Bulletin of the American Physical Society
APS March Meeting 2017
Volume 62, Number 4
Monday–Friday, March 13–17, 2017; New Orleans, Louisiana
Session H5: Bacterial Populations - Interactions and Growth |
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Sponsoring Units: DBIO Chair: Jeff Gore, MIT Room: 264 |
Tuesday, March 14, 2017 2:30PM - 2:42PM |
H5.00001: Highly multiplexed and spatially resolved phylogenetic census of microbial consortia Hao Shi, Iwijn De Vlaminck Microbes in the environment frequently live in complex biofilm communities. The spatial relationships between individual cells within a biofilm can provide insights into the ecology and function of the microbial community. Fluorescence in-situ hybridization experiments have revealed the exquisite spatial organization of microbial communities in a variety of environments. However, technical limitations of fluorescence imaging have so far significantly limited the number of observable taxons in a single experiment. We have developed a versatile method to perform highly multiplexed spatial census of microbial communities. We will present results from application of this technique to human oral biofilms. [Preview Abstract] |
Tuesday, March 14, 2017 2:42PM - 2:54PM |
H5.00002: Synchronization and survival of connected bacterial populations Shreyas Gokhale, Arolyn Conwill, Tanvi Ranjan, Jeff Gore Migration plays a vital role in controlling population dynamics of species occupying distinct habitat patches. While local populations are vulnerable to extinction due to demographic or environmental stochasticity, migration from neighboring habitat patches can rescue these populations through colonization of uninhabited regions. However, a large migratory flux can synchronize the population dynamics in connected patches, thereby enhancing the risk of global extinction during periods of depression in population size. Here, we investigate this trade-off between local rescue and global extinction experimentally using laboratory populations of \textit{E. coli} bacteria. Our model system consists of co-cultures of ampicillin resistant and chloramphenicol resistant strains that form a cross-protection mutualism and exhibit period-3 oscillations in the relative population density in the presence of both antibiotics. We quantify the onset of synchronization of oscillations in a pair of co-cultures connected by migration and demonstrate that period-3 oscillations can be disturbed for moderate rates of migration. These features are consistent with simulations of a mechanistic model of antibiotic deactivation in our system. The simulations further predict that the probability of survival of connected populations in high concentrations of antibiotics is maximized at intermediate migration rates. We verify this prediction experimentally and show that survival is enhanced through a combination of disturbance of period-3 oscillations and stochastic re-colonization events. [Preview Abstract] |
Tuesday, March 14, 2017 2:54PM - 3:06PM |
H5.00003: Population genetics with selection on multiple phases of microbial growth Michael Manhart, Bharat Adkar, Eugene Shakhnovich Microbial populations undergo multiple stages of growth, including a lag phase, an exponential growth phase, and a stationary phase. Both laboratory and wild populations may experience multiple cycles of these growth dynamics as they explore new environments, or new resources become available. Mutations typically have pleiotropic effects on multiple phases of growth, and the evolutionary fate of these mutations may depend on all of these effects. We use a simple model of population growth to quantify how selection acts on these different growth phases. The model shows how tradeoffs between the phases can give rise to complex population dynamics including frequency-dependent selection, stable and unstable coexistence of multiple strains, and non-transitive selection, where the very notion of a fitness landscape breaks down. In particular, the model predicts how to tune the competition conditions to alter the balance of these tradeoffs. We compare these results to growth data on E. coli strains having mutations in the enzyme adenylate kinase. These strains show evidence of such tradeoffs, which we verify in direct competition experiments. [Preview Abstract] |
Tuesday, March 14, 2017 3:06PM - 3:18PM |
H5.00004: Maintenance of cooperation in evolving heterogenous populations with motility Marianne Bauer, Steffen Rulands, Joerg Martin, Erwin Frey The presence of cooperation in nature is a fundamental, still unsolved problem in biology. We study the evolution of cooperation in populations with different motility rates. We show under what conditions cooperation can be maintained in such populations using a simple implementation of the prisoner's dilemma and fitness update mechanism. Specifically, we show why cooperation can be maintained for surprisingly large costs and high motility rates, and discuss the average motility that is selected after time evolution [Preview Abstract] |
Tuesday, March 14, 2017 3:18PM - 3:30PM |
H5.00005: Host-pathogen interactions and bacterial survival under phage fluctuations Antun Skanata, Edo Kussell Environmental changes can have profound effects on ecosystems, leading to drastic outcomes such as extinction and desertification. Quantifying, predicting, and ultimately preventing those transitions is a key problem in the field. Our previous work in microbial systems has shown that fluctuations in environments drive transitions to alternate evolutionary optima, which can be either smooth or abrupt. The long term growth rate, an analog of free energy for population dynamics, has been used to distinguish under what conditions those transitions will occur. Our framework, which uses the mean field approximation to compute the long term growth rate in fluctuating environments, is uniquely positioned to treat more complex dependencies that allow coexistence among species sharing resources or infected by common pathogens. Here we present a simple model of a bacterial community subjected to fluctuating phage infections that outlines the regimes where species diversity results in long-term stability. We identify prevalent, but often counter-intuitive, strategies that bacteria use to protect against infection, and find a new general principle in the evolution of phage resistance. Our results, which predict the transition regimes, have implications for a broad range of ecological models. [Preview Abstract] |
Tuesday, March 14, 2017 3:30PM - 3:42PM |
H5.00006: Biofilm growth program and architecture revealed by single-cell live imaging Jing Yan, Benedikt Sabass, Howard Stone, Ned Wingreen, Bonnie Bassler Biofilms are surface-associated bacterial communities. Little is known about biofilm structure at the level of individual cells. We image living, growing \textit{Vibrio cholerae} biofilms from founder cells to ten thousand cells at single-cell resolution, and discover the forces underpinning the architectural evolution of the biofilm. Mutagenesis, matrix labeling, and simulations demonstrate that surface-adhesion-mediated compression causes V. \textit{cholerae} biofilms to transition from a two-dimensional branched morphology to a dense, ordered three-dimensional cluster. We discover that directional proliferation of rod-shaped bacteria plays a dominant role in shaping the biofilm architecture, and this growth pattern is controlled by a single gene. Competition analyses reveal the advantages of the dense growth mode in providing the biofilm with superior mechanical properties. We will further present continuum theory to model the three-dimensional growth of biofilms at the solid-liquid interface as well as solid-air interface. [Preview Abstract] |
Tuesday, March 14, 2017 3:42PM - 3:54PM |
H5.00007: Morphodynamics of growing bacterial colony Pushpita Ghosh, Prasad Perlekar, Navdeep Rana Self-organization into multicellular communities is a natural trend of most of the bacteria. Mutual interactions and competition among the bacterial cells in such multicellular organization play essential role in governing the spatiotemporal dynamics. We here present the spatiotemporal dynamics of growing bacterial colony using theory and a particle-based or individual-based simulation model of nonmotile cells growing utilizing a diffusing nutrient/food on a semi-solid surface by their growth and division forces and by pushing each-other through sliding motility. We show how the resource competition over a fixed amount of food, the diffusion coefficient of the nutrient and the random genetic noise govern the morphodynamics of a single species and a well-mixed two-species bacterial colonies. Our results show that for a very low initial food concentrations, colony develops fingering pattern at the front, while for intermediate values of initial food sources, the colony undergoes transitions to branched structures at the periphery and for very high values of food colony develops smoother fronts. [Preview Abstract] |
Tuesday, March 14, 2017 3:54PM - 4:06PM |
H5.00008: Killing to Fluctuate, or: How Death and Reproduction Drive a Fluctuation-Response Relation in Biofilms Arben Kalziqi, Peter Yunker, Jacob Thomas Unlike equilibrium atomic solids, biofilms do not experience significant thermal fluctuations at the constituent level. However, cells inside the biofilm stochastically die and reproduce, provoking a mechanical response. We investigate the mechanical response of biofilms to the death and reproduction of cells by measuring surface-height fluctuations of biofilms with two mutual predator strains of \textit{Vibrio cholerae} which kill one another on contact via the Type VI Secretion System. Biofilm surface topography is measured in the homeostatic limit, wherein cell division and death occur at roughly the same rate, via white light interferometry. Although biofilms are far from equilibrium systems, measured height correlation functions line up with expectations from a generalized fluctuation-response relation derived from replication and death events, as predicted by Risler et al. (PRL 2015). Using genetically modified strains of \textit{V. cholerae} which cannot kill, we demonstrate that extracted effective temperatures increase with the amount of death and reproduction. Thus, high-precision measurement of surface topography reveals the physical consequences of death and reproduction within a biofilm, providing a new approach to studying interactions between bacteria and cells. [Preview Abstract] |
Tuesday, March 14, 2017 4:06PM - 4:18PM |
H5.00009: Experimental Population Dynamics in Fluid Flows Severine Atis, Bryan T. Weinstein, Patrick Soddard, Andrew W. Murray, David R. Nelson Transport dramatically alters the evolutionary dynamics of populations. The diffusive transport of microbial populations has been well explored on agar plates; striking genetic segregation patterns in the populations are observed as a result of the small population size near the expanding front. We show that these patterns are modified when the microbial populations grow on the top of an extremely viscous fluid. Both \textit{E. coli} and \textit{S. Cerevisea} colonies appear to induce radial flows by emitting surfactants allowing them to rapidly colonize new territory. We discuss how changing the fluid's properties alters the morphology and evolutionary dynamics of the populations, and demonstrate that imposed fluid flows can be used to study the interplay between evolution and advection. [Preview Abstract] |
Tuesday, March 14, 2017 4:18PM - 4:30PM |
H5.00010: Mathematical Modeling the Geometric Regularity in Proteus Mirabilis Colonies Bin Zhang, Yi Jiang \textit{Proteus Mirabilis} colony exhibits striking spatiotemporal regularity, with concentric ring patterns with alternative high and low bacteria density in space, and periodicity for repetition process of growth and swarm in time. We present a simple mathematical model to explain the spatiotemporal regularity of \textit{P. Mirabilis} colonies. We study a one-dimensional system. Using a reaction-diffusion model with thresholds in cell density and nutrient concentration, we recreated periodic growth and spread patterns, suggesting that the nutrient constraint and cell density regulation might be sufficient to explain the spatiotemporal periodicity in \textit{P. Mirabilis} colonies. We further verify this result using a cell based model. [Preview Abstract] |
Tuesday, March 14, 2017 4:30PM - 4:42PM |
H5.00011: Growth Mechanism of Microbial Colonies Minhui Zhu, K. Michael Martini, Neil H. Kim, Nicholas Sherer, Jia Gloria Lee, Thomas Kuhlman, Nigel Goldenfeld Experiments on nutrient-limited {\it E. coli\/} colonies, growing on agar gel from single cells reveal a power-law distribution of sizes, both during the growth process and in the final stage when growth has ceased. We developed a Python simulation to study the growth mechanism of the bacterial population and thus understand the broad details of the experimental findings. The simulation takes into account nutrient uptake, metabolic function, growth and cell division. Bacteria are modeled in two dimensions as hard circle-capped cylinders with steric interactions and elastic stress dependent growth characteristics. Nutrient is able to diffuse within and between the colonies. The mechanism of microbial colony growth involves reproduction of cells within the colonies and the merging of different colonies. We report results on the dynamic scaling laws and final state size distribution, that capture in semi-quantitative detail the trends observed in experiment. [Preview Abstract] |
Tuesday, March 14, 2017 4:42PM - 4:54PM |
H5.00012: Diffusion-mediated growth rules allow assembly of metabolically efficient colony Yipei Guo, Mikhail Tikhonov, Michael P. Brenner The typical self-assembly program examines how specific interaction rules can lead to the assembly of desired structures from individual building blocks. This is a natural approach when looking at macromolecular structures that are held together by molecular interactions. However, spatially-structured colonies such as biofilms emerge from cell growth, analogous to allowing building blocks to replicate. The final arrangement of different cell types depends on the response of these cells (switching between states, growth rate, etc.) to local concentrations of diffusible chemicals such as metabolites and morphogens. Here we consider the simplest possible set of rules that can arise in a colony of cells that exchange intermediates and carry out an overall reaction. We found that incorporating diffusion-mediated growth rules into the colony's self-assembly program not only gives rise to a diverse range of structures, it can also solve the optimization problem of achieving the metabolically most efficient structure. While agent-based simulations have commonly been used to explore the effect of specific interaction mechanisms, this self-assembly perspective brings new types of questions: what structures are easier to assemble, what structures can be obtained with a minimal set of rules. [Preview Abstract] |
Tuesday, March 14, 2017 4:54PM - 5:06PM |
H5.00013: Crosstalk Regulates the Capacity for Robust Collective Decision Making in Heterogeneous Microbial Communities Tahir Yusufaly, James Boedicker Microbial communities frequently communicate via quorum sensing (QS), where cells produce, secrete, and respond to a threshold level of an autoinducer (AI) molecule, thereby modulating density-dependent gene expression. However, the biology of QS remains incompletely understood in heterogeneous communities, where crosstalk between distinct QS systems leads to novel effects. Such knowledge is necessary both for understanding signaling in real microbial communities, and for the rational design of synthetic communities with designer properties. As a step towards this goal, we investigate the effects of crosstalk between Gram-negative bacteria communicating via LuxI/LuxR-type QS systems, with acyl-homoserine lactone (AHL) AI molecules. After mapping QS in a heterogeneous community onto an artificial neural network model, we systematically analyze how heterogeneity regulates the community's capability for stable yet flexible decision making. We find that there are preferred distributions of interactions which provide optimal tradeoffs between capacity, or the number of different decisions a population can make, and robustness, or the tolerance of the community to disturbances. We compare our results to inferences made from experimental data, and critically discuss implications for the biological significance of crosstalk. [Preview Abstract] |
Tuesday, March 14, 2017 5:06PM - 5:18PM |
H5.00014: Modeling the role of quorum sensing in interspecies competition in biofilms Avaneesh V. Narla, Ned S. Wingreen, David B. Borenstein Bacteria grow on surfaces in complex immobile communities known as biofilms, composed of cells embedded in an extracellular matrix. Within biofilms, bacteria often communicate, cooperate, and compete within their own species and with other species using Quorum Sensing (QS). QS refers to the process by which bacteria produce, secrete, and subsequently detect small molecules called autoinducers as a way to assess the local population density of their species, or of other species. QS is known to regulate the production of extracellular matrix. We investigated the possible benefit of QS in regulating matrix production to best gain access to a nutrient that diffuses from a source positioned away from the surface on which the biofilm grows. We employed Agent-Based Modeling (ABM), a form of simulation that allows cells to modify their behavior based on local inputs, e.g. nutrient and QS concentrations. We first determined the optimal fixed strategies (that do not use QS) for pairwise competitions, and then demonstrated that simple QS-based strategies can be superior to any fixed strategy. In nature, species can compete by sensing and/or interfering with each other's QS signals, and we explore approaches for targeting specific species via QS-interference. [Preview Abstract] |
Tuesday, March 14, 2017 5:18PM - 5:30PM |
H5.00015: Light, Imaging, Vision: An interdisciplinary undergraduate course Philip Nelson Students in physical and life science, and in engineering, need to know about the physics and biology of light. In the 21st century, it has become increasingly clear that the quantum nature of light is essential both for the latest imaging modalities and even to advance our knowledge of fundamental processes, such as photosynthesis and human vision. But many optics courses remain rooted in classical physics, with photons as an afterthought. I'll describe a new undergraduate course, for students in several science and engineering majors, that takes students from the rudiments of probability theory to modern methods like fluorescence imaging and Förster resonance energy transfer. After a digression into color vision, students then see how the Feynman principle explains the apparently wavelike phenomena associated to light, including applications like diffraction limit, subdiffraction imaging, total internal reflection and TIRF microscopy. Then we see how scientists documented the single-quantum sensitivity of the eye seven decades earlier than `ought' to have been possible, and finally close with the remarkable signaling cascade that delivers such outstanding performance. A new textbook embodying this course will be published by Princeton University Press in Spring 2017. [Preview Abstract] |
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