassy dynamics regulate 3D transitions in bacterial colonies Invited Speaker: Sho C Takatori A key step in the development of many bacterial colonies and biofilms is a transition from a two-dimensional (2D) monolayer into a three-dimensional (3D) structure. In this talk, we explore the mechanisms behind the 2D-to-3D transition of motile Pseudomonas aeruginosa colonies. We show that the viscous shear stresses and dynamic pressures arising from bacterial swarming allow cells to overcome cell-substrate adhesion, leading to rate-dependent buckling into the third dimension. Furthermore, we show that bacterial monolayers exhibit a crossover from a swarming state to a kinetically-arrested, glassy-like state above an onset density, resulting in a distinct 2D-to-3D transition. In our approach, we combine experimental observations of P. aeruginosa colonies at single-cell resolution, molecular dynamics simulations of active particles, and theories of 2D fluid films. We develop a dynamical state diagram to predict the various buckling mechanisms governing the 2D-to-3D transitions in bacterial colonies. |
Tuesday, March 16, 2021 8:36AM - 8:48AM Live |
E13.00002: Intrinsic Rhythms in a Giant Single-Celled Organism and the Interplay with Time-Dependent Drive, Explored via Self-Organized Macroscopic Waves Eldad Afik, Tony J.B. Liu, Elliot M. Meyerowitz Living Systems often seem to follow, in addition to external constraints and interactions, an intrinsic predictive model of the world — a defining trait of Anticipatory Systems. |
Tuesday, March 16, 2021 8:48AM - 9:00AM Live |
E13.00003: Nonequilibrium polarity-induced chemotaxis: emergent Galilean symmetry and exact scaling exponents Saeed Mahdisoltani, Riccardo Ben Alì Zinati, Charlie Duclut, Andrea Gambassi, Ramin Golestanian A generically observed mechanism that drives the self-organization of living systems is interaction via chemical signals among the individual elements--which may represent cells, bacteria, or even enzymes. Here we propose a novel mechanism for such interactions, in the context of chemotaxis, which originates from the polarity of the particles and generalizes the well-known Keller-Segel interaction term. We study the resulting large-scale dynamical properties of a system of such chemotactic particles using the exact stochastic formulation of Dean and Kawasaki along with dynamical renormalization group analysis of the critical state of the system. At this critical point, an emergent ``Galilean'' symmetry is identified, which allows us to obtain the dynamical scaling exponents exactly; these exponents reveal superdiffusive density fluctuations and non-Poissonian number fluctuations. We expect our results to shed light on how molecular regulation of chemotactic circuits can determine large-scale behavior of cell colonies and tissues. |
Tuesday, March 16, 2021 9:00AM - 9:12AM Live |
E13.00004: The role of eDNA in the formation of biofilm streamers Giovanni Savorana, Alessandra Vitale, Leo Eberl, Roman Stocker, Roberto Rusconi, Eleonora Secchi Across many different habitats, bacteria are often found as sessile communities embedded in a self-secreted matrix of extracellular polymeric substances (EPS). The biofilm matrix enhances bacterial resistance to harsh environmental conditions and antimicrobial treatments. Nevertheless, little is known about how environmental features shape its microstructure and chemical composition. |
Tuesday, March 16, 2021 9:12AM - 9:24AM Live |
E13.00005: Genome-scale simulations of Escherichia coli colony morphologies and genetic demixing Ilija Dukovski, Alexander Golden, Daniel Segrè, Kirill S Korolev
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Tuesday, March 16, 2021 9:24AM - 9:36AM Live |
E13.00006: Tubulation and dispersion of oil by growth of marine bacteria on oil droplets Vincent Hickl, Gabriel Juarez Bacteria on surfaces exhibit collective behaviors such as active turbulence and active stresses, which result from their motility, growth, and interactions with the local surroundings. However, interfacial deformations on soft surfaces and liquid interfaces caused by active growth, particularly over long time scales, are not well understood. Here, we describe experimental observations on the emergence of tubular structures arising from the growth of rod-shaped bacteria at the interface of oil droplets in water. Using microfluidics and time-lapse microscopy, we quantify the dimensions and growth rates of individual tubular structures as well as bulk biofilm formation on hundreds of droplets over 72 hours. We find that tubular structures are composed of an inner filament of oil stabilized by an outer shell of bacteria and are comparable in size to the initial droplet radius. These oil filaments then undergo breakup into smaller microdroplets dispersed within the bacterial shell. Finally, we describe how oil tubes, microdroplets, and bacteria break off from the droplet into its surroundings. This work provides insight into active stresses at deformable interfaces and improves our understanding of oil biodegradation and its influence on the transport of oil droplets in the ocean. |
Tuesday, March 16, 2021 9:36AM - 9:48AM Live |
E13.00007: Chemotactic smoothing of bacterial populations Tapomoy Bhattacharjee, Daniel Amchin, Ricard Alert, Jenna Ott, Sujit Datta How do bacterial populations regulate morphology? Previous studies have identified several key factors that play a role in population morphogenesis, such as differential growth, intercellular mechanics, substrate interactions, and osmotic stresses. Here, we describe a previously undocumented mechanism by which bacterial populations regulate their morphology: via self-generated chemotaxis, biased motion in response to a self-generated nutrient gradient. Using experiments on 3D-printed bacterial populations, we demonstrate that this mechanism causes perturbations in population morphology to self-smooth, and characterize its dependence on cellular motility and initial population morphology. Further, by combining continuum-scale simulations with a linear stability analysis, we identify two distinct modes in which chemotaxis smooths a population: through differential cellular motility in response to either morphology-dependent nutrient availability or morphology-dependent nutrient sensing. Our analysis quantifies the rate at which these modes smooth perturbations in general, providing a framework by which chemotactic smoothing can be predicted and controlled. |
Tuesday, March 16, 2021 9:48AM - 10:00AM Live |
E13.00008: Light-regulated cell aggregation in confinement Alexandros Fragkopoulos, Jeremy Vachier, David Zwicker, Michael Wilczek, Marco G. Mazza, Oliver Baeumchen Photoactive microbes live in complex environments with spatially and temporally fluctuating light conditions. They have adapted to such habitats by switching their metabolic activity from photosynthesis to aerobic respiration in unfavorable light conditions. We demonstrate that under confinement this adaptation in a suspension of soil-dwelling Chlamydomonas reinhardtii cells leads to a spontaneous separation into regions of high and low cell densities. We show that the inhibition of the photosynthetic machinery is necessary but insufficient to generate the observed aggregation. Microfluidic experiments, simulations, and mean-field theory approaches demonstrate that the emergence of microbial aggregations is governed by the oxygen concentration field inside the microhabitat. In fact, in regions where the energy production is completely arrested by both, the photosynthetic and respiratory systems, the cell speed decreases resulting in an aggregation, which thus takes the form of the underline oxygen field. |
Tuesday, March 16, 2021 10:00AM - 10:12AM Live |
E13.00009: Density phase transition of spatially confined bacteria Yuya Karita, Oskar Hallatschek Microbes often colonize spatial niches such as colonic crypts in a gut or glands on skin. Understanding colonization and competition processes within each spatial niche is fundamental to interpret metagenomic data. In this study, we culture fly-gut-derived Acetobacter indonesiensis cells in microfluidics, and find three distinct density states sharply depending on the chamber depth. The critical depth for the transition is shown to be determined by the ratio of the diffusion constant and growth rate of cells. With a reaction-diffusion model, we show that the density-dependent diffusion stabilizes the intermediate density phase. Our results not only propose a basic null model for microbial niche colonization but also suggest novel active matter physics of proliferating and diffusing particles. |
Tuesday, March 16, 2021 10:12AM - 10:24AM Live |
E13.00010: Trail following in bacteria Katherine Copenhagen, Joshua Shaevitz Bacteria form coordinated structures out of millions of cells while individuals only sense and interact with their local environment, thus they are an excellent model system for studying active matter physics. One tool that bacteria use is stigmergy, the same mechanism ants use to form pheromone trails. When individual cells move into unexplored regions on a substrate they modify their environment, signaling other bacteria to follow in their paths. This trail following behavior plays an important role in the life cycle of several different types of bacteria including colony expansion in P. aeruginosa, and the formation of streams in M. xanthus. We study the motion of individual M. xanthus cells as they create and follow along trails. Through the use of a 3D confocal profilometer, we map out the height of a surface as cells move across it and find that single cells are capable of forming physical furrows in the substrate which other cells then move along. The patterns that arise from stigmergy are widespread in biology and much can be learned from this microscopic view of individuals creating and interacting with measurable trails. |
Tuesday, March 16, 2021 10:24AM - 10:36AM Live |
E13.00011: Growth and characteristic layering of Myxococcus xanthus active nematic droplets Cassidy Yang, Joshua Shaevitz Myxococcus xanthus is a social bacterium that exhibits nematic interactions in large populations due to its rod-like shape. When starved, the cells collectively bead from surfaces to form 3D droplet-like aggregates known as fruiting bodies, which are comprised of hundreds of thousands of cells and are crucial for sporulation and survival. We find that these aggregates break symmetry and are often elongated in shape with distinctively non-uniform contact angles. Topographical surface height measurements allow us to characterize the disparate axial and radial growth rates of these droplets, which suggest that different mechanisms underly the axial and radial dynamics. We have recently shown that the early growth of fruiting bodies occurs as a series of 2D layers that are seeded at the position of topological defects in the nematic order field.1 Here, we investigate the role of layering in the axial growth during further stages of fruiting bodies development. By tracking sparsely labelled cells, we also make progress towards understanding constrained 3D cell motion within these dense fruiting bodies. |
Tuesday, March 16, 2021 10:36AM - 10:48AM Live |
E13.00012: Bacteria growth and self-organization at liquid interfaces can buckle and deform oil droplets Gabriel Juarez Bacteria growth, colony formation, and the emergence of structure in biofilms at interfaces are relevant to many natural and industrial processes. Here we present experimental work where we use microfluidics and time-lapse microscopy to examine the growth of rod-shaped bacteria on stationary oil droplets with maximum diameters ranging from 10 to 200 micrometers. After 72 hours, we observe that droplets above a critical diameter become living oil-water interfaces while droplets below a critical diameter do not change at all. The emergence of the rich behavior of living oil-water interfaces is a result of the coupling between the adsorption and growth of bacteria at finite-area liquid interfaces. The interplay between bacteria morphology and interfacial curvature results in the self-organization of a monolayer of cells with long-range orientational order at the droplet surface. As cell growth and division continue, the stress generated from cell-cell steric interactions gives rise to the emergence of mesoscale collective motion followed by the deformation of the droplet surface, including buckling and tubulation. This setup functions as a useful model system to gain insight into active stresses at deformable interfaces and improves our understanding of microbial oil biodegradation. |
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