Bulletin of the American Physical Society
APS March Meeting 2018
Volume 63, Number 1
Monday–Friday, March 5–9, 2018; Los Angeles, California
Session P49: Evolutionary and Ecological Dynamics - IIIFocus
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Sponsoring Units: DBIO GSNP Chair: Kirill Korolev, Boston University Room: LACC 511A |
Wednesday, March 7, 2018 2:30PM - 3:06PM |
P49.00001: Ecological feedback in quorum-sensing microbial populations Invited Speaker: Erwin Frey Bacteria and other microbes can communicate with each other using chemical languages. They release small signaling molecules called autoinducers into their surroundings and sense the levels of the autoinducers in the environment. The response to these autoinducers – known as quorum sensing – can regulate how whole communities of microbes grow and behave; for example, autoinducers can alter the ability of microbes to infect humans or enable the microbes to collectively switch on light production. Recent experiments suggest that, in a population of genetically identical microbes, some individuals may produce autoinducers while others do not. The coexistence of these different phenotypes in one population may enable different individuals to perform different roles, or act as a bet-hedging strategy that helps the population to survive if it is later exposed to a stressful situation. It is not clear how microbes regulate autoinducer production so that only some individuals produce these molecules. In this talk a theoretical model will be presented that addresses this question. In the model, the microbes shape their environment by producing autoinducers and can respond to this self-shaped environment by changing their level of autoinducer production. The coupling between ecological and population dynamics through quorum sensing can induce phenotypic heterogeneity in microbial populations, suggesting an alternative mechanism to stochastic gene expression in bistable gene regulatory circuits. |
Wednesday, March 7, 2018 3:06PM - 3:18PM |
P49.00002: Adaptive Immunity Constrains the Composition and Fate of Large Bacterial Populations Madeleine Bonsma-Fisher, Dominique Soutière, Sidhartha Goyal Many bacteria possess an adaptive immune system called CRISPR-Cas which allows them to 'remember' phage attacks by inserting pieces of phage DNA, called spacers, into their genome. Experiments have shown that the abundance of spacer types in a bacterial population under phage attack is both highly dynamic and can vary by orders of magnitude between spacer types, yet in our analysis we observed stability in the overall spacer abundance distribution. Bacteria can also up-regulate Cas protein expression through the quorum-sensing pathway. |
Wednesday, March 7, 2018 3:18PM - 3:30PM |
P49.00003: Swim/stick tradeoffs for gut bacterial symbionts Brandon Schlomann, Travis Wiles, Elena Wall, Karen Guillemin, Raghuveer Parthasarathy For microorganisms motility is primarily a dispersal mechanism, enabling them to find new environments at an energetic cost, and yet it is widespread in species of symbiotic bacteria that have adapted to long-term residence in the intestine. Deciphering the costs and benefits of gut bacterial motility will inform our understanding of the ecology and biophysics of the intestinal microbiome, specifically the interplay between the spatial structures of the host environment and its bacterial communities. I’ll present work that investigates these issues by using light sheet microscopy to observe native and genetically perturbed bacterial communities in the intestines of live, larval zebrafish. Our findings reveal a novel benefit of motility: when directed towards an upstream chemotactic cue, motility is extremely effective at countering downstream peristaltic transport. However, the benefits of motility are fragile: small chemical perturbations that impede motility lead to massive population losses via peristaltic transport out of the gut. Together, these results offer insight into how bacterial motility dictates population-scale spatial structure and dynamics in the intestine. |
Wednesday, March 7, 2018 3:30PM - 3:42PM |
P49.00004: Invasion-Induced Phase Transitions in Microbial Ecosystems Samuel Bray, Yuhang Fan, Bo Wang It is a challenge to predict the outcome of introducing new species to a microbial community, especially those with poorly defined ecological interactions. Therefore, we studied a model community of two cross-feeding species, with small molecule resources in the system explicitly modeled. We challenged this community with invaders displaying three strategies: complete competitors for the common energy source, parasites that use shared resources produced by native species, and a third adopting both strategies. With analytical and numerical analysis, we defined phase diagrams of post-invasion community compositions in the space of community mutuality and invader fitness. As invader fitness increases, complete competitors cannot coexist with the native community, resulting in first-order transitions across phase boundaries, while parasites can be integrated into the community, leading to second-order phase transitions. We tested other communities, some with nonlinear interactions, and observed this correspondence between phase transition order and outcome of invasions (species loss vs. integration) is general. Our work can serve as a theoretical basis for understanding biodiversity changes in a community upon invasion by foreign species |
Wednesday, March 7, 2018 3:42PM - 3:54PM |
P49.00005: Forecasting Critical Transitions and Bifurcation Diagrams of Natural Populations Amin Ghadami, Eleni Gourgou, Bogdan I. Epureanu Recent studies demonstrate that several early warning signals based on the analysis of measured time series can successfully provide an alarm when an ecological system approaches a tipping point. However, predicting key aspects of the system's future stability and dynamics still remains a challenge. |
Wednesday, March 7, 2018 3:54PM - 4:06PM |
P49.00006: Effect of Temporal Environmental Fluctuations on Microbial Competition Vilhelm Woltz, Clare Abreu, Jeffrey Gore Environmental fluctuations, such as seasonal or diurnal variation, can affect species diversity. A major challenge in ecology is to predict how such disturbances will affect the outcome of interspecies competition. When temporal variation is imposed on additive linear models, such as the Lotka-Volterra competition model, the parameters and variables can be replaced by their time averages. The outcome of a fluctuating environment should therefore be the same as that of a constant environment with the time-averaged parameters and variables, according to these simple models. To test this prediction, we drew from previous results, which showed that increasing mortality shifts pairwise outcomes from dominance of the slow grower at low mortality to dominance of the fast grower at high mortality, with coexistence or bistability at intermediate mortality. By fluctuating between low and high mortality, we were able to produce the time-averaged result: bistability or coexistence. These results argue that simple models can provide powerful insight into how changing environments will lead to changing structure of communities. |
Wednesday, March 7, 2018 4:06PM - 4:18PM |
P49.00007: Engineering transitions between alternative stable states in a microbial ecosystem Daniel R. Amor, Christoph Ratzke, Jeffrey Gore Temporary perturbations (such as exposure to antibiotics) can threaten the stability of microbial ecosystems such as the human microbiome. However, there is still little knowledge on the mechanisms driving long-term community dynamics after short-term perturbations. Here, we experimentally study transitions between stable states in a two-species laboratory ecosystem, in which bistability results from the fact that the two species are inhibiting each other via incompatible pH modifications of the environment. We found that a broad range of temporary perturbations induced transitions from one stable state but not the other, revealing a striking difference in resilience between the two states. Interestingly, it was the slow growing species that dominated in the more resilient state, in contrast with the theoretical prediction from the Lotka-Volterra model (in which the fast grower is generally favored by short-term perturbations). Guided by a modified model, we found that Allee effects (cooperative growth) acting on the fast grower are able to explain its low resilience to perturbations. Our results illustrate that cooperative growth dynamics may play an important role in determining the resilience of complex communities to environmental perturbations. |
Wednesday, March 7, 2018 4:18PM - 4:30PM |
P49.00008: Ecological Suicide in Microbes Christoph Ratzke, Jonas Denk, Jeffrey Gore The growth and survival of organisms often depend on interactions between them. In many cases, these interactions are positive and caused by a cooperative modification of the environment. However, organisms can similarly display negative interactions by changing the environment in ways that are detrimental for them. Here we find an extreme type of negative interactions, in which bacteria modify the environmental pH to such a degree that it leads to a rapid extinction of the whole population, a phenomenon we call ecological suicide. Promoting bacterial growth can drive populations extinct whereas inhibiting bacterial growth by the addition of harmful substances – like antibiotics – can rescue them. Moreover, ecological suicide can cause oscillatory dynamics, even in single-species populations. We find ecological suicide in a wide variety of microbes, suggesting that it could play a significant role in microbial ecology and evolution. |
Wednesday, March 7, 2018 4:30PM - 4:42PM |
P49.00009: Neutral evolution in the presence of long-range dispersal Jayson Paulose, Oskar Hallatschek Stochastic effects have an outsize influence on the genetics of range |
Wednesday, March 7, 2018 4:42PM - 4:54PM |
P49.00010: Birth-death and immigration models, with mutations and carrying capacity. Renaud Dessalles, Thomas Chou, Maria D'Orsogna
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Wednesday, March 7, 2018 4:54PM - 5:06PM |
P49.00011: Mapping clone extinction and resurrection to intermittent hematopoietic stem cell differentiation: Analysis of a decade-long clone tracking study in rhesus macaque Song Xu, Sanggu Kim, Irvin Chen, Thomas Chou Recently, virally tagged hematopoietic stem cells (HSCs) were autologously transplanted into rhesus macaques and peripheral blood cells were sampled and sequenced over 14 years to quantify the proliferation of each viral tag. Through mathematical modeling and statistical analysis of the data, we develop a simple mechanistic picture of hematopoiesis of tagged cells. We show that HSC self-renewal in the bone marrow leads to heterogeneity in clone sizes, which can ultimately lead to the heterogeneity seen in clone sizes observed in the peripheral blood. The magnitude of the temporal variations of clone abundances in the sampled blood is controlled by intermittent HSC differentiation, described by a Poisson process. Experimental data are analyzed using a new statistic that is insensitive to the unknown underlying HSC clone heterogeneity, from which least-squares estimates of key parameters in our model were inferred. |
Wednesday, March 7, 2018 5:06PM - 5:18PM |
P49.00012: Extinction phase transitions in correlated external noise Matthew Small, Alexander H Oniwa Wada, Thomas Vojta We investigate the non-equilibrium phase transition between survival and extinction of biological populations in the presence of global temporal fluctuations of the environmental conditions. Such temporal disorder gives rise to an unusual type of critical point dubbed infinite-noise critical point [1]. It is characterized by enormous density fluctions that increase without limit at criticality. As a result, a typical population decays much faster than the ensemble average which is dominated by rare events. Here we show that long-range power-law correlations of the environmental noise further increase these effects, i.e., they accelerate the decay of a typical population but slow down the decay of the ensemble average. We determine the complete critical behavior of the extinction transitions, we establish a relation of our results to fractional random walks, and we illustrate them by Monte Carlo simulations. |
Wednesday, March 7, 2018 5:18PM - 5:30PM |
P49.00013: Modeling Population Dynamics of Antimicrobial Peptides in Bacterial Culture Paul Talledo, Siddhartha Sarkar, Sattar Taheri-Araghi, Andrej Kosmrlj Antimicrobial peptides (AMPs) are broad-spectrum antibiotics that utilize electrostatics to target bacteria selectively. Despite our knowledge of the molecular structure and membrane interactions of AMPs, their population dynamics are still poorly understood. We developed a model that quantifies the kinetics of AMPs that inhibits the growth of a bacterial culture by considering the binary state for individual cells’ physiology: (1) natural growth and (2) fully inhibited growth. These simulations are inspired by our experimental data where the minimum inhibitory concentration (MIC) of AMPs is dependent on the cell density. We hypothesize that bacteria killed by AMP LL-37 absorb additional AMPs, thus effectively reducing the available concentration of AMPs' for attacking the remaining cells. Our model recapitulates the experimental behavior and suggests that dead bacteria absorb on the order of 108 AMPs. Furthermore, our model allows us to infer a few parameters that are not accessible from direct experimental measurements. Specifically, we can quantify the killing rate of bacteria and the number of AMPs sequestered by each individual cells. |
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