Bulletin of the American Physical Society
APS March Meeting 2020
Volume 65, Number 1
Monday–Friday, March 2–6, 2020; Denver, Colorado
Session G23: Evolutionary and Ecological Dynamics I: Population EcologyFocus
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Sponsoring Units: DBIO GSNP Chair: Jeffrey Gore, Massachusetts Institute of Technology MIT Room: 304 |
Tuesday, March 3, 2020 11:15AM - 11:51AM |
G23.00001: The price of a shortcut Invited Speaker: Wenying Shou I will discuss the importance of quantitative mathematical modeling in biology. I will also experiment with a different presentation style where scientific work is described through story-telling. My talk will be accessible to specialists who study physical biology and to general audience with little knowledge of biology. I also hope to get feedback from the audience on how well this style worked for them. |
Tuesday, March 3, 2020 11:51AM - 12:03PM |
G23.00002: Long-term Nutrient Cycling in a Materially Closed Ecosystem Luis de Jesús Astacio, Zeqian Li, KAUMUDI PRABHAKARA, Seppe Kuehn Closed Microbial Ecosystems (CES) are hermetically sealed microbial communities that support self-sustaining nutrient cycles using only light as an input. CESs have been proposed as controlled model systems to understand the principles governing ecosystem organization and persistence. However, we do not yet understand how the nutrient cycling capabilities of a CES depend on its community structure and composition. To address this question, we present a new method for making precision measurements of carbon cycling in CES using low-cost piezoresistive pressure sensors. With these devices, we quantify carbon cycling rates in a set of CESs over periods of months. Our data show that previously studied synthetic CES comprised of model organisms exhibit declining carbon cycling rates on long-timescales. We go on to self-assemble CESs using the phototrophic alga Chlamydomonas reinhardtii combined with complex, soil-derived, bacterial communities. We find that these CESs persistently cycle carbon on timescales of many weeks. Also, we characterize the limiting nutrients in these CESs as well as their community-level metabolic capabilities. Finally, we use next-generation sequencing to characterize the taxonomic and metagenomic composition of these persistent microbial biospheres. |
Tuesday, March 3, 2020 12:03PM - 12:15PM |
G23.00003: Growth and form control population dynamics of cellular aggregates Alexander Golden, Kirill S Korolev While the colony morphology reflects the interplay of biophysical processes such as nutrient diffusion, motility, and growth. How these processes control genetic correlations within the population remains an open question. To understand how growth morphology influences evolutionary dynamics, we have developed a numerical model of two-dimensional colonies in which microbes grow by consuming a diffusible nutrient and have a density-dependent motility. We show that this model can reproduce a diverse family of shapes observed in the experiments. Many of these morphologies exhibit a qualitatively different pattern of genetic drift compared to microbial colonies with a moderately rough front, which have been the focus of previous work. We report the scaling exponents for both morphological and genetic quantities for each of the growth regime. Most importantly, we show the consequences of the transition from pulled to pushed expansions in two-dimensional models with nutrient diffusion. |
Tuesday, March 3, 2020 12:15PM - 12:27PM |
G23.00004: Synergistic effects of nitrogen and phosphorous on the growth of algal cells reveled by a microfluidic platform Fangchen Liu, Mohammad Yazdani, Nicole Goulding Wagner, Beth A. Ahner, MingMing Wu A sudden growth of photosynthetic algal cells causes Harmful Algal Bloom (HAB), depleting water resources and disrupting the balance of aqua ecosystems. HAB is an emerging environmental problem acerbated by climate change and population growth. Despite the urgency of the problem, there still lacks a systematic understanding of the environmental conditions (physical, chemical, and biological) under which HABs occur. In this presentation, we studied the growth of a model algal strain, Chlamydomonas reinhardtii, under a dual concentration gradient of nitrogen (N) and phosphorous (P) and found that N and P synergistically promoted algal cell growth. Interestingly, no discernible response was observed under single nutrient gradient. We also demonstrated the potential application of the newly developed microfluidic platform that integrated the array microhabitat format with dual gradient generation, enabling fast screening of environmental factors for algal growth studies. Future investigations will include the dynamics of bacterial community under controlled environmental condition. |
Tuesday, March 3, 2020 12:27PM - 12:39PM |
G23.00005: Dynamics of prey-predator: effect of cooperative interaction and inertial forces Dipanjan Chakraborty, Rumi De A swarm of preys when attacked by a predator is known to rely on their cooperative interactions to escape. We present a simple theoretical model to investigate the effect of cooperative interactions on the survival chances of a prey group while chased by a predator. Our study shows that very short-range or very long-range interactions are not beneficial for preys to escape. However, in the intermediate range of interaction, an optimality criterion can be established where the survival probability of the prey group is maximum. We further explore the effect of inertial forces on the survival chances and escape trajectories of the prey group. Interestingly, we observe a transition from non-survival to survival of the prey group as a function of increasing predator mass. Our analysis also shows that prey group size and predator strength have an immense effect on this survival regime. |
Tuesday, March 3, 2020 12:39PM - 12:51PM |
G23.00006: Representing spatially extended ecological oscillators by kinetic Ising models with memory Vahini Reddy Nareddy, Jonathan Machta, Karen Abbott, Shadisadat Esmaeili, Alan Hastings Synchronous behavior in spatially-extended ecological systems can be modeled by noisy, coupled oscillators. If the individual oscillators are in a two-cycle regime, the transition to synchrony as a function of noise strength and coupling strength has been shown to be in the Ising universality class [1]. On the other hand, a nearest neighbor Ising model may not provide an accurate description of non-universal properties. In this talk we will discuss the question of accurately representing a system of coupled, noisy two-cycle oscillators by an Ising model. We show that an accurate representation requires a kinetic Ising model with a self-interaction (memory) term. Even if this kinetic Ising model with memory includes only nearest-neighbor couplings in the dynamics, its equilibrium states are described by a Hamiltonian with more distant neighbor coupling and multi-spin terms. Using maximum likelihood methods we are able to infer an accurate kinetic Ising representation of synthetic data from a noisy lattice map system. We also discuss applications to field data in ecology. |
Tuesday, March 3, 2020 12:51PM - 1:03PM |
G23.00007: Ocean currents promote rare species diversity in protists Paula Villa Martin, Ales Bucek, Tom Bourguignon, Simone Pigolotti Oceans host communities of plankton composed of a huge number of rare species that, as estimated in metagenomic studies, decay as a steep power law of their abundance. We propose that the way oceanic currents limit protists dispersal is a key factor of such biodiversity pattern. We introduce a spatially explicit coalescence model able to reconstruct species ancestry and diversity in the presence of currents. Our model predicts a steep power law decay of the species abundance distribution and a steep increase of the number of observed species with sample size. Metagenomic studies of planktonic protist communities show excellent agreement with our results. |
Tuesday, March 3, 2020 1:03PM - 1:15PM |
G23.00008: Spatial segregation as a necessity for beneficial gene loss in cross-feeding bacterial communities: a kinetic perspective on the Black Queen Hypothesis Mario Di Salvo, Sima Setayeshgar, James McKinlay Cross-feeding communities are common across diverse environments, such as soil, water, and host microbiomes. The Black Queen Hypothesis (BQH) [1] asserts that some metabolic functions are leaky and thus provide a public resource within a community. The public resource allows some community members to lose genes for the production of that resource as long as at least one member continues to produce the resource. Nitrogen fixation as a process that leaks ammonium is used as an example to explain why only certain prokaryotes encode nitrogenase. We explore the emergence of mutualistic cross-feeding in bacterial cocultures in the context of the BQH. We pair a slow-growing nitrogen-fixing cooperator with fast-growing fermentative partners that can either also fix nitrogen gas or require the product, ammonium. We demonstrate that spatial heterogeneity is necessary for the emergence of a partner strain that loses nitrogen-fixation. |
Tuesday, March 3, 2020 1:15PM - 1:27PM |
G23.00009: Localization transitions in age-structured populations Takashi Nozoe, Edo Kussell We discuss age-structured population models that exhibit a range of collective phenomena including phase transitions and population-level oscillations. We present an analysis that predicts the lineage properties of single cells, and demonstrate how the optimal lineage in a population undergoes a qualitative change in its statistical properties as model parameters are varied past a localization transition point that is analytically computed. We observe aging dynamics of the population in the localized phase, and illustrate connections with other problems in evolutionary dynamics. |
Tuesday, March 3, 2020 1:27PM - 1:39PM |
G23.00010: Formation of Phage Lysis Patterns and Implications on Co-Propagation of Phages and Motile Host Bacteria Jing Chen Coexistence of bacteriophages, or phages, and their host bacteria plays an important role in maintaining the microbial communities. In natural environments with limited nutrients, motile bacteria can actively migrate towards locations of richer resources. Although phages are not motile themselves, they can infect motile bacterial hosts and spread in space via the hosts. Therefore, in a migrating microbial community coexistence of bacteria and phages implies their co-propagation in space. Here, we combine an experimental approach and mathematical modeling to explore how phages and their motile host bacteria coexist and co-propagate. When lytic phages encountered motile host bacteria in our experiments, a sector-shaped lysis zone formed. Our mathematical model indicates that local nutrient depletion and the resulting inhibition of proliferation and motility of bacteria and phages are the key to formation of the lysis pattern. The model further reveals the straight radial boundaries in the pattern as a tell-tale sign for coexistence and co-propagation of bacteria and phages. Emergence of such a pattern, albeit insensitive to extrinsic factors, requires a balance between the intrinsic physiology of phages and bacteria, which likely results from co-evolution of phages and bacteria. |
Tuesday, March 3, 2020 1:39PM - 1:51PM |
G23.00011: Spatial competition of toxin-secreting strains of yeast Andrea Giometto, Andrew Murray, David R. Nelson Antagonistic interactions are widespread among microbes and can affect the structure and composition of microbial communities. Theoretical models of well-mixed population genetics with antagonistic interactions predict that a stronger competitor can invade a weaker one only if its initial population is larger than a critical inoculum size. In spatially-extended populations, the invasion of one competitor by another can be mapped to a nucleation problem and the invasion is predicted to be successful only above a critical nucleation size. To test these predictions, we have genetically engineered two strains of the baker’s yeast Saccharomyces cerevisiae to release two different toxins, whose production rates we can vary independently. These strains allowed us to study how antagonistic interactions affect the population dynamics and population genetics of spatially-structured populations at different levels of toxin production, i.e. at different relative strengths of the two competitors. We show that, both in spatially-structured and in well-mixed populations, a toxin-producing strain can displace another toxin-producing strain only if the initial inoculum is larger than a critical threshold, even if the invader strain enjoys a selective advantage. |
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