Bulletin of the American Physical Society
APS March Meeting 2023
Volume 68, Number 3
Las Vegas, Nevada (March 5-10)
Virtual (March 20-22); Time Zone: Pacific Time
Session S06: Bacterial Communities IFocus
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Sponsoring Units: DBIO Chair: Sujit Datta, Princeton University Room: Room 129 |
Thursday, March 9, 2023 8:00AM - 8:12AM |
S06.00001: A population-level resolution to the colonization-dispersal tradeoff Ghita Guessous When utilizing solid substrates such as chitin, individual microbial cells must resolve the tradeoff between colonizing them for growth and dispersing from them to explore new nutrient patches. As such, we studied the strategies of chitin utilization of two different bacterial species: one favoring attachment of cells to particles and another, detachment from them. Careful mechanistic analyses of these two strategies revealed that even though individual cells were subject to the aforementioned tradeoff, bacterial populations could circumvent it through their production of localized public goods. We speculate on the ecological forces that may tune bacterial strategies for solid substrate utilization. |
Thursday, March 9, 2023 8:12AM - 8:24AM |
S06.00002: Topographic Changes in Heteroresistant Bacterial Communities Adam J Krueger, Peter Yunker, David Weiss, Bikash Bogati Antimicrobial resistance (AMR) is a current and growing threat to global health. AMR has already caused millions of deaths worldwide and continues to lead a more than 10% treatment failure rate. Without effective antimicrobials, modern medical advances such as transplants, chemotherapy, and treatment of premature infants may also not be safe to perform. Due to the lack of sensitivity of traditional susceptibility tests, AMR has largely been treated as binary – microbial populations are considered either resistant or susceptible to a drug – while AMR is actually analog – heteroresistance, persistence, and tolerance as examples. We focus on bacterial heteroresistance, which occurs when an isogenic strain of bacteria possesses phenotypically resistant and susceptible sub-populations. This susceptibility phenotype is extremely common, contributes to chronic infections, and has been correlated with treatment failure. |
Thursday, March 9, 2023 8:24AM - 8:36AM |
S06.00003: Self-organized canals enable long range directed material transport in bacterialcommunities Shiqi LIU, Liang Yang, Yingdan Zhang, Zi Jing SENG, Haoran Xu, Yilin Wu, Ye Li Long-range material transport is essential to maintain the physiological functions of |
Thursday, March 9, 2023 8:36AM - 8:48AM |
S06.00004: Morphological instability of growing competing bacterial colonies Alejandro Martinez-Calvo, Carolina Trenado-Yuste, Ned S Wingreen, Sujit S Datta In nature, bacteria are frequently found in colonies, a communal lifestyle that is known to provide advantages to the group, such as resistance to stressors, adhesion to surfaces, and collective access and processing of resources. Bacterial colonies can consist of cells with different heritable phenotypes sharing and competing for space and essential resources. Recent experiments on 2D growing multi-strain colonies have shown that cells become segregated into single-strain sectors, developing a morphological instability in which the interface between two sectors forms a dented, rough shape. To understand the mechanisms underlying such instability, we consider a minimal continuum model that incorporates cell growth and cell-substrate friction, both of which can vary between single-strain sectors. Stability analysis and numerical simulations suggest that a segregated multi-strain colony becomes morphologically unstable when sectors grow at different rates and exhibit different cell-substrate friction forces. Our model recapitulates the experimental observations, which suggests that a minimal mechanistic description captures the morphodynamics of multi-strain growing bacterial colonies. Moreover, our theoretical framework is not restricted to bacterial colonies, and can be extended to other growth-driven processes in living matter and ecological systems, such as developmental processes, the expansion of heterogeneous tumors, or engineered living materials. |
Thursday, March 9, 2023 8:48AM - 9:24AM |
S06.00005: One to many and many to one: how phenotypic heterogeneity scaffolds communal carbon-harvesting by marine bacteria Invited Speaker: Julia Schwartzman Phenotypic heterogeneity shapes the behavior of clonal bacterial populations. The existence of heterogeneous sub-populations can increase the resilience of a clonal collective, allowing the collective to perform otherwise unattainable physiological functions. However, understanding the cellular mechanisms of how heterogeneity allows novel behaviors to emerge in clonal populations remains a challenge. In this talk, I'll present recent work on how phenotypic heterogeneity facilitates the collective growth and reproduction of a marine bacterium that eats polysaccharides from brown algae, allowing a division of labor. I'll demonstrate that this highly reproducible growth process emerges when cells require local density to access nutrients. I hope to convince you that the functional consequences of such phenotypic heterogeneity have likely been under-appreciated in the context of microbial ecology. |
Thursday, March 9, 2023 9:24AM - 9:36AM |
S06.00006: Predicting metabolomic profiles from microbial composition through neural ordinary differential equations Tong Wang, Xu-Wen Wang, Kathleen Lee-Sarwar, Augusto A Litonjua, Scott T Weiss, Yizhou Sun, Sergei Maslov, Yang-Yu Liu Characterizing the metabolic profile of a microbial community is crucial for understanding its biological function and its impact on the host or environment. Metabolomics experiments directly measuring these profiles are difficult and expensive, while sequencing methods quantifying the species composition of microbial communities are well-developed and relatively cost-effective. Computational methods that are capable of predicting metabolomic profiles from microbial compositions can save considerable efforts needed for metabolomic profiling experimentally. Yet, despite existing efforts, we still lack a computational method with high prediction power, general applicability, and great interpretability. Here we develop a new method — mNODE (Metabolomic profile predictor using Neural Ordinary Differential Equations), based on a state-of-the-art family of deep neural network models. We show compelling evidence that mNODE outperforms existing methods in predicting the metabolomic profiles of human microbiomes and several environmental microbiomes. Moreover, in the case of human gut microbiomes, mNODE can naturally incorporate dietary information to further enhance the prediction of metabolomic profiles. Besides, susceptibility analysis of mNODE enables us to reveal microbe-metabolite interactions, which can be validated using both synthetic and real data. The presented results demonstrate that mNODE is a powerful tool to investigate the microbiome-diet-metabolome relationship, facilitating future research on precision nutrition. |
Thursday, March 9, 2023 9:36AM - 9:48AM |
S06.00007: Fluctuations in biofilm topographies: characterization and dynamics Pablo Bravo, Siu Lung Ng, Kathryn MacGillvray, Brian Hammer, Peter Yunker During biofilm development, colonies grow from sub-micron heights to heights of hundreds of microns. Using white-light interferometry, we measure the biofilm topography of a diverse cohort of microbes with nanometer resolution in the vertical direction, across colonies that span multiple millimeters in radius. We characterize the fluctuations through scale-free metrics like the Hurst exponent and fractal dimension, as well as standard ISO metrics. We explore the emergence of self-similarity in the profiles, as well as low amplitude and high wavelength modes close to their steady state. We then reconcile our experimental observations with well established analytical models and recent bacterial colonies representations. |
Thursday, March 9, 2023 9:48AM - 10:00AM |
S06.00008: Heterogeneity in a developing biofilm Jung-Shen B Tai, Jing Yan, Christopher M Waters Biofilm is an important lifestyle of bacteria where individual cells form aggregates embedded in a secreted matrix. Biofilm development is known to consist of three stages: initial attachment, maturation, and dispersal. However, whether individual cells display phenotypic heterogeneity in biofilm formation and the consequence of such heterogeneity in biofilm development is still largely unknown. Using Vibrio cholerae as a model organism, we aim to reveal the spatiotemporal pattern and heterogeneity of gene expression and second-messenger molecule concentration at the single-cell level. By combining fluorescent reporters and high-resolution time-lapse imaging, we found various levels of heterogeneity in a developing biofilm in expression of biofilm relevant genes such as matrix production and quorum sensing, as well as heterogeneity in cyclic-di-GMP concentration, a critical second-messenger molecule that modulates sessile-to-motile transition in many bacterial species. The heterogeneity was also found to couple to the biofilm’s mechanical environment and structural organization. Our study elucidates how biofilm regulation and heterogeneity, cell organization, and mechanical environment are correlated in driving biofilm development. |
Thursday, March 9, 2023 10:00AM - 10:12AM |
S06.00009: Mathematical Modeling of Spatio-temporal Organization of Biofilm Structure Mohammad Nooranidoost, NG Cogan Biofilms are initiated by individual polymer producing bacteria in aqueous. These polymers form a network combined with the fluid solvent creating a gel-like fluid that exhibits complex, viscoelastic rheological behavior and is involved in biofilm development and integrity. In this work, we developed a mathematical model to describe the spatio-temporal organization of the biofilm components in various settings. The biofilm is modeled as a multi-phase system where each volume in space is fractionally occupied by the polymeric network and the fluid solvent. The polymeric network is modeled as a chemically active, viscoelastic fluid that induces viscoelastic stresses and osmotic pressure due to the chemical reactions of the active polymers. The fluid solvent is modeled as a Newtonian fluid. Each fluid moves with its own velocity and the difference in velocities develop a drag force between the phases, coupling the mechanics. Using numerical methods similar to those used to solve the Navier-Stokes equations, we investigated the dynamics and motion of the biofilm. Our numerical results help characterize the role of polymeric networks and various extracellular polymeric substances in the pattern formation of the biofilm structure. |
Thursday, March 9, 2023 10:12AM - 10:24AM |
S06.00010: Force balance and surface interactions play an important role in determining bacterial colony growth rate Aawaz R Pokhrel, Gabi Steinbach, Siu L Ng, Brian Hammer, Peter Yunker Bacteria often live in surface attached, densely packed communities called biofilms. Though biofilms expand both across and perpendicular to the surface they sit on, we lack a systematic framework that would allow us to assess the impact of vertical growth on horizontal expansion. Here, we use interferometry to measure the three-dimensional surface morphology of biofilms grown on different surfaces. We find that colonies that grow at different rates exhibit different shapes. In particular, we observe that as the colony contact angle increases the horizontal expansion rate decreases; this observation holds across many different strains and species. More cells are necessary to increase the radius of a steep biofilm than the radius of a shallow biofilm, so higher contact angle biofilms expand at a slower rate than lower contact angle biofilms. We show that contact angle depends on the balance between three forces at the biofilm edge in a manner reminiscent of the Young equation for sessile drops. Thus, we find that mechanical interactions and shape of a colony play a crucial role in determining colony growth rate. |
Thursday, March 9, 2023 10:24AM - 10:36AM |
S06.00011: Mechanics of biofilm adhesion to ultra-thick polymer brushes Katherine E Powell, Jessica Faubel, Jennifer E Curtis Intractable biofilms cause tremendous problems in health and industrial settings. This work explores whether and how fluid-like interfaces conferred by ultra-thick polymer brushes have the potential to limit biofilm adhesion. We explore the hypothesis that the lack of sizable mechanical cues to adhering bacteria prevents the bacteria from entering a biofilm state and hence, limits biofilm formation and attachment to the substrate. While polymer brushes have been used in previous studies to minimize biofilm attachment, the mechanism relied upon the physiochemical properties of densely grafted, antifouling polymers. The giant tunable hyaluronan polymer brushes used in this investigation can be grown to be up to 10-100 times thicker than those previously used and have distinct mechanical properties that alter the physical cues provided to bacteria. In this study, we quantify bacterial adhesion and biofilm state while varying the mechanical properties of the brushes by manipulating their grafting density, growth conditions, and post-growth chemical modification, allowing for the creation of brushes of varying height and stiffness. This study will offer insight into a possible new way to thwart biofilm formation and guidance for the design of future surface coatings. |
Thursday, March 9, 2023 10:36AM - 10:48AM |
S06.00012: Rheology of the Environment Regulates Bacterial Growth Anna M Hancock, Sujit S Datta Many bacterial communities inhabit complex environments such as soils and biopolymer gels secreted by a host or the bacteria themselves. In these settings, the cellular surroundings are rheologically complex, subjected to flow, and frequently have limited nutrient availability. Within the human body alone, the rheological properties of a microbe's environment can change drastically depending on location in the body and host physiology. Here, by probing bacterial growth in granular hydrogel matrices with defined structural and rheological properties, we demonstrate that the rheology of the environment modulates flow-induced transport of essential nutrients—thereby regulating bacterial metabolism and cellular physiology. Our work thus reveals a new mechanism, beyond mechanosensing, by which mechanics modulates microbial behavior. |
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