Bulletin of the American Physical Society
APS March Meeting 2022
Volume 67, Number 3
Monday–Friday, March 14–18, 2022; Chicago
Session M05: Ecological and Evolutionary Dynamics IIIFocus Recordings Available
|
Hide Abstracts |
Sponsoring Units: DBIO Chair: Daniel Weissman, Emory Room: McCormick Place W-178A |
Wednesday, March 16, 2022 8:00AM - 8:36AM |
M05.00001: A new evolutionary perspective on drug(g)ability Invited Speaker: Brandon Ogbunu Drug(g)ability is a classical concept in pharmacology that describes properties of drug targets in some cases, and of small molecules in others. In this seminar, I unpack this ambiguity, and introduce new metrics that quantify the likelihood that (i) a given drug is effective across alleles, and that (ii) alleles are treatable by a panel of drugs. Further, we resolve drug-variant interactions into very specific higher-order terms between mutations that construct alleles and drug environments. We interpret these results in light of modern questions in evolutionary biomedicine and in the context of the growing science of higher-order complex biological systems. |
Wednesday, March 16, 2022 8:36AM - 8:48AM |
M05.00002: Stability criteria for the consumption and exchange of essential resources Theo L Gibbs, Yifan Zhang, Zachary R Miller, James P O'Dwyer Models of pairwise interactions have informed our understanding of when ecological communities will have stable equilibria. However, these models do not explicitly include the effect of the resource environment, which has the potential to refine our understanding of when a group of interacting species will coexist. Recent consumer-resource models incorporating the exchange of resources alongside competition exemplify this: such models can lead to either stable or unstable equilibria, depending on the resource supply. On the other hand, these recent models focus on a simplified version of microbial metabolism where the depletion of resources always leads to consumer growth. Here, we model an arbitrarily large system of consumers governed by Liebig's law, where species require and deplete multiple resources, but each consumer's growth rate is only limited by a single one of these multiple resources. Consumed resources that do not lead to growth are leaked back into the environment, thereby tying the mismatch between depletion and growth to cross-feeding. We show that feasible equilibria can be either stable or unstable. We identify special consumption and production networks which protect the community from instability when resources are scarce. Using simulations, we demonstrate that the qualitative stability patterns we derive analytically apply to a broader class of network structures and resource inflow profiles, including cases in which species coexist on only one externally supplied resource. Our stability criteria relate to classic stability results for pairwise interactions, but also demonstrate how environmental context can shape coexistence patterns when ecological mechanism is modeled directly. |
Wednesday, March 16, 2022 8:48AM - 9:00AM |
M05.00003: High-dimensional characterization of phototroph-heterotroph interactions Chandana Gopalakrishnappa, Zeqian Li, Seppe Kuehn Phototrophic and heterotrophic microbes are ubiquitous in ecosystems from soils to lakes and oceans. Interactions between them lie at the heart of global biogeochemistry, ecosystem productivity, and biofuel generation. However, relatively little is known about how the chemical nature of the environment affects their interactions. Using a high throughput droplet-based microfluidic platform, we have assayed phototroph-heterotroph interactions across a wide range of availability of the non-substitutable nutrients - carbon, nitrogen, and phosphorus. The system under study comprises the alga Chlamydomonas reinhardtii as the phototroph and Escherichia coli as the heterotroph. In contrast to the prevailing view that microbial interactions are governed by nutrient competition, we have found that the interactions in our system are governed by the initial pH and buffering capacity which are themselves set by the nutrient availability. Low pH and buffering capacities result in nutrient-dependent interactions whereas high pH and buffering capacities result in nutrient-independent inhibition of the heterotroph. Our work presents a new view of how the chemical environment impacts phototroph-heterotroph interactions. |
Wednesday, March 16, 2022 9:00AM - 9:12AM |
M05.00004: Genomic structure predicts metabolite dynamics in microbial communities Karna Gowda, Derek J Ping, Madhav Mani, Seppe Kuehn The metabolic activities of microbial communities play a defining role in the evolution and persistence of life on Earth, driving redox reactions that give rise to global biogeochemical cycles. Community metabolism emerges from a hierarchy of processes, including gene expression, ecological interactions, and environmental factors. In wild communities, gene content is correlated with environmental context, but predicting metabolite dynamics from genomes remains elusive. Here we show, for the process of denitrification, that metabolite dynamics of a community are predictable from the genes each member of the community possesses. A simple linear regression reveals a sparse and generalizable mapping from gene content to metabolite dynamics for genomically-diverse bacteria. A consumer-resource model correctly predicts community metabolite dynamics from single-strain phenotypes. Our results demonstrate that the conserved impacts of metabolic genes can predict community function, enabling the prediction of metabolite dynamics from metagenomes, designing denitrifying communities, and discovering how genome evolution impacts metabolism. |
Wednesday, March 16, 2022 9:12AM - 9:24AM |
M05.00005: Unique functional structure of the Yellowstone hot spring microbial mats revealed by multi-omics studies Zeqian Li, Amanda Shelton, Frederick De St Pierre Bunbury, Arthur Grossman, Devaki Bhaya, Feiqiao B Yu, Seppe Kuehn The alkaline siliceous hot spring microbial mats of Yellowstone National Park are ideal model systems to study the geo-eco-evolutionary processes of microbial communities. The hot spring mats exhibits special community structures and functions, such as adaptation of closely related species to environmental conditions, fine-scale diversity, and extensive recombination events. However, the mats' structure on a community level is largely unknown. Using a multi-omics dataset, including metagenomic data of samples across various environmental parameters, metatranscriptomic data of full diel cycles, and single-cell sequencing data, we extensively studied the mats' community composition, genomic structure, and metabolic activities. We showed how environmental parameters determine community composition and gene content to facilitate nutrient cycling. Genomics studies showed genome diversity on a functional level across environmental conditions. Our results provide a unique example of how environments shape structure and function of microbial communities. |
Wednesday, March 16, 2022 9:24AM - 9:36AM |
M05.00006: Constrained proteome allocation affects coexistence in models of competitive microbial communities Leonardo Pacciani-Mori Microbial communities are ubiquitous and play crucial roles in many natural processes, but despite their importance there are many of their aspects that we still don't fully understand. There is a growing amount of evidence that the structure and composition of microbial communities are intertwined with the metabolism of the species that inhabit them, suggesting that properties at the intracellular level such as the allocation of cellular proteomic resources must be taken into account when describing microbial communities with a population dynamics approach. In this talk, we reconsider one of the theoretical frameworks most commonly used to model population dynamics in competitive ecosystems, MacArthur's consumer-resource model, in light of experimental evidence showing how proteome allocation affects microbial growth. This new framework allows us to describe community dynamics at an intermediate level of complexity between classical consumer-resource models and biochemical models of microbial metabolism, accounting for temporally-varying proteome allocation subject to constraints on growth and protein synthesis in the presence of multiple resources. In particular, we study this consumer-proteome-resource model analytically and numerically to determine the conditions that allow the coexistence of multiple species. |
Wednesday, March 16, 2022 9:36AM - 9:48AM |
M05.00007: Alternative sources of information for adaptation to varying environments BingKan Xue, Leo H Law Two types of adaptation strategies have been widely studied for organisms in varying environments. The "sensing" strategy assumes that organisms are able to gather information from the present environment and adapt their traits, thus maximizing their fitness at all times. The "bet-hedging" strategy, on the other hand, allows a population to survive by maintaining a diversity of traits among individuals, so that the average fitness is less affected by environmental fluctuation. Because the bet-hedging strategy does not make use of environmental information, it is expected to perform worse than the sensing strategy, unless the cost of gathering external information is prohibitive. Here, we demonstrate a different type of strategy that utilizes an internal source of information to improve performance. For example, an organism may choose to forage or not depending on how much energy reserve it has; the reserve level effectively serves as a memory of past environments. In general, the trait of an organism may depend on an internal state, which does not directly interact with the environment but becomes correlated with it due to past selection. We show that this strategy using internal information can outperform bet-hedging and even approach the sensing strategy. |
Wednesday, March 16, 2022 9:48AM - 10:00AM |
M05.00008: Nutrient availability controls coupling between algae and bacteria Kaumudi H Prabhakara, Derek J Ping, Seppe Kuehn Photosynthetic (phototrophic) microbes are responsible for fixing nearly half of the carbon dioxide on the planet. Mircobial phototrophs perform this feat in the context of communities, where they form tight associations with non-photosynthetic (heterotrophic) microbes. Carbon flow between phototrophs and heterotrophs forms the basis of biomass production in ecosystems across the globe and is critical for the global carbon cycle. Despite the importance of phototroph-heterotroph communities, we do not understand how these consortia assemble and function. In particular, it is unclear how the availability of nutrients influences community assembly. To address this quesion, we grow complex bacterial consortia, obtained from soil, in the presence of the photosynthetic alga, Chlamydomonas reinhardtii. We ask how the frequency of exogenous nutrient supply influences community assembly. We find that when exogenous nutrients are supplied infrequently, the composition of the bacterial community in the presence of the alga converges across replicate communities over time. Our analysis reveals that this convergence arises from the down-regulation of certain bacterial taxa in presence of C. reinhardtii. Our study shows that when the frequency of externally supplied nutrients is low, phototrophs control bacterial community assembly, but when nutrients are supplied frequently, bacterial community assembly is decoupled from the phototroph. We hypothesize that this coupling arises from carbon exchange between the alga and bacteria. |
Wednesday, March 16, 2022 10:00AM - 10:12AM |
M05.00009: Environment complexity and nativeness control the level of coarse-graining at which community assembly is reproducible Mikhail Tikhonov, Jacob Moran, Ryan S McGee Experiments demonstrate that microbial communities sampled from nature and reassembled in laboratory replicates exhibit reproducibility at a coarse taxonomic level (family), yet a high variability at finer scales (species). As was recently shown, the former is ensured by metabolic constraints, while the latter is allowed by functional degeneracy within a family, and multistability of population dynamics. Is the family-level classification special (due to universality of metabolic rules), or should we expect the level at which reproducibility is observed to depend on experimental conditions? What are the theoretical expectations, and what experimentally accessible control parameters could allow predictions to be tested? To address such questions, we built a theoretical framework where a microscopic "ground truth" based on consumer-resource dynamics can be systematically compared to a hierarchy of coarse-grained descriptions. Here, we investigate how the level of coarse-graining at which replicate communities are reproducible is controlled by both environment complexity and environment "nativeness" - the extent to which the test environment resembles the natural context from which the community is originally derived. |
Wednesday, March 16, 2022 10:12AM - 10:24AM |
M05.00010: Howbet-hedging species survive competition in fluctuating environments XIAO ZHOU, BingKan Xue Understanding the coexistence of species in a changing environment is an important problem in ecology. Bet-hedging is a strategy that helps species survive in such changing environments. However, studies of bet-hedging have often focused on unlimited growth of a single species, neglecting competition with other coexisting species. To account for competition, it is important to study the extinction risk of one species in the presence of others. We show that, when both environmental and demographic fluctuations are considered, there are three contributions to the extinction risk. The first is the usual demographic contribution due to stochastic reproduction and selection processes in finite populations. The second, due to the fluctuation of population growth rate caused by environmental changes, may counterintuitively reduce the extinction risk for small populations. This is a manifestation of the "storage effect" studied in community ecology. The third contribution, unique to bet-hedging species that diversify into multiple phenotypes, comes as the phenotype composition fluctuates with time. We illustrate all three contributions and examine how they depend on environmental correlations and population sizes. |
Wednesday, March 16, 2022 10:24AM - 10:36AM |
M05.00011: Ecological diversification of rapidly adapting populations Daniel Wong, Benjamin H Good Microbial populations, owing to their large size, continually produce new mutations. Some mutations influence the competitive fitness of individuals, which compete with each other in a process known as clonal interference. Other mutations allow the population to diversify into distinct ecological niches, as has been directly observed in laboratory experiments. However, despite the empirical relevance of both clonal interference and ecological diversification in microbial populations, their interplay is not well understood theoretically. To address this gap, we study the dynamics of a simple class of consumer resource models in which individuals acquire mutations that alter their resource uptake rates. We focus on large, clonally interfering populations, where ecological and evolutionary timescales cannot be fully separated. In this regime, we find that the few highly fit individuals that dominate the future population are strongly influenced by the ecological environment set by the bulk population. This delayed feedback between evolutionary and ecological processes manifests as a dynamical "priority effect" for resident ecotypes, impeding diversification. |
Wednesday, March 16, 2022 10:36AM - 10:48AM |
M05.00012: Phenotypic Heterogeneity Facilitates Survival While Hindering the Evolution of Drug Resistance Joshua D Guthrie, Daniel A Charlebois Drug resistance has recently been shown to emerge from non-genetic mechanisms, such as "persistence" in quiescent microbes and fluctuations in gene expression in actively replicating cells, as well as genetic mutations. However, it is still unclear if non-genetic drug resistance affects the evolution of genetic drug resistance. We develop deterministic and stochastic population models that incorporate resource competition to quantitatively investigate the transition from non-genetic to genetic resistance during the exposure to static and cidal drugs. We find that non-genetic resistance facilitates the survival of cell populations during drug treatment, but that it hinders the development of genetic resistance due to the competition between the non-genetically and genetically resistant subpopulations. |
Follow Us |
Engage
Become an APS Member |
My APS
Renew Membership |
Information for |
About APSThe American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics. |
© 2024 American Physical Society
| All rights reserved | Terms of Use
| Contact Us
Headquarters
1 Physics Ellipse, College Park, MD 20740-3844
(301) 209-3200
Editorial Office
100 Motor Pkwy, Suite 110, Hauppauge, NY 11788
(631) 591-4000
Office of Public Affairs
529 14th St NW, Suite 1050, Washington, D.C. 20045-2001
(202) 662-8700