Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities

Abstract

A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences between the microbes and their chemical environment through the consumption and production of metabolites. By analyzing a generalized consumer resource model that explicitly includes cross-feeding, stochastic colonization, and thermodynamics, we show that complex microbial communities generically exhibit a transition as a function of available energy fluxes from a "resource-limited" regime where community structure and stability is shaped by energetic and metabolic considerations to a diverse regime where the dominant force shaping microbial communities is the overlap between species' consumption preferences. These two regimes have distinct species abundance patterns, different functional profiles, and respond differently to environmental perturbations. Our model reproduces large-scale ecological patterns observed across multiple experimental settings such as nestedness and differential beta diversity patterns along energy gradients. We discuss the experimental implications of our results and possible connections with disorder-induced phase transitions in statistical physics.

arXiv comment26 pages, 19 figures

References in corpus (12)

• Scikit-learn: Machine Learning in Python
• From Quantum Chaos and Eigenstate Thermalization to Statistical Mechanics and Thermodynamics
• Genetic Demixing and Evolutionary Forces in the One-Dimensional Stepping Stone Model
• A phase transition between the niche and neutral regimes in ecology
• Marginally Stable Equilibria in Critical Ecosystems
• A collective phase in resource competition in a highly diverse ecosystem
• A generalized model of island biodiversity
• The effect of population abundances on the stability of large random ecosystems
• Diversity, stability, and reproducibility in stochastically assembled microbial ecosystems
• Public good diffusion limits microbial mutualism
• Trade-off shapes diversity in eco-evolutionary dynamics
• An analytically tractable model for community ecology with many species

Cited by in corpus (13)

• A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns
• Effect of resource dynamics on species packing in diverse ecosystems
• Modeling microbial cross-feeding at intermediate scale portrays community dynamics and species coexistence
• The Community Simulator: A Python package for microbial ecology
• Diverse communities behave like typical random ecosystems
• Constrained optimization as ecological dynamics with applications to random quadratic programming in high dimensions
• Cross-feeding Creates Tipping Points in Microbiome Diversity
• Closed ecosystems extract energy through self-organized nutrient cycles
• Exclusion of the fittest predicts microbial community diversity in fluctuating environments
• The advantage of leakage of essential metabolites and resultant symbiosis of diverse species
• Geometry of ecological coexistence and niche differentiation
• Thermodynamic constraints on the assembly and diversity of microbial ecosystems are different near to and far from equilibrium
• Mathematical modeling and intuition in microbiology: a perspective