Bulletin of the American Physical Society
APS March Meeting 2022
Volume 67, Number 3
Monday–Friday, March 14–18, 2022; Chicago
Session B05: Physics of Bacterial Communities: Structure and MechanicsFocus Recordings Available
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Sponsoring Units: DBIO DFD DSOFT Chair: Jing Yan, Yale University Room: McCormick Place W-178A |
Monday, March 14, 2022 11:30AM - 11:42AM |
B05.00001: Universal biofilm height dynamics Pablo Bravo, Siu Lung Ng, Brian Hammer, Peter Yunker Bacterial colonies play important roles in ecology and medicine, as they are sources of infection and they account for a large percentage of biomass on Earth. However, fundamental questions remain about the nature and dynamics of the vertical growth of biofilms. Through interferometry, we can capture their height dynamics with nanometer precision. With this tool, we characterize their growth and show that current literature models do not capture the behavior of the system on short and long timescales. |
Monday, March 14, 2022 11:42AM - 11:54AM |
B05.00002: Bacteriophage-driven spatial structuring of Pseudomonas aeruginosa biofilms Robert E Edmiston, Hemaa Selvakumar, Joshua S Weitz, Stephen P Diggle, Jennifer E Curtis Bacteriophages (“phage”) are viruses that exclusively infect bacteria and are promising alternatives to antibiotics in eliminating biofilms. However, the interaction of phage with biofilm structure remains underexplored. We have shown that, in Pseudomonas aeruginosa biofilms, lytic phage can induce a dramatic rearrangement of the rod-shaped cells into ordered, laterally aligned “stacked” aggregates. This is due to the entropic depletion force, which arises from the exclusion of smaller particles from the vicinity of bacterial cells. Critically, as phage infect and lyse cells, progeny phage and biopolymers accumulate in the extracellular space, eventually attaining the densities required for the depletion force to operate. This phenomenon poses a novel problem for phage therapy: the very agent used to destroy infecting bacteria may instead promote their flourishing by restructuring surviving cells into phage-resistant aggregates. In this talk, I will identify the conditions under which phage-induced aggregation occurs and discuss their relevance to human infections. I will then provide evidence that stacked aggregates confer greater protection from phage than the typical biofilm environment. |
Monday, March 14, 2022 11:54AM - 12:06PM |
B05.00003: A Computational Model of Interface Formation in Bacterial Colonies Joseph Larkin, Gürol Süel, Alan Gillman, Jake McCool, Caelan Brooks, Andrew Mugler Bacterial colonies benefit from heterogeneity: cells differentiate into diverse physiology and gene expression states. During growth, these states form patterns. To uncover the functional relevance of emergent patterns, we must model how they arise from cellular growth, phenotype inheritance, and interactions. Here we present an agent-based model to predict patterns formed by motile and matrix-producing cells in growing Bacillus subtilis colonies. By incorporating phenotype inheritance, differential cell interactions, and escape of outer motile cells, our model predicts the emergence of a pattern: matrix surrounds a fractal-like motile population. We find that some properties of the motile-matrix pattern depend on the initial arrangement of cells, while others do not. Using box-counting, we show that the emergent interface exhibits a fractal dimension that increases as cells grow but eventually saturates as the thickness of the peripheral matrix layer exceeds the capacity of inner cells to push it away. The presence of the fractal interface correlates with larger colony growth rates and increases the proximity of motile and matrix cells, potentially promoting resource sharing. Our results illustrate how population-level properties emerge from the interactions of individual cells. |
Monday, March 14, 2022 12:06PM - 12:42PM |
B05.00004: Confinement-induced self-organization in growing bacterial colonies Invited Speaker: Luca Giomi When confined in a long channel, colonies of rod-shaped sessile bacteria are observed to form highly ordered structures, where the cells are aligned along the channel's longitudinal direction. By contrast, freely expanding colonies on an open surface, give rise to a "mosaic" of microdomains consisting of mutually aligned cells, but whose average orientation does not propagate over the length scale of the entire colony. In this talk, I will describe our recent theoretical and experimental efforts toward understanding the origin of these fascinating examples of self-organisation in growing active matter. |
Monday, March 14, 2022 12:42PM - 12:54PM |
B05.00005: Growth of bacterial biofilms at interfaces Japinder Nijjer, Thomas Henzel, Changhao Li, qiuting zhang, Sulin Zhang, Tal Cohen, Jing Yan In many ecological niches, growth of bacterial biofilms is mechanically coupled to their surroundings. However, how the mechanical environment shapes the growth of biofilms is still unknown. Using Vibrio cholerae as a model biofilm former, we investigate the growth of biofilms at the interface between a glass and a gel substrate. We find that the stiffness of the encasing gel determines the overall biofilm morphology. When surrounded by a soft gel, biofilms grow into a bulbous shape, that grows in a nearly shape-preserving manner, whereas when surrounded by a stiff gel, biofilms grow into a penny-like shape, that becomes apparently thinner over time. Furthermore, we elucidate the role that biofilm-surface adhesion plays on overall shape morphogenesis. Finally, we demonstrate the effect that shape has on the emergence of cell ordering and cell trajectories during biofilm development. |
Monday, March 14, 2022 12:54PM - 1:06PM |
B05.00006: A segmentation clock patterns cellular differentiation in a bacterial biofilm Kwang-Tao Chou, Dong-yeon D Lee, Jian-geng Chiou, Leticia Galera-Laporta, San Ly, Jordi Garcia-Ojalvo, Jian-geng Chiou, Gürol M Süel Contrary to multicellular organisms that display segmentation during development, communities of unicellular organisms are believed to be devoid of such sophisticated patterning. Unexpectedly, we find that gene expression underlying the nitrogen stress response of a developing Bacillus subtilis biofilm becomes organized into a ring-like pattern. Mathematical modeling and genetic probing of the underlying circuit indicate that this patterning is generated by a clock-and-wavefront mechanism, similar to that driving vertebrate somitogenesis. We experimentally validated this hypothesis by showing that predicted nutrient conditions can even lead to multiple concentric rings, resembling segments. We additionally confirmed that this patterning mechanism is driven by cell-autonomous oscillations. Importantly, we show that the clock and wavefront process also spatially patterns sporulation within the biofilm. Together, these findings reveal a biofilm segmentation clockthat organizes cellular differentiation in space and time, thereby challenging the paradigm that such patterning mechanisms are exclusive to plant and animal development. |
Monday, March 14, 2022 1:06PM - 1:18PM |
B05.00007: Impact of Spatial Structure on Heteroresistance Adam J Krueger, Pablo Bravo, Gabi Steinbach, Aawaz R Pokhrel, David Weiss, Peter Yunker Microbes are very social, as they perform much of their metabolism outside of their bodies by secreting various `public goods’ into the environment around them. Many of these public goods are antagonistic, deadly toxins produced to kill susceptible competitors. These toxins can be highly effective and are the source of most antibiotics. For survival, bacteria have evolved defense mechanisms to resist antibiotics delivered by competitors. While traditionally treated as binary – microbial populations are either resistant or susceptible to a drug – due to the lack of sensitivity in susceptibility tests, antibiotic susceptibility is analog. Heteroresistance sits between the extremes and occurs when an isogenic strain shows different levels of phenotypic resistance. This is common, occurring in over 25% of toxin-strain combinations, contributing to increasing numbers of chronic infections, treatment complications, and death in humans. |
Monday, March 14, 2022 1:18PM - 1:30PM |
B05.00008: An Agent-Based Model of Spatially Structured Bacterial Populations Louis R Nemzer Although more computationally intensive, agent-based models have many advantages over alternative simulation approaches. In particular, stochastic processes and the resulting emergent behaviors can be modeled more realistically. Here, we discuss the Stochastic Agent-Based Network-Fixation Computed Topology with Undirected Migration (SANCTUM) model. In it, agents are given qualitative or quantitative "phenotypes" and placed in one of a set of patches connected by migration paths. Each patch has a fixed number of available spaces, as well as specific properties, like antibiotic concentration. Agents undergo growth, death, and migration steps stochastically based on their phenotype and patch characteristics. Sigmoidal growth and resource limitations previously modeled using the Lotka-Volterra equations instead emerge naturally based on the number of unoccupied spaces within a patch. Using SANCTUM, we can assess the impact of network topology on the chance that a rare mutation - for example, one that confers increased antibiotic resistance - will take over a population. In this way, the evolutionary pressures that act on heterogeneous populations can be explored more systematically. Future work can extend the model to test the effectiveness of "drug sanctuaries," in which the use of certain drugs is restricted for certain patches and/or times to suppress the emergence of resistance. Similar work can be done for proposed ‘adaptive therapy’ regimes to treat cancer which seek to maximize the effectiveness of chemotherapy or radiation by carefully controlling selection pressures. Thus, SANCTUM can serve as a platform for in silico testing of novel treatment approaches based on understanding the underlying population and evolutionary dynamics. |
Monday, March 14, 2022 1:30PM - 1:42PM |
B05.00009: Spreading rates of bacteria colonies depend on substrate stiffness and permeability Merrill E Asp, Minh-Tri Ho Thanh, Alison E Patteson Many bacterial species develop surface-dwelling multi-cellular colonies known as biofilms. Biofilm growth is widely regarded to depend on physical properties of the underlying substrate, such as substrate stiffness and porosity. Biofilm studies are however largely restricted to agar substrates, which have complex mechanical properties and in which stiffness and porosity cannot be independently tuned. Here, we report the use of synthetic polyacrylamide hydrogels with tunable stiffness and controllable pore size to assess the effects of substrate mechanics on biofilm development. We use time lapse microscopy to track the growth and form of expanding Serratia marcescens colonies and traction force microscopy to measure forces the bacteria exert on the surface. We find that biofilm colony growth increases on purely elastic substrates with increasing substrate stiffness, unlike what is found on traditional agar substrates. We also find that bacteria-generated traction forces increase with greater substrate stiffness. Our results suggest that the transport and spread of bacteria can be independently modified and controlled by substrate stiffness and new models of biofilm growth based on the contribution of substrate mechanics are needed. |
Monday, March 14, 2022 1:42PM - 2:18PM |
B05.00010: Mechanophysiology of Bacterial Microcolonies Invited Speaker: Nicolas Biais While bacterial physiology has been historically studied on bacteria swimming freely in rich media, there is no doubt that this is rarely their natural habitat. Many bacteria will form small aggregates of a few tens to a few thousands cells, called microcolonies, that can either represent their usual state or the precursors of more structured biofilms. Type IV pili are ubiquitous prokaryotic appendages involved in the mechanical interactions between many bacteria. We will show how the internal and external forces shaping Type IV pili mediated microcolonies can alter the physiology of the bacteria within these microcolonies. Similarly to what has been shown for eukaryotic cells, mechanical cues can control the physiological fate of bacteria from death to antibiotic resistance. |
Monday, March 14, 2022 2:18PM - 2:30PM |
B05.00011: Exploring bacterial swarm development through smart microscopy Hannah Jeckel, Konstantin Neuhaus, Kazuki Nosho, Knut Drescher The introduction of novel, rapid methods of microscopy has enabled researchers to capture large amounts of data in a short amount of time, however the tradeoff between spatial resolution, time resolution and potential damage to biological samples from laser exposure remains unsolved. This creates the necessity of approaches to not only acquire large datasets, but smart datasets, in the sense that imaging is limited to only capture the most relevant and necessary information. Such a smart microscopy setup can be achieved for example by coupling image analysis to the microscope control, allowing on-the-fly adjustments of experimental settings such as imaging sites or exposure time. We followed this approach to create a fully automated microscope setup that adaptively performs experiments without the need for manual intervention. Here, I will describe how we take advantage of this system to investigate biological and biophysical processes in a developing bacterial swarm, following its changes as the community expands over several orders of magnitude in space. |
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