Bulletin of the American Physical Society
APS March Meeting 2022
Volume 67, Number 3
Monday–Friday, March 14–18, 2022; Chicago
Session T05: Statistical Mechanics of Active Matter and Microbial EcologyFocus Recordings Available
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Sponsoring Units: DBIO Chair: Marco Polin, Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC) Room: McCormick Place W-178A |
Thursday, March 17, 2022 11:30AM - 12:06PM |
T05.00001: Overcoming physical obstacles: a collective microbial solution to a shared problem Invited Speaker: Diana Fusco Bacterial biofilms are the most pervasive life form on the planet having adapted to a wide range of living conditions. While invading new territory in the wild, biofilms periodically encounter physical barriers, including populations of other bacteria that can be so densely packed to completely halt the forward motion of individual cells. How do biofilms overcome such a challenge? |
Thursday, March 17, 2022 12:06PM - 12:18PM |
T05.00002: The Role of Quenched Noise in the Evolution of Populations undergoing Range Expansions Jimmy Gonzalez, Daniel A Beller, Jayson J Paulose, Wolfram Möbius Inferring or predicting evolutionary outcomes in populations growing on surfaces requires understanding the causes and consequences of genetic spatial structure, an area that has received much attention recently. However, much remains to be understood about the role that variability in the environment plays in the evolution of these growing populations, which may have far-reaching consequences, e.g., for the emergence of antibiotic resistance in bacterial colonies. To make progress, it is essential to understand the interplay between intrinsic demographic noise caused by genetic drift and extrinsic environmental noise that arises from interactions with landscape features, such as nutrient-rich regions of increased growth. To study the interactions between these two regimes of noise, we conduct multi-species Eden model simulations of population growth in heterogeneous landscapes, and we analyze the results through the "lenses" of population genetics and geometric optics. This allows us to characterize how repeated lensing effects from landscape features shapes the advancing colony front and creates a distinct genetic lineage structure. By connecting population genetic measures to the landscape heterogeneity, we distinguish between genetic drift and environmental noise signatures. |
Thursday, March 17, 2022 12:18PM - 12:30PM |
T05.00003: Modelling finger-like pattern formation in a bacteria colony growing at an interface using dynamical self-consistent field theory Robert A Wickham, Drake M Lee Fascinating finger-like patterns are observed at the edge of Pseudomonas aeruginosa bacteria colonies that grow at the effectively two-dimensional interface between agar and glass. We study this pattern formation phenomenon by simulating a dynamical self-consistent field theory. The twitching bacteria are modelled as self-propelled rods pushing against the agar-glass adhesion force, represented as a bath of passive particles. Fingers emerge in our simulation as regions of dense, nematically-aligned rods that move along the nematic director. We examine how a perturbation to an initially flat colony edge can evolve into a set of fingers. We investigate the relationship between the strength of the self-propulsive force and the finger speed. Introducing a random spatial variation in the agar-glass adhesion strength leads to finger shapes and finger motion similar to what is observed in experiments. |
Thursday, March 17, 2022 12:30PM - 12:42PM |
T05.00004: Calibrating active forces of gliding bacteria through self-buckling Maximilian Kurjahn, Stefan Karpitschka Abstract. Self-buckling, first described in 1778 by Leonard Euler, is the buckling of a flexible column under its own weight if its length exceeds a critical value. Here we transfer the principle of self-buckling to gliding filamentous cyanobacteria, one of the oldest lifeforms on earth with manifold potential applications in economics and ecology. These phototrophic organisms form long and flexible filaments that actively glide over solid surfaces. However, the force generation mechanism of their gliding apparatus is not yet understood. We quantify their propulsion forces by systematic self-buckling experiments: Filaments that glide onto an obstacle buckle if their body length exceeds a certain critical value. Adapting Euler’s self-buckling theory to the properties of self-propelling filaments, we derive the active force density from the critical length and an independent calibration of the bending rigidity. Our results indicate that self-buckling also plays a crucial role in natural habitats. In conjunction with polydisperse length distributions and stimuli-dependent propulsion forces, rich structures emerge, enabling colonies to adapt to an ever changing environment. |
Thursday, March 17, 2022 12:42PM - 12:54PM |
T05.00005: A phase diagram for bacterial swarming Avraham Beer Bacterial swarming is a rapid mass-migration, in which thousands of cells spread collectively to colonize surfaces. Physically, swarming is a natural example for active particles that use energy to generate motion. Accordingly, understanding the constraints physics imposes on these dynamics is essential for understanding the mechanisms underlying swarming. We present new experiments of swarming Bacillus subtilis mutants with different aspect ratios and at different densities. Analysing the dynamics reveals a rich phase diagram of qualitatively distinct swarming regimes, describing how cell shape and population density govern the dynamical characteristics of the swarm. In particular, we show that under standard conditions, bacteria inhabit a region of phase space that is associated with rapid mixing and robust dynamics, with homogeneous density and no preferred direction of motion. The results suggest that bacteria have adapted their physical properties to optimize the principle functions assumed for swarming. |
Thursday, March 17, 2022 12:54PM - 1:06PM |
T05.00006: Self-organization of bacterial colonies through quorum sensing and motility regulation Julien Tailleur, Yongfeng Zhao, Agnese Curatolo, Nan Zhou, Chenli Liu, Adrian Daerr, Jiandong Huang, Alberto Dinelli, Jérémy O'Byrne, Peter K Sollich Equilibrium statistical mechanics predicts how the self-assembly of a passive material emerges from the competition between energy and entropy. Out of equilibrium, no such principle applies and generic self-organization mechanisms are scarce. In this talk I will discuss how the regulation of motility allows bacterial colonies to self-organize in space and time. I will show how reciprocal control may lead to static phase separation with colocalization or demixing between competing strains [1], but also how non-reciprocal interactions may lead to travelling waves and dynamic patterns. For a precise type of reciprocal interactions, I will show that bacterial mixtures can be mapped onto passive colloidal systems. This mapping shows that passive self-assembly is embedded into the phenomenology accessible to bacterial suspensions. It also provides powerful principles to account for---and control---the organization of bacterial ecosystems. |
Thursday, March 17, 2022 1:06PM - 1:18PM |
T05.00007: Co-existence and extinction due to surfing viral infections in a spatially expanding bacterial colony Godwin Stephenson, Amit Nadig, Toshi Parmar, Vijay K Krishnamurthy, Namiko Mitarai, Sandeep Krishna, Shashi Thutupalli Despite their relevance in natural environments, the spatio-temporal consequences of the interactions between phages and bacteria remain largely unexplored. In the most well-studied setting, i.e. plaque formation, phages infect a uniform background of bacteria, within which the phages spread diffusively, causing the plaque front to grow linearly as a function of time. Here, we investigate the dynamics of the spread of the infection due to a phage-lambda during the range expansion of an E coli colony; the phages "surf" the front of the growing bacterial colony by hitchhiking on E coli that are advected due to growth of the bacteria in the colony, resulting in an anisotropic spread of the phages -- ballistically in the direction of colony growth and diffusively in the lateral direction (occurring over timescales of many hours and millimetric length scales). We identify microscopic processes -- of the phage release during lysis (occurring on short millisecond timescales at length scales close to that of a single bacterium) and local nematic alignment of the rod-like E coli bacteria (occurring on timescales comparable to the bacterial growth rate and on the length scales of a few bacteria) -- that enhance the advective effects driving the hitchhiking behavior. Altogether, the interplay between the phage infection, cell replication and transport processes -- all involving multiple length and time scales, ranging from diffusion of individual phages to single-cell lysis events to colony-level patterns -- result in a panoply of dynamical patterning phenomena. Combining our experiments with simulations, we explain the multiple spatio-temporal dynamical regimes -- from coexistence of the uninfected bacteria, resistant (lysogenic) cells and phages to fixed points where the entire population turns resistant or remains uninfected. |
Thursday, March 17, 2022 1:18PM - 1:30PM |
T05.00008: Cellular sensing governs the stability of chemotactic fronts Ricard Alert, Sujit Datta In contexts ranging from embryonic development to bacterial ecology, cell populations migrate chemotactically along self-generated chemical gradients, often forming a propagating front. I will theoretically show that the stability of such chemotactic fronts to morphological perturbations is determined by limitations in the ability of individual cells to sense and respond to the chemical gradient. Specifically, I will argue that cells at bulging parts of a front are exposed to a smaller gradient, which slows them down and promotes stability, but they also respond more strongly to the gradient, which speeds them up and promotes instability. We predict that this competition leads to chemotactic fingering when sensing is limited at too low chemical concentrations. Guided by this finding and by experimental data on E. coli chemotaxis, we suggest that the cells' sensory machinery might have evolved to avoid these limitations and ensure stable front propagation. Finally, as sensing of any stimuli is necessarily limited, the principle of sensing-induced stability may operate in other types of directed migration such as durotaxis, electrotaxis, and phototaxis. |
Thursday, March 17, 2022 1:30PM - 1:42PM |
T05.00009: Bacteria bioluminesce in response to fluid shear Sumit Kumar Birwa, Raymond E Goldstein, Nuno M Oliveira Many bacteria display bioluminescence, through which they convert chemical energy into light that illuminates the sea. While it is known that mechanical stress can trigger bioluminescence in eukaryotes such as dinoflagellates, it has often been suggested that this is not true for bacteria. Here, we combine imaging and rheology experiments to show that bacteria indeed emit light in response to shear within seconds of stimulation. The light intensity increases sigmoidally with shear rate and the response to shear ramps exhibits species-dependent hysteresis. This response is consistent with that of shear-activated ion channels in eukaryotic cells leading to calcium signaling, and hysteresis is a common feature of ion channels in other systems. We capture the full range of observations with a two-state adaptive kinetic model with the time scale for opening and closing of channels of the order of seconds. The time scale for adaptation of the total number of channels to shear is larger and introduces the unsteadiness in the system that leads to hysteresis. |
Thursday, March 17, 2022 1:42PM - 1:54PM |
T05.00010: Light-induced phase separation and pattern formation by phototactic micro-algae Raphael Jeanneret, Nicolas Desprat, Isabelle Eisenmann Excess of light can be hazardous and lethal for photosynthetic organisms. When intensity is too high, the motile micro-algae Chlamydomonas reinhardtii therefore reorient itself to swim away from the incident light (negative phototaxis). We recently discovered that a collection of such migrating cells can be unstable, whereby small spatial fluctuations in cell density can trigger the local densification of the system and the formation of dynamic branching patterns, whose features depend on the global cell density, the intensity of light and the concentration of extra-cellular calcium. Mutants with deficient eyespots (organelle for light detection) still perform negative phototaxis but do not exhibit branching patterns. This new kind of instability originates from the strong coupling between cell density and light fields through both negative phototaxis and light scattering by the individual cells. Here I will present our results on the quantitative characterization of the patterns as well as the simple model we developed in order to rationalise our observations. We believe our findings will help to better understand the phototactic reorientation mechanism of the algae and will provide a simple protocol to quantitatively assess phototactic abilities of micro-algae populations. |
Thursday, March 17, 2022 1:54PM - 2:06PM |
T05.00011: Phototaxis of the dominant marine pico-eukaryote Micromonas sp.: from population to single cell. Marco Polin, Richard J Henshaw, Raphael Jeanneret Micromonas is a unicellular photosynthetic pico-eukaryote globally dominant in marine ecosystems. Although previously been described as strongly phototactic, its phototactic strategy and indeed its motility are currently poorly understood. It is also unclear how light is detected, given that the tiny cells do not possess the eyespot typical of larger unicellular green algae: the organism is essentially blind. Here we first perform population-scale phototactic experiments to show that this organism actively responds to a wide range of light wavelengths and intensities. These population responses follow a simple drift-diffusion framework displaying a all-or-none-type response to light. Single-cell tracking experiments detail thoroughly the way Micromonas sp. explore its environment. The extracted motility resembles the run-and-reverse styles of motion commonly observed in marine prokaryotes but with long stopping periods between runs and no specific pattern in the sequence of reversals. The associated peculiar microscopic changes upon photostimulation are finally described and integrating those into jump-diffusion simulations produces phototactic drifts that are quantitatively compatible with those obtained experimentally at the population level. These drifts match the natural sedimentation speed of cells, providing the cells with a mechanism to stay within the photic zone. We conclude with a perspective on the possible mechanism that the cells might utilize to recognise where the light is coming from. |
Thursday, March 17, 2022 2:06PM - 2:18PM |
T05.00012: Microbial narrow-escape is facilitated by wall interactions Antoine Allard, Mathieu Souzy, Jean-Francois Louf, Idan Tuval, Marco Polin Cells have evolved efficient strategies to probe their surroundings and navigate through complex environments. From metastatic spread in the body to swimming cells in porous materials, escape through narrow constrictions - a key component of any structured environment connecting isolated micro-domains - is one ubiquitous and crucial aspect of cell exploration. Here, using the model microalgae Chlamydomonas reinhardtii, we combine experiments and simulations to achieve a tractable realization of the classical Brownian narrow escape problem in the context of active confined matter. Our results differ from those expected for Brownian particles or leaking chaotic billiards and demonstrate that cell-wall interactions substantially modify escape rates and, under generic conditions, expedite spread dynamics. |
Thursday, March 17, 2022 2:18PM - 2:30PM |
T05.00013: How encounters at the microscale prime microbial ecosystems Jonasz J Slomka, Roman Stocker Microorganisms control the global biogeochemistry of the oceans through interactions between individual cells and between cells and particles of organic matter. Prominent examples include marine snow formation by phytoplankton following a phytoplankton bloom or bacterial degradation of marine snow responsible for carbon export from the upper ocean in the biological pump. A variety of physical mechanisms can drive these interactions, including diffusion, active swimming, gravitational settling and turbulent mixing, and the concept of encounter rates provide a unifying framework to describe them. However, the corresponding collision kernels, which map the physical mechanisms to the frequency of encounters, have been traditionally computed for inanimate particles. Here, we first describe the impact of elongation, sinking and turbulence on marine snow formation, and later we describe the impact of elongation and fluid shear on the encounters between motile bacteria and sinking particles of organic matter. Overall, our results demonstrate that microbial traits must be taken into account to accurately predict encounter rates at the microscale, which govern the large carbon flux in the ocean's biological pump. |
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