Bulletin of the American Physical Society
APS March Meeting 2019
Volume 64, Number 2
Monday–Friday, March 4–8, 2019; Boston, Massachusetts
Session E63: Evolutionary and Ecological Dynamics III: Community EcologyFocus
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Sponsoring Units: DBIO GSNP Chair: Kirill Korolev, Boston University Room: BCEC 259A |
Tuesday, March 5, 2019 8:00AM - 8:36AM |
E63.00001: Dynamics of microbiota communities during physical perturbation. Invited Speaker: Carolina Tropini The consortium of microbes living in and on our bodies is intimately connected with human biology and deeply influenced by physical forces. Despite incredible gains in describing this community, and emerging knowledge of the mechanisms linking it to human health, understanding the basic physical properties and responses of this ecosystem has been comparatively neglected. Most diseases have significant physical effects on the gut; diarrhea alters osmolality, fever and cancer increase temperature, and bowel diseases affect pH. Furthermore, the gut itself is comprised of localized niches that differ significantly in their physical environment, and are inhabited by different commensal microbes. Understanding the impact of common physical factors is necessary for engineering robust microbiota members and communities; however, our knowledge of how they affect the gut ecosystem is poor. |
Tuesday, March 5, 2019 8:36AM - 8:48AM |
E63.00002: Evolution of Multicellular Specialization in Dynamic Fluids Gurdip Uppal, Dervis Can Vural Multicellularity and division of labor mark a major transition in the development of life. In this study, we determine the conditions for multicellular specialization to occur starting with a system of generalists that secrete two public goods. We look at two different fitness functions where either both public goods are necessary for any fitness gain or where either one is sufficient for a fitness gain. We denote these by AND and OR respectively, to resemble the logical AND and OR functions. Social structures arise naturally from our advection-diffusion-reaction model as self-replicating Turing patterns. We see that an AND structure is necessary for the specialists to stay together in the same social structure. Specialists in the OR case dissociate into separate groups of pure specialists. We look at the effects of varying the cost of cooperation and mutation rate on the emergence of specialization. When trade-off costs are small, we see that spatial structure can help facilitate the transition to specialization for either fitness function. At larger trade-offs in the AND case, we see that generalists are more stable. |
Tuesday, March 5, 2019 8:48AM - 9:00AM |
E63.00003: Pinning and pulsed expansion in a spatially expanding bacterial mutualism Arolyn Conwill, Jeffrey Gore Range expansions occur when a population expands in space due to dispersal and growth. These expansions can result from environmental change, introduction of invasive species, or evolutionary adaptation that enables a population to move into previously unoccupied territory. Theoretical work has shown that fragmented habitats and seasonal growth (discrete space and discrete time) can result in pinning and pulsed invasions in expanding populations with an Allee effect. However, it is not clear how underlying population dynamics such as limit cycle oscillations influence these phenomena. We probe this question in an experimental model system consisting of an oscillating bacterial mutualism inhabiting discrete population patches and subject to periodic growth cycles. For low nearest-neighbor migration rates, the mutualism cannot expand, and the population is pinned in place. For high nearest-neighbor migration rates, the mutualism expands at pulsed speeds. Furthermore, our experimental results are consistent with a mechanistic model prediction that the period of population oscillations locks into specific values during pulsed invasion, emphasizing the interplay between ecological interactions and spatial structure. |
Tuesday, March 5, 2019 9:00AM - 9:12AM |
E63.00004: Survival probabilities of mutants with antagonistic interactions Maxim O Lavrentovich, David R Nelson Strains within a population interact not only via competition due to varying growth rates, but also via secretion of toxins, predation, parasitism, and other adaptations which result in frequency-dependent selection. These dynamics often play out in a spatial context, such as at the frontier of a growing spherical cell mass, or on the surface of a Petri dish. We study how a mutant, interacting antagonistically with a wild-type strain (i.e., the mutant grows more slowly in the presence of the wild-type), survives in two-dimensional populations with flat and curved geometries, representing, for example, the Petri dish surface and cell mass frontier, respectively. The antagonistic interactions significantly diminish the survival probability of the mutant even when, in isolation, the mutant grows much faster than the wild-type strain. We show that the survival probability can be thought of as a kind of "nucleation rate" of the mutant strain. The predictions of classical nucleation theory agree with our simulation results and provide an important modification, due to the antagonistic interactions, of the classic Kimura formula for the survival probability. We comment on both the effects of small-number fluctuations and the curved population geometry. |
Tuesday, March 5, 2019 9:12AM - 9:24AM |
E63.00005: Measuring cellular memory and heterogeneity at the single-cell level Tamas Szekely, Zhihao Cai, Martin Sauzade, Eric Brouzes, Gabor Balazsi Microbial populations live in a wide range of ecological settings. In changing environments, survival is improved by heterogeneity. In contrast, in stable environments the population is best off when cells adopt the single optimal phenotype. In a clonal population, heterogeneity occurs at the phenotypic (protein) level; as cellular protein levels vary over time, phenotypes can change dynamically, with the timescale given by “cellular memory”. However, the population-level distribution of phenotypes remains stable, optimised by evolution to its ecological setting. An interesting situation occurs when a population moves from one setting to another. In this case, one can encounter a bimodal population in a constant environment for which it is not adapted. How does evolution shape this population? We examine this in yeast containing a synthetic gene circuit that gives a phenotypically bimodal population. We expose cells to a stable environment and observe changes in heterogeneity. Using a microfluidic platform, we measure the cellular memory of many single cells. Thus, we investigate the relationship between fitness, cellular memory and phenotype distribution during evolution in a constant environment. |
Tuesday, March 5, 2019 9:24AM - 9:36AM |
E63.00006: Bet-hedging strategies in expanding populations Paula Villa Martín, Miguel Angel Muñoz, Simone Pigolotti Ecological species can spread their extinction risks in uncertain environments by adopting a bet hedging strategy, i.e. by diversifying individual phenotypes. We present a theory of bet-hedging for populations colonizing unknown environments that fluctuate either in space or time. We find that diversification is more favorable strategy in this scenario than for well-mixed populations, supporting the view that range expansions promote diversification. For slow rates of variation, spatial fluctuations open more opportunities for bet-hedging than temporal variations. Opportunities for bet-hedging reduce In the limit of frequent environmental variation, regardless of the nature of these fluctuations. These conclusions are robust against stochasticity induced by finite population sizes. |
Tuesday, March 5, 2019 9:36AM - 9:48AM |
E63.00007: Competition in dense bacterial biofilms through killing and replication Gabi Steinbach, Michael Siulung, Brian K. Hammer, Peter Yunker Typically, biofilms feature many different microbial species and strains. This diversity presents a challenge, as individuals must compete for resources and space. In response, microbial species have evolved antagonistic mechanisms such as the Type VI secretion system (T6SS). This is a contact-dependent toxin-delivery system that enables the injection of fatal toxins into other bacteria as well as eukaryotic cells. Previous studies have shown that such an antagonistic one-on-one interaction causes an initially well-mixed culture to phase separate, providing protection by number. We study biofilms consisting of V. cholerae, which express T6SS, as an experimentally controllable and practically relevant system of mutual killers. While we observe phase separation, the typical size of clonal patches stops changing much earlier than expected. In experimental and numerical studies of mutual killing strains of V. cholerae, we show that a protective layer of debris forms at the interface between patches, which slows down further killing. This poses major consequences for the role of antagonistic interactions and the survival dynamics in biofilms. |
Tuesday, March 5, 2019 9:48AM - 10:00AM |
E63.00008: Phase Transition Behavior in Yeast Populations Under Stress Stephen W. Ordway, Dawn M. King, David Friend, Christine Noto, Snowlee Phu, Wendy Olivas, Sonya Bahar Nonequilibrium phase transition behavior has recently been observed in computational models of evolutionary dynamics (Scott et al., 2013; King et al. 2017). Dynamical signatures predictive of population collapse have been observed in yeast populations under stress (Dai et al., 2012). We experimentally investigate the population response of Saccharomyces cerevisiae to biological stressors (temperature and salt concentration) in order to investigate the dynamical behavior of the system in the vicinity of population collapse. While both conditions lead to population decline, the dynamical characteristics of the population response differ significantly depending on the stressor. Under temperature stress, the population undergoes a sharp change with significant fluctuations within a critical temperature range, indicative of a continuous absorbing phase transition. In the case of salt stress, the response is much more gradual. |
Tuesday, March 5, 2019 10:00AM - 10:12AM |
E63.00009: A neural network model predicts the consequences of crosstalk in bacterial quorum sensing James Boedicker, Kalinga Pavan T Silva, Tahir Yusufaly Many bacteria use chemically similar molecules to communicate, resulting in crosstalk between bacterial signaling networks. Such crosstalk can have unexpected consequences for decision making in heterogeneous communities of cells. Here we examine crosstalk within a community composed of five strains of Bacillus subtilis, with each strain producing a variant of the quorum sensing peptide ComX. Co-cultures of these strains create in a mixture of ComX variants, resulting in variable levels of gene expression in each strain. To predict gene regulation in communities producing multiple signals, we implement a neural network model. Experimental quantification of crosstalk between pairs of strains parametrized the model, enabling the accurate prediction of activity within the full five-strain network. Interactions weights between the five signaling networks were both positive and negative, of variable magnitude, and asymmetric. Signal crosstalk within the five-strain community results in multiple community-level quorum sensing states, each with a unique combination of quorum sensing activation among the five strains. The community-level signaling state was influenced by the ratio of strains as well as dynamics of community composition. |
Tuesday, March 5, 2019 10:12AM - 10:24AM |
E63.00010: Production of a biofilm polymer can benefit bacteria when grown in co-culture under low iron conditions Vernita Gordon, Jaime B Hutchison, Karishma S Kaushik, Christopher A Rodesney, Thomas Lilieholm, Layla Bakhtiari Biofilm formation is associated with resistance to antibiotics and the immune system. The opportunistic human pathogen Pseudomonas aeruginosa forms biofilm infections in lungs, wounds, and on medical devices. However, its ability to form biofilms originated in this bacterium’s native environment, primarily plants and soil. Such environments are polymicrobial and resource-limited. The P. aeruginosa extracellular polysaccharide Psl can bind iron and, for the strain PAO1, is also the dominant “glue” holding together multicellular aggregates and biofilms. Here, we quantify early biofilm growth using time-lapse confocal microscopy. We find that aggregates of P. aeruginosa have a growth advantage over single cells of P. aeruginosa in the presence of Staphylococcus aureus in low-iron environments. This growth advantage is linked to aggregates' high Psl content and to the production of an active factor by S. aureus. We posit that this may have been linked to the evolutionary development of the strong biofilm-forming tendencies of P. aeruginosa. |
Tuesday, March 5, 2019 10:24AM - 10:36AM |
E63.00011: Oxygen dynamics in a two-dimensional microbial ecosystem Alexander Petroff, Frank Tejera, Albert J Libchaber Ecosystems persist over geological timescales by continuously cycling nutrients. However, we lack a quantitative model of how diverse organisms organize with respect to one another. We observe these dynamics in a quasi-two-dimensional microbial ecosystem, in which all microbes live within the penetration depths of oxygen and light. This community is composed of both photosynthetic bacteria, which produce sugars and oxygen, and aerobic bacteria, which consume oxygen and sugars. Shinning a light on the community drives a nutrient cycle between these two groups of microbes. Illuminating a spot, we measure the resulting distribution of oxygen. Under normal conditions, diffusion alone stabilizes oxygen gradients. However, at freezing temperatures or low atmospheric oxygen concentration, the kinetics of microbial oxygen production and consumption dominate. Surprisingly, after three weeks, the initially uniform distribution of oxygen in the spot becomes an annulus. We present a robust method to invert the measured oxygen concentration for the distribution of oxygen sources and sinks. |
Tuesday, March 5, 2019 10:36AM - 10:48AM |
E63.00012: Thermodynamic constraints on cross-feeding in bacterial population Tong Wang, Chen Liao, Sergei Maslov Overflow metabolism refers to the strategy of cells using fermentation instead of the more energetically-efficient respiration, even when the oxygen is available. Cross-feeding between two bacterial strains growing on a single primary carbon source can be established when one bacterial strain consumes overflow metabolites excreted by the other bacterial strain. Many overflow pathways are thermodynamically controlled and thermodynamic constraints on them are not included to consider the cross-feeding of overflow metabolites between two strains in the past. Motivated by experimental results of acetate cross-feeding polymorphism, in this paper, we developed a single cell growth model with coarse-grained metabolic pathways including proteome allocation and thermodynamic constraints on the overflow pathway. The model can accurately capture the flux of thermodynamically controlled overflow pathway and growth rate of cells under different growth conditions. Moreover, when it is applied to study the cross-feeding, the model can reveal the short-term dynamics and long-term dynamics of cross-feeding stable polymorphism seen in experiments. |
Tuesday, March 5, 2019 10:48AM - 11:00AM |
E63.00013: How can unsuccessful invaders drive long-term shifts in community state? Daniel R. Amor, Christoph Ratzke, Jeffrey Gore The stability of virtually all microbial communities is frequently challenged by the arrival of new individuals that could potentially invade the system. This urges for a deeper understanding of how invasions can interfere the dynamics of microbial communities. I will present a bistable model system to study the dynamics between alternative stable states in microbial ecosystems. By introducing additional species into the system, we observed induced transitions between stable states. Interestingly, in many cases the invading species did not survive in the final community state, making these species what we call a “transient invader.” This suggests that short-term invasions (such as infections) could be a common mechanism driving transitions between stable states in microbial communities. |
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