Bulletin of the American Physical Society
APS March Meeting 2023
Volume 68, Number 3
Las Vegas, Nevada (March 5-10)
Virtual (March 20-22); Time Zone: Pacific Time
Session K08: Ecological Dynamics IIIFocus
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Sponsoring Units: DBIO Chair: Antun Skanata, Syracuse University Room: Room 131 |
Tuesday, March 7, 2023 3:00PM - 3:36PM |
K08.00001: The structure-function problem in microbial communities Invited Speaker: Seppe Kuehn Microbial communities exhibit complex abundance dynamics driven by a myriad of interactions between constituents. Despite the apparent complexity of their dynamics, communities consistently perform critical functions across the biosphere including protecting hosts from pathogens and driving global biogeochemical cycles. How do functional aspects of communities emerge from interactions between constituents? How does the structure of a collective – the genotypes present, their phenotypes and interactions – determine emergent community function? How does Nature construct such robustly functional communities? |
Tuesday, March 7, 2023 3:36PM - 3:48PM |
K08.00002: Global patterns in gene content soil microbiomes emerge from ecological interactions Kyle Crocker, Milena S Chakraverti-Wuerthwein, Madhav Mani, Karna Gowda, Seppe Kuehn Correlations between the genetic or taxonomic composition of microbial communities and their environment are ubiquitous, with examples ranging from microbiome composition changing with host diet to changes with local nutrient conditions in the ocean. We do not understand how these patterns emerge from the complex interactions present in microbiomes, however. Here, leveraging a global dataset of soil metagenomes, we identify a pattern in gene content of soil microbiomes. The two enzymes that complete the first step in bacterial denitrification (Nar, Nap) exhibit opposite trends with pH: Nar increases at low pH, while Nap decreases. Lab enrichment experiments recapitulate this pattern, confirming that pH is causal. Experiments with isolates possessing these two enzymes reveal the surprising result that Nar-genotypes die during denitrification in acidic conditions – despite their ecological dominance at low pH. However, in communities of both genotypes, Nar dominates at low pH. We show that this outcome emerges from Nar specialization in nitrate utilization and Nap specialization in the utilization of the byproduct nitrite, which is toxic at low pH. Using experiments and simulations, we argue that this resource-sharing interaction arises due to trade-offs that constrain bacterial traits, likely giving rise to the global trend in gene abundances. Our results show how physiology drives ecological interactions that give rise to emergent patterns on a global scale. |
Tuesday, March 7, 2023 3:48PM - 4:00PM |
K08.00003: Mapping prediction error versus information content of coarse-grained descriptions of microbial ecosystems Jacob Moran, Mikhail Tikhonov Sequencing-based technologies allow resolving the composition of microbial ecosystems to strain-level detail; however, coarser representations are often found to be more reproducible and more predictive of community-level properties. The general principles for selecting an appropriate level of description for modeling remain elusive. We have recently developed a framework to begin addressing such challenges in the context of a standard ecological model of resource competition, where organisms are described functionally by a list of characteristics at an arbitrary level of detail. We build on this work to systematically compare all possible coarse-grained descriptions by explicitly quantifying their prediction power and information content. We show that coarse-grained descriptions can provide similar predictiveness as microscopic, but at a fraction of the entropy budget, allowing us to define an optimal "good-enough" description for predicting a property of interest. Finally, we demonstrate that the selected optimum can either increase or decrease in complexity as a function of community diversity, depending on the property we aim to predict. We discuss how investigating these behaviors nuances the notion of "emergent simplicity" in microbial ecology. |
Tuesday, March 7, 2023 4:00PM - 4:12PM |
K08.00004: Ecosystems self-organize to capture atypically large energy in a model of coupled redox transformations Akshit Goyal, Avi I Flamholz, Alexander P Petroff, Arvind Murugan In ecosystems, organisms survive by extracting energy through metabolism, transforming matter and consequently, interacting with others. Yet, we do not understand how much energy ecosystems can capture from their surroundings while obeying the constraints imposed by such metabolic transformations. Here, we systematically study the energy capture efficiency and convergent features of self-organized ecosystems, by means of a new conceptual model which combines ecology with thermodynamically-constrained redox transformations. We find that constraint-satisfying ecosystems show convergent thermodynamic features: namely the set of resource fluxes, network of coupling between transformations, and total energy capture. However, the degree of convergence depends inversely on the potential of the external energy input, with the most convergent ecosystems being nearly energy-limited. Finally, we observe that the dynamics of self-organization produces ecosystems that are extremely efficient at capturing energy, even when compared with machines engineered to maximize energy capture. Our results highlight the role of redox transformations, and the constraints they impose, in organizing ecosystems towards convergent functional non-equilibrium states with atypically large energy capture. |
Tuesday, March 7, 2023 4:12PM - 4:24PM |
K08.00005: How does toxin production maintain diversity in ecological systems? Ga Ching Lui, Sidhartha Goyal Competition promotes survival of the fittest, and one of the strategies bacteria can adopt to attain a higher fitness compared to its competitors is through the production of toxins. Intuitively, the presence of toxins should widen the gap in fitness differences between species and thus driving down diversity. The effects of toxins on diversity become less straightforward when one considers the following factors: (1) the trade-offs in strategies, (2) the cost and (3) the regulation of toxin production. Considering the interplay between these factors, under what regimes does toxin production, if possible, promote diversity? Specifically, by using a coarse-grained model of metabolism which satisfies proteome constraints, we show transitions from low to high diversity, and suggest diversity can be maintained by toxin production through two routes: (i) coexistence at steady state, and (ii) persistence through oscillations or chaos. Counterintuitively, the presence of toxins can equalize fitness differences while the toxin producers can act as keystone species, without which the entire system would simply collapse, and may have a role by either of the routes in sustaining diversity beyond the upper limits as suggested by competitive exclusion principle. |
Tuesday, March 7, 2023 4:24PM - 4:36PM |
K08.00006: Multi-strain phage-induced clearance of Pseudomonas aeruginosa Jacopo Marchi, Sophia Zborowsky, Laurent Debarbieux, Joshua S Weitz Antibiotic resistant bacteria are a serious global health threat. As a |
Tuesday, March 7, 2023 4:36PM - 4:48PM |
K08.00007: Recovering Population and Growth Rate of Bacteria Within a Two-Tank Interconnected Chemostat Model using Data Assimilation Susan Rogowski, Nick Cogan, Aseel Farhat The chemostat is a popular laboratory device that is used for growing and maintaining a population of microorganisms. The well-studied single chemostat model is often not realistic for real-world applications such as monitoring populations of microorganisms like lake plankton. Instead, models using a finite number of interconnected chemostats, the so-called gradostat model, often provide more insight for applications that occur in large environments, such as lakes or reservoirs, where liquid mediums are not necessarily well-mixed. Additionally, gradostats have been shown to improve the performances of bioprocesses through decreasing residence time or increasing species persistence. Extensive studies have been done on the behavior and steady state solutions of the general gradostat model. However, it still remains a common problem that, given a noisy set of data observed from one tank, one must estimate and reconstruct the parameters and state variables for the remaining tanks. In this study, we consider a two-tank gradostat model where data is collected from the outflow of the second tank. From here, we develop a data assimilation algorithm to recover the growth rate and population dynamics for the first tank. We conclude with some discussion on extending this model to a larger number of tanks and how data would need to be collected within the larger model to accurately recover the growth and population dynamics. |
Tuesday, March 7, 2023 4:48PM - 5:00PM |
K08.00008: Additivity and asymmetricity in microbial community coalescence Jinyeop Song, Jiliang Hu, Jeffrey C Gore Community coalescence, a process of mixing between two or more pre-existing ecological communities, plays an important role in assembly of natural and engineered microbiomes. Despite the large importance of this process, the quantitative patterns of community coalescence remain elusive. Using both theory and experiment with bacterial microcosms, we show that species pool size and interspecies interaction strengths determine the additivity and asymmetricity in community coalescence. Additivity decreases and eventually reaches a plateau as species pool size and interspecies interactions increase, providing evidence of community maturation in niche theory. Asymmetricity increases as interspecies interaction strengths increase, providing evidence of emergent cohesiveness. We further show that such features are well matched with population dynamics modelling. Taken together, our results demonstrate that the outcome of coalescence exhibits predictable statistical features depending on the species pool size and interspecies interaction strength. |
Tuesday, March 7, 2023 5:00PM - 5:36PM |
K08.00009: Nutrients' control over microbial communities Invited Speaker: Martina Dal Bello Resource availability is a major structuring force of natural communities that has been the object of theoretical exploration since the formulation of the principle of competitive exclusion at the beginning of the XX century. By contrast, experiments on the effects of changes in resource pools on the diversity and structure of communities have lagged behind, with resource-diversity relationship being especially underexplored in the microbial realm. By experimentally manipulating the quality and quantity of available nutrients in natural microbial microcosms, my work aims at bridging the gap between theory and experiments and gaining a mechanistic understanding of the principles governing how available nutrients shape microbial communities. In this talk, I will show that the number and quality of available nutrients determine community richness, while their quantity solely affects community structure. I will interpret these results in the light of consumer resource models and I will highlight the connections between features of microbial metabolism promoted by available nutrients and observed changes in community outcomes. |
Tuesday, March 7, 2023 5:36PM - 5:48PM |
K08.00010: Competition at the edge of expanding populations Daniel W Swartz, Hyunseok Lee, Kirill S Korolev, Mehran Kardar Microbes, cancer cells, and invasive species often spread across space forming a continuous two-dimensional population in a process known as range expansion. At the edge of this growth, mutants are likely to arise and rapidly colonize new territory. These mutants may colonize new territory either faster or slower than their wildtype ancestors, leading to a nontrivial morphology of the expansion front near the mutant colony. In this work, we couple a model of surface growth to a model of one-dimensional competition to describe this behavior. In silico, we find that the colony morphologies generated by new mutants in this model match those seen in microbial invasion experiments. We also make analytical predictions for how the speed of mutant invasion depends on the speed at which the population colonizes new territory. We summarize our results into three general classes. The mutant can either invade the wildtype purely due to its competitive advantage, or due to an overwhelming colonization advantage. Finally, we uncover a third case where the effects of colonization rate and competitive ability become mixed. Taken together our results not only elucidate many subtleties associated with mutant establishment, but also pave the way for a more universal description of evolutionary and ecological processes in growing populations that is also very amenable to theoretical analyses. |
Tuesday, March 7, 2023 5:48PM - 6:00PM |
K08.00011: Lab-evolved multicellular organisms exhibit long-range flows that overcome nutrient diffusion limits Emma P Bingham, Nishant Narayanasamy, William C Ratcliff, Peter Yunker, Shashi Thutupalli Large organisms face a challenge in transporting nutrients from outside to inside and waste from inside to outside. Early multicellular organisms were likely undifferentiated groups of cells and therefore would not have had specialized circulatory systems. Diffusion thus limits how far and fast nutrients can travel into these clusters of cells, setting a microscopic upper bound on size. Using a model organism for multicellularity, snowflake yeast, which has undergone ~5,000 generations of selection for larger size, we have observed that evolved clonal yeast clusters defy diffusion limits and grow exponentially to millimeter sizes. We present a possible mechanism for this: live clusters exhibit metabolically-driven flows when cultured in liquid media. Using micron-sized fluorescent beads, we have observed that fluid flows at 5-10 um/s into the bottom of the cluster and out through the top. We hypothesize that these flows are created due to variation in fluid density caused by gradients of nutrients or waste products. These results suggest that early multicellular organisms could have relied on physical processes alone — before the development of circulatory systems — in order to achieve large sizes in spite of diffusion limits. |
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