Bulletin of the American Physical Society
APS March Meeting 2022
Volume 67, Number 3
Monday–Friday, March 14–18, 2022; Chicago
Session F05: Ecological and Evolutionary Dynamics IIFocus Recordings Available
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Sponsoring Units: DBIO Chair: Daniel Weissman, Emory Room: McCormick Place W-178A |
Tuesday, March 15, 2022 8:00AM - 8:36AM |
F05.00001: Ecological Dynamics in Health and Infection Invited Speaker: Micaela Martinez
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Tuesday, March 15, 2022 8:36AM - 8:48AM |
F05.00002: Acid stress and cross-feeding provide a dynamic mechanism of microbial coexistence Avaneesh V Narla, Kapil Amarnath, Sammy Pontrelli, Jiajia Dong, Tolga Caglar, Brian R Taylor, Julia Schwartzman, Uwe Sauer, Otto X Cordero, Terence T Hwa Despite the ubiquity of microbial diversity observed across environments, mechanisms of cooperativity that enable species coexistence beyond the classical limit of one-species-per-niche have been elusive. Here we report the observation of a transient but substantial cross-feeding of internal metabolites between two marine bacterial species under acid stress, and further establish through quantitative physiological characterization of the individual strains that this cross-feeding is central to the coexistence of these species in growth-dilution cycles. The coculture self-organizes into a limit cycle in which acid-stressed producers excrete various internal metabolites upon entering growth arrest, enabling the cross-feeders to grow, restore medium pH, and protect the producers from death. These results establish a mechanism in which functional niches are dynamically emergent from self-inhibited growth of a fast-growing species and subsequent resource sharing that allows a slower-growing species to sufficiently grow to enable coexistence. |
Tuesday, March 15, 2022 8:48AM - 9:00AM |
F05.00003: Community Assembly in Time-Varying Environments Avaneesh V Narla, Terence T Hwa, Arvind Murugan We study community assembly in time-varying environments such as growth-dilution or circadian cycles and find conditions under which the competitive exclusion principle may be violated. We find self-organized resource sharing results in "dynamic niches". For example, a fast-growing species might modify the environment (e.g., pollution) in a way that eventually limits its own growth; if a slower-growing pollution-resistant species can sufficiently grow in the modified environment, such species could co-exist in growth-dilution cycles of specific timescales. Such communities feature species with different instantaneous growth rates but are nevertheless stabilized by repeatedly going through unstable transients in composition. We abstract general conditions under which physiological interactions conspire with environmental variations to create such dynamic niches. We further quantify the robustness and susceptibility of such dynamic coexistence. The dynamic niches described here disappear in any limit of a constant environment such as a chemostat and thus cannot be predicted using any effective averaged environment. Thus, our work suggests distinct ecological principles for coexistence in fluctuating environments. |
Tuesday, March 15, 2022 9:00AM - 9:12AM |
F05.00004: A minimal model of cross-feeding in microbial communities Daniel Amchin, Alejandro Martinez-Calvo, Hongbo Zhao, Carolina Trenado Yuste, Sujit Datta The active exchange of resources in biological systems can give rise to complex emergent phenomena. For example, many bacterial communities employ metabolic cross-feeding—a process of importance to physiology, ecology, and industry—in which bistability and oscillations are observed but not well understood. Here, we present a minimal model of bacterial cross-feeding that enables us to establish biophysical rules underlying these non-linear phenomena. Because the metabolic network described by our model manifests in many diverse biological systems, our results help to provide quantitative and generalizable principles to guide future work. |
Tuesday, March 15, 2022 9:12AM - 9:24AM |
F05.00005: Complementary resource preferences spontaneously emerge in diauxic microbial communities Zihan Wang, Sergei Maslov Many microbes grow diauxically, utilizing the available resources one at a time rather than simultaneously. The properties of communities of microbes growing diauxically remain poorly understood, largely due to a lack of theory and models of such communities. Here, we develop and study a minimal model of diauxic microbial communities assembling in a serially diluted culture. We find that, unlike co-utilizing communities, diauxic community assembly repeatably and spontaneously leads to communities with complementary resource preferences, namely communities where species prefer different resources as their top choice. Simulations and theory explain that the emergence of complementarity is driven by the disproportionate contribution of the top choice resource to the growth of a diauxic species. Additionally, we develop a geometric approach for analyzing serially diluted communities, with or without diauxie, which intuitively explains several additional emergent community properties, such as the apparent lack of species which grow fastest on a resource other than their most preferred resource. Overall, our work provides testable predictions for the assembly of natural as well as synthetic communities of diauxically shifting microbes. |
Tuesday, March 15, 2022 9:24AM - 9:36AM |
F05.00006: Structure-function landscape of a closed microbial ecosystem Luis M de Jesus Astacio, Chandana Gopalakrishnappa, Seppe Kuehn Ecosystem persistence depends on emergent stable nutrient cycles to replenish resources. In a previous study, we established closed microbial ecosystems (CES) as models of nutrient cycling in ecosystems. CES are materially closed microbial communities that persist by supporting self-sustaining nutrient cycles using only light as an input. We showed that CES composed of bacterial communities and a model phototrophic alga self-assemble to cycle carbon for months. Furthermore, we showed that replicate CES that persistently cycle carbon exhibit a conserved set of metabolic capabilities despite strong differences in the taxonomy of the bacteria present. However, fully exploring the dependence of carbon cycling on community composition is experimentally challenging. Therefore, we developed a consumer-resource model of emergent carbon cycling in CES. The model incorporates thermodynamic considerations of metabolic reactions and recycling of necromass. Our model recapitulates the dependence of phototroph-heterotroph interactions in the establishment of carbon cycles. Using this model, we present a detailed exploration of how the bacterial catabolic traits and community structure impact emergent nutrient cycling in CES. |
Tuesday, March 15, 2022 9:36AM - 9:48AM |
F05.00007: Modeling multi-trophic ecosystems with consumer resource model Zhijie Feng, Pankaj Mehta, Robert A Marsland, Maria Yampolskaya MacArthur's consumer-resource model describes the ecological dynamics of a simple two trophic-layer ecosystem where consumers compete for a pool of resources (e.g herbivores compete for plants). However, real ecosystems often possess multiple trophic layers (e.g. carnivores, herbivores, plants) that all interact to determine ecosystem dynamics. Inspired by this observation, we analyze a generalization of MacArthur's consumer model with multiple trophic layers using methods from statistical physics. For the three-layer model, we discuss the new properties of the model, connection with constrained optimization, and present a mean-field solution for the multi-trophic layer model using the cavity method. We show that the introduction of additional trophic layers into an ecosystem can result in both quantitative and qualitative changes in ecosystem-level properties. |
Tuesday, March 15, 2022 9:48AM - 10:00AM |
F05.00008: Learning and Control for Evolutionary Processes Obinna A Ukogu, Colin LaMont, Ceyhun Eksin, Armita Nourmohammad Evolutionary selection can be interpreted as exerting an optimal control on population trajectories over many generations. As the field of synthetic biology grows, researchers are increasingly preoccupied with effectuating artificial selection on laboratory populations. However, many systems of interest exhibit unknown, or partially unknown, stochastic dynamics. In these settings it is desirable to learn the system dynamics while applying a knowledge-dependent optimal control subject to a cost function. Here we show that studying a deterministic analog of a stochastic system highlights the tradeoff between control and learning. This perspective will allow for the development of nearly optimal Bayesian algorithms for simultaneous learning and control, with applications to experiments to synthetic biology and immuno-therapy for HIV treatment. |
Tuesday, March 15, 2022 10:00AM - 10:12AM |
F05.00009: Coarse-graining ecological dynamics in the face of unkown microscopic details Jacob Moran, Mikhail Tikhonov Any description of microbial communities necessarily ignores some details of the underlying diversity. What predictions can be robust to such omissions and coarse-grained descriptions? Here, building on the theoretical framework of resource competition, we introduce an eco-evolutionary model that allows organisms to be described at an arbitrary level of detail, enabling us to formally study the hierarchy of possible coarse-grained descriptions. Within this model, we demonstrate that the ability of coarse-graining schemes to appropriately describe a community depends on the quantity we aim to predict (e.g., invasion rates versus strain abundances). We further show that robustness of predictions to coarse-graining requires two conditions: the ecological context in which we test a coarse-grained prediction must remain highly diverse, and this diversity must be derived from a sufficiently similar environment as the one used for testing. We use our model to argue that studying communities away from their natural eco-evolutionary context may eliminate the very reasons that make a coarse-grained description an adequate characterization of the natural diversity. |
Tuesday, March 15, 2022 10:12AM - 10:24AM |
F05.00010: Pinpoint ecological niches and metabolic essentiality of microbial communities using both metagenomics and metaproteomics Tong Wang, Leyuan Li, Daniel Figeys, Yang-Yu Liu Microbes rely on various proteins to carry out functions, which are crucial for their metabolism and competitiveness in the community. In a given environment, a microbe usually expresses a fraction of its genomic capabilities as protein functions. It is not clear yet how microbial genomic capabilities map to their protein functions. In addition, how the role of one protein in the metabolic network and ecological competition shapes the mapping remains to be revealed either experimentally or through modeling. Here, we propose to compare the network degree and redundancy of each protein between the genomic content network obtained from metagenome and the protein content network obtained from metaproteome. We find that the difference in network degree and redundancy of each protein can characterize the ecological niches and metabolic essentiality. Furthermore, we develop an ecological model with the mapping from the genomic capabilities to protein functions that can reproduce the pattern of difference in network degree and redundancy. These results provide better insights into the metabolic and ecological functions of proteins and shed light on the impact of community competition on the selective expression of functions. |
Tuesday, March 15, 2022 10:24AM - 10:36AM |
F05.00011: A PDE Model for Protocell Evolution and the Origin of Chromosomes via Multilevel Selection Daniel B Cooney, Fernando W Rossine, Dylan H Morris, Simon A Levin The origin of chromosomes was a major transition in the evolution of complex cellular life. To model this phenomenon, we consider a simple protocell composed of two types of genes: a ``fast gene'' with an advantage for gene-level self-replication and a ``slow gene'' that confers an advantage for protocell-level reproduction. Using a PDE describing the dynamics genetic composition of protocells under within-cell and between-cell competition, we find that the gene-level advantage of fast replicators casts a long shadow on the dynamics of protocell evolution: no level of between-protocell competition can produce coexistence of the fast and slow replicators when the two genes are equally needed for protocell-level reproduction. By introducing a ``dimer replicator'', a linked pair of the slow and fast genes, we see that the possibility of genetic linkage can help to overcome this shadow of lower-level selection and promote coexistence of the fast and slow genes via multilevel selection. |
Tuesday, March 15, 2022 10:36AM - 10:48AM |
F05.00012: Robust Altruism by Similarity in Multifaceted Phenotypes Linnea Bavik, Rohan S Mehta, Daniel B Weissman We study the evolution of altruistic behavior under a model where individuals choose to cooperate with each other by comparing a set of always-visible continuous tags, and find the generic maintenance of robust cooperation when individuals carry more than one tag. Our model marries existing weak and strong selection results in the literature, addresses previous challenges to prior model formulations and supports the viability of a simple memory-less mechanism for cooperation in a well-mixed population. Robust cooperation is buoyed by a regime of weak positive selection that serves as a buffer for the strongly selected cycles of high cooperation. |
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