Bulletin of the American Physical Society
APS March Meeting 2019
Volume 64, Number 2
Monday–Friday, March 4–8, 2019; Boston, Massachusetts
Session P63: Evolutionary and Ecological Dynamics IV: Community Assembly and Interspecies InteractionsFocus
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Sponsoring Units: DBIO GSNP Chair: Carolina Tropini, University of British Columbia Room: BCEC 259A |
Wednesday, March 6, 2019 2:30PM - 3:06PM |
P63.00001: Combinatorial ecology in the simple fruit fly gut microbiome Invited Speaker: Will Ludington The gut microbiome is an ecosystem within an animal host that impacts health and disease in mysterious ways. Complex interactions between individual species can produce unexpected results, often involving feedbacks with the host physiology. Discovering general principles of microbiome-host systems can benefit human health and also teach us about how groups of interacting organisms behave differently from their separate parts. To deconstruct this complexity, my lab develops a microbiome model using the fruit fly as the host and its natural set of just five stably colonizing gut bacteria as the microbiome. We reconstruct this system combinatorially, starting with germ-free flies, to ask how bacteria influence each other’s ability to colonize the gut and how these interactions influence physiology of the fly. We find that colonization ability of new species is strongly influenced by previous colonizers due both to spatial and metabolic interactions. These interactions also shape host fitness, altering the lifespan and reproduction of flies. We introduce new mathematical tools called epistatic filtrations to calculate microbiome interactions. The fly gut serves as an effective combinatorial model to dissect the gut microbiome. |
Wednesday, March 6, 2019 3:06PM - 3:18PM |
P63.00002: Predictability in the assembly of microbial communities Jeffrey Gore Multispecies microbial communities are essential for the health of the planet as well as the human body. A major challenge is to develop a predictive understanding of which species will be able to coexist in a given environment. This task is potentially made even more difficult if there are strong higher-order interactions between species, in which the presence of a third species changes the nature of the interaction between two other species. In a series of laboratory experiments we have demonstrated that pairwise competitive outcomes are typically sufficient to predict the composition of simple communities containing three species. These results argue that higher-order interactions, while undoubtedly present, are typically not so strong as to make prediction impossible. |
Wednesday, March 6, 2019 3:18PM - 3:30PM |
P63.00003: Alternative stable states in microbial communities induced by environmental fluctuations Vilhelm Andersen Woltz, Clare I Abreu, Jeffrey Gore Environmental fluctuations are pervasive in ecosystems, from daily and yearly variations in temperature to gut microbes receiving influxes of resources. In experiments with soil microbes, we have observed that a fluctuating environment causes a two-species community to exhibit alternative stable states that depend on the initial abundances of each species. Environmental disturbances were administered via daily dilutions of bacteria competitions. The magnitude of the daily dilution factor determines the fraction of cells discarded and therefore the depth of disturbance to the environment. We found the outcome of a competition with a fluctuating dilution factor to be the same as that with a constant dilution factor equal to the average of the fluctuating dilution factors. This outcome is in line with a prediction of the Lotka-Volterra competition model with an added global mortality rate: an environment with a fluctuating death rate equilibrates to the same fixed point as one with the time-averaged added mortality rate. We also observed fluctuation-induced alternate stable states in a more complex community with three species. These results suggest that, at least in a simple ecosystem, a fluctuating environment and a constant environment are in fact equivalent. |
Wednesday, March 6, 2019 3:30PM - 3:42PM |
P63.00004: Increasing Temperature Favors Slower-Growing Bacterial Species Simon Lax, Clare I Abreu, Jeffrey Gore Temperature is among the cardinal environmental variables which affect the growth and survival of microorganisms. Although the effects of temperature on the growth rates and metabolic activities of individual species is a central focus of microbiology, the manner in which temperature regulates competition between species is less well understood. Using a simple adaptation of the Lotka-Voltera competition models, we hypothesize that temperature should have generic effects on microbial competition, such that slower-growing species should consistently be favored by increasing temperature. We demonstrate that this prediction holds true in experimental pairwise competitions between a diverse set of species, and discuss how a community-wide death rate and the growth rates of the individual species interact to shape competitive landscapes. Finally, we show that pairwise dynamics are predictive of competitive outcomes in more complex communities, suggesting it should be possible to make general predictions for how communities might react to warming environments. |
Wednesday, March 6, 2019 3:42PM - 3:54PM |
P63.00005: Decomposition of generalized Lotka-Volterra systems and microbiome recovery Eric Jones, Jean Carlson In the gut microbiome the successful administration of fecal microbiota transplantation (FMT) will convert a person's diseased microbial composition into a healthy one. We model these "healthy'' and "diseased'' microbial states as idealized ecological species, and characterize their behavior by homogenizing the properties of their constituitive microbial populations in a process called "steady state reduction'' (SSR). This method decomposes a generalized Lotka-Volterra (gLV) system of many microbial species into two-dimensional (2D) subsystems that each span a pair of steady states of the high dimensional model and obey gLV dynamics. We investigate an experimentally derived model of antibiotic-induced C. difficile infection (CDI), and study the clinically relevant transition between CDI-vulnerable (diseased) and CDI-resilient (healthy) states with the 2D subspace generated by SSR. Specifically, we investigate the ability of FMT to convert a diseased state into a healthy state, and observe that a delay in FMT administration following antibiotics may undermine its success. |
Wednesday, March 6, 2019 3:54PM - 4:06PM |
P63.00006: What’s love got to do with it? Stable marriage in microbial ecosystems limited by two essential nutrients Sergei Maslov, Veronika Dubinkina, Yulia Fridman, Parth Pratim Pandey Microbial communities routinely have several alternative stable states observed for the same environmental parameters. A possibility of sudden and irreversible transitions between these states (regime shifts) complicates external manipulation of these systems. Can we predict which specific perturbations may induce such regime shifts and which would have only a transient effect? To study this topic we introduce and study a model of a microbial ecosystem colonized by a large number of specialist species. Each species can be limited by essential nutrients of two types, e.g. carbon and nitrogen, each represented in the environment by multiple metabolites. We demonstrate that our model has an exponentially large number of potential stable states realized for different nutrient fluxes. Using game theoretical methods adapted from the stable marriage problem, we predict all of these states based only on ranked lists of competitive abilities of species for each of the nutrients. We show that several mutually uninvadable stable states are generally feasible for a given set of environmental conditions, and explore an intricate network of discontinuous transitions between these states upon changes of nutrient fluxes. |
Wednesday, March 6, 2019 4:06PM - 4:18PM |
P63.00007: The Minimum Environmental Perturbation Principle Robert Marsland, Wenping Cui, Pankaj Mehta Variational principles have served as powerful conceptual tools throughout all areas of physics, often providing some geometrical intuition for the behavior of an otherwise intractable model. Variational principles have also been found for some of the paradigmatic models of theoretical ecology, but they usually lack a clear physical interpretation, and are therefore of limited use for building intuition. In this talk, I will show that competition among consumers for a common pool of resources leads to steady-state resource concentrations that solve a constrained optimization problem. Specifically, the magnitude of the environmental perturbation induced by resource consumption is minimized, subject to the constraint that the per-capita growth rate of each consumer species in the regional pool is zero or negative. This "Minimum Environmental Perturbation Principle" applies to a wide class of models with arbitrarily large numbers of species and resource types, whether the resources are substitutable or essential. But it is broken by environmental feedbacks, whereby consumers return resources to the environment as metabolic byproducts or decaying biomass. |
Wednesday, March 6, 2019 4:18PM - 4:30PM |
P63.00008: Higher order interaction inhibits bacterial invasion of a producer-predator microbial community Harry Mickalide, Seppe Kuehn Microbial communities must resist invasion in order to maintain biodiversity, stabilize industrial bioreactors, and preserve human microbiome health. It is widely believed that the more diverse a microbial community is, the more resistant to invasion it will be, and that this increased invasion resistance arises from a niche complementarity effect: more diverse communities consume a greater range of resources and thus eliminate niches for would-be invaders. Here we show that in a community of the algae Chlamydomonas reinhardtii (producer) and the ciliate Tetrahymena thermophila (predator), invasions by the bacteria Escherichia coli fail even when there is a niche of resources available to the bacteria. In contrast, bacteria successfully invade communities of algae or ciliates alone. We attribute the invasion resistance of the algae-ciliate community to a higher-order (3-way) interaction: the algae inhibits the bacteria’s ability to aggregate which leaves the bacteria vulnerable to the ciliate’s predation. This method of invasion resistance requires both the algae and the ciliate to be present and thus provides an example of diversity leading to invasion resistance due to a higher-order interaction rather than niche complementarity. |
Wednesday, March 6, 2019 4:30PM - 4:42PM |
P63.00009: Bacterial cohesion predicts spatial distribution in the larval zebrafish intestine Brandon Schlomann, Travis Wiles, Elena Wall, Karen Guillemin, Raghuveer Parthasarathy Are there general biophysical relationships governing the spatial organization of the gut microbiome? Despite growing realization that spatial structure impacts microbial ecological dynamics, it is unclear in any animal gut whether structure is governed by predictive, unifying rules, of if it results from contextual, species-specific behaviors. I’ll present work that explores this question through light sheet fluorescence microscopy of live, larval zebrafish that are raised germ-free and then associated with model microbial communities consisting of fluorescently tagged, symbiotic bacteria. Through comparative study of seven different species in isolation, we uncovered an unexpected and striking correlation between bacterial cohesion—the degree to which bacteria auto-aggregate—and position along the length of the intestine. We propose that this relationship emerges from the mechanical response of communities to flows generated by peristaltic contractions, and test this idea with genetic and antibiotic perturbations that modulate bacterial cohesion. The generality of this phenomenon points to bacterial cohesion as an ideal target for precision microbiome engineering. |
Wednesday, March 6, 2019 4:42PM - 4:54PM |
P63.00010: Spatial dynamics of multispecies mutualism Kirill Korolev, Rajita Menon Ecosystems function via a network of interactions between the species. Many of these interactions require physical proximity and are therefore affected by the spatial distribution of the species. We explore spatial structure that emerges due to facilitation and mutualism in multispecies communities and investigate its effects on ecosystem dynamics. In addition to one-way and two-way metabolite exchanges, interactions in multispecies community include loops of cyclic cross-feeding and higher order interactions such as collective mutualism. Collective mutualism requires that several species simultaneously contribute to a particular task such as digestion of a complex polysaccharide. We show that collective interactions become increasingly unstable to demographic fluctuations as the number of participating species increases. Such higher order interactions can nevertheless be stabilized by a network of reciprocal cross-feeding. We show how our results connect to the theory of nonequilibrium phase transitions and discuss the implications of our findings for the design of synthetic microbial communities. |
Wednesday, March 6, 2019 4:54PM - 5:06PM |
P63.00011: Dynamics of a predator-prey system with multiple predation strategies Ritwika Vallomparambath PanikkasserySu, Justin Yeakel, Ajay Gopinathan Predator foraging behavior includes hunting, scavenging, and stealing. Despite a wealth of literature about predator-prey dynamics, studies with different predator behavioral modalities are rare. We use non-linear dynamics to understand how populations evolve in predator-prey systems with multiple predator behaviors. Predator-prey interactions are summarized by coupled differential equations describing predator and prey population fluxes. The predator population is described by a single variable while the prey population is described by three – alive prey, prey being eaten by predators and is available for stealing, and dead prey available for scavenging. The size of each prey group serves as a proxy for the proportion of the relevant predator behavior. Fixed point analysis yields two trivial and one non-trivial fixed point, and the latter depends on predator death rate, prey growth rate, and relative strengths of different predator-prey interactions. Numerical simulations yield at least three distinct families of solutions depending on interaction strengths between prey types and predator – i.e., the system has multiple bifurcations. Finally, we show that hunting is more prevalent than scavenging or stealing. |
Wednesday, March 6, 2019 5:06PM - 5:18PM |
P63.00012: Investigating the role of pairwise interactions in microbial community assembly James Brunner, Nicholas Chia Using metabolic and ecological modeling, we investigate the question: is microbial co-occurrence in the human gut a result of pairwise interactions, or do higher order interactions play a signicant role? We perform model tting on data from pairwise bacterial growth experiments to produce deterministic and stochastic growth models for pairs and triplets of bacterial species. We measure the accuracy of the predictions given by the triplet models to asses the extent to which pairwise interaction parameters can explain triplet outcomes. We also use metabolic models to assess bacterial growth in pairs and triplets. Pairwise metabolic modeling can be used to determine interaction parameters between species, using for example dynamic ux balance analysis (dFBA). We compare the apparent pairwise interaction parameters derived from pair community models and triplet community models to determine whether or not constraint based metabolic modeling of communities depends strongly on only pairwise interactions, or if higher order interactions must be taken into account. |
Wednesday, March 6, 2019 5:18PM - 5:30PM |
P63.00013: Immigration-induced phase transition in a regulated multispecies birth-death process Song Xu, Thomas Chou Power-law-distributed species counts or clone counts arise in many biological settings such as multispecies cell populations, population genetics, and ecology. This empirical observation that the number of species ck represented by k individuals scales as negative powers of k is also supported by a series of theoretical birth-death-immigration (BDI) models. However, we show how a simple global population-dependent regulation in a neutral BDI model destroys the power law distributions. Simulation of the regulated BDI model shows a high probability of observing a high-population species that dominates the total population. Further analysis reveals that the origin of this breakdown is associated with the failure of a mean-field approximation for the expected species abundance distribution. We find an accurate estimate for the expected distribution 〈ck〉 by mapping the problem to a lower-dimensional Moran process, allowing us to also straightforwardly calculate the covariances 〈ckcl〉. Finally, we exploit the concepts associated with energy landscapes to explain the failure of the mean-field assumption by identifying a phase transition in the quasi-steady-state species counts triggered by a decreasing immigration rate. |
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