Predicting Regime Shifts in Microbial Ecosystems: Nutrient Competition, Phage Dynamics, and Stable Marriage Models

Abstract

Microbial ecosystems frequently exhibit multiple alternative stable states under identical environmental conditions, separated by abrupt regime shifts. These shifts complicate the understanding, manipulation, and control of such systems, with significant implications for natural, industrial, and health-related contexts. In this talk, I present a unified framework combining insights from nutrient competition and phage-bacteria interactions to explore these dynamics.
First, I will discuss models that predict stable states in microbial ecosystems based on different resource utilization strategies. The first model [1] describes communities of diauxically growing microbes, where species dynamically switch between nutrient preferences depending on environmental availability. In contrast, the second model [2] focuses on specialist species, each limited by two essential nutrients, such as carbon and nitrogen, represented by multiple metabolites. Both models draw inspiration from the stable marriage problem in economics, developed by Gale and Shapley in the 1960s and awarded the Nobel Prize in Economics in 2012. Using ranked tables of species' competitive abilities for nutrients, these models identify all feasible stable states and the specific environmental conditions—characterized by nutrient fluxes—where they occur. This framework reveals a complex network of transitions between stable states and highlights perturbations that induce regime shifts versus those with transient effects.
Next, I address alternative stable states in phage-bacteria systems, building on the findings in [3]. These systems demonstrate how bacterial growth rates, phage burst sizes, and defense mechanisms like CRISPR and abortive infection drive regime shifts. For example, a fast-growing bacterium may exclude slow-growing one via nutrient depletion, but phage predation can invert this dynamic, favoring the slower-growing bacterium.
References:
[1] Goyal A, Dubinkina V, Maslov S. Multiple stable states in microbial communities explained by the stable marriage problem. ISME J. 2018;12: 2823–2834. https://doi.org/10.1038/s41396-018-0222-x
[2] Dubinkina V, Fridman Y, Pandey PP, Maslov S. Multistability and regime shifts in microbial communities explained by competition for essential nutrients. eLife. 2019;8:e49720. https://doi.org/10.7554/eLife.49720
[3] Maslov S, Sneppen K. Regime shifts in a phage-bacterium ecosystem and strategies for its control. mSystems. 2019;4:e00470-19. https://doi.org/10.1128/mSystems.00470-19