Dynamic coexistence driven by physiological transitions in microbial communities

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(16)

Published: April 17, 2025

Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes often modify their environments so strongly that they forced out of the state into stressed, nongrowing Such dynamics typical ecological succession nature and serial-dilution cycles laboratory. Here, we introduce a phenomenological model, Community State Model, to gain insight dynamic coexistence due changes physiological states during cyclic succession. Our model specifies preference each along global coordinate, taken be biomass density community, but is otherwise agnostic specific (e.g., nutrient starvation, stress, aggregation), order focus on self-consistency conditions combinations states, “community states,” stable ecosystem. We identify three key features such dynamical communities contrast starkly with steady-state communities: enhanced community stability through staggered dominance different increased tolerance diversity fast growing dominating distinct requirement late-growing species. These features, derived explicitly for simplified models, proposed here as principles aiding understanding complex communities. shifts ecosystem from bottom–up studies based fixed, idealized interspecies interaction top–down accessible macroscopic observables rates total density, enabling quantitative examination community-wide characteristics.

Language: Английский

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Paradox of the Sub‐Plankton: Plausible Mechanisms and Open Problems Underlying Strain‐Level Diversity in Microbial Communities

Environmental Microbiology, Journal Year: 2025, Volume and Issue: 27(4)

Published: April 1, 2025

ABSTRACT Microbial communities are often complex and highly diverse, typically with dozens of species sharing spatially‐restricted environments. Within these species, genetic ecological variation exists at a much finer scale, closely related strains coexisting competing. While the coexistence in has been heavily explored over past two decades, we have no self‐consistent theory how this diversity is maintained. This question challenges our conventional understanding coexistence, framed around clear phenotypic differences. In review, synthesise plausible mechanisms underlying strain‐level (termed microdiversity), focusing on niche‐based such as nutrient competition, neutral migration, evolutionary horizontal gene transfer. We critically assess strengths caveats mechanisms, acknowledging key gaps that persist linking similarity to divergence. Finally, highlight origin maintenance microdiversity could pose major challenge thinking. articulate call‐to‐arms for dialogue between well‐designed experiments new theoretical frameworks address grand conceptual microbial biodiversity.

Language: Английский

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Dynamic coexistence driven by physiological transitions in microbial communities

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 12, 2024

Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes often modify their environments so strongly that they forced out of the state into stressed or non-growing Such dynamics typical ecological succession nature and serial-dilution cycles laboratory. Here, we introduce a phenomenological model, Community State to gain insight dynamic coexistence due changes physiological Our model bypasses specific (e.g., nutrient starvation, stress, aggregation) lead different combinations states, referred collectively as "community states", specifying preference each along global coordinate, taken here be total community biomass density. We identify three key features such dynamical communities contrast starkly with steady-state communities: increased tolerance diversity fast rates dominating enhanced stability through staggered dominance requirement on for inclusion late-growing species. These features, derived explicitly simplified models, proposed principles aiding understanding complex communities. shifts focus ecosystem from bottom-up studies based idealized inter-species interaction top-down accessible macroscopic observables density, enabling quantitative examination community-wide characteristics.

Language: Английский

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The Architecture of Metabolic Networks Constrains the Evolution of Microbial Resource Hierarchies

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(9)

Published: Aug. 23, 2023

Microbial strategies for resource use are an essential determinant of their fitness in complex habitats. When facing environments with multiple nutrients, microbes often them sequentially according to a preference hierarchy, resulting well-known patterns diauxic growth. In theory, the evolutionary diversification metabolic hierarchies could represent mechanism supporting coexistence and biodiversity by enabling temporal segregation niches. Despite this ecologically critical role, extent which substrate can evolve diversify remains largely unexplored. Here, we used genome-scale modeling systematically explore evolution across vast space network genotypes. We find that only limited number readily evolve, corresponding most commonly observed genome-derived models. further show how novel is constrained architecture central metabolism, determines both propensity change ranks between pairs substrates effect specific reactions on hierarchy evolution. Our analysis sheds light genetic mechanistic determinants microbial hierarchies, opening new research avenues understand evolution, evolvability, ecology.

Language: Английский

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Self-organized biodiversity in biotic resource systems through pairwise encounters

Chaos Solitons & Fractals, Journal Year: 2024, Volume and Issue: 188, P. 115607 - 115607

Published: Oct. 4, 2024

Language: Английский

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