A balance between environmental filtering and competitive exclusion modulates the macroecology of alternative stable states in microbial communities

Abstract

Predicting the assembly and stability of microbial ecosystems is fundamentally challenged by the stochas-ticity inherent in historical contingencies. Although these dynamics often appear reproducible at coarse taxonomic or functional scales, the mechanisms governing fine-grained species-level variation and the emergence of alternative stable states remain an unresolved problem in ecology. Bridging the gap between individual species variability and the emergence of predictable community-level attractors is essential for a mechanistic understanding of ecosystem resilience. Here, by analyzing replicate microbial communities assembled in vitro, we demonstrate that community structure is built upon individual species exhibiting robustly bimodal abundance distributions. Each taxon exists in either a high- or low-abundance state. We show that the collective configuration of these binary species states--a phenomenon also observed in natural systems--drives the correlation structure between community members and defines a set of discrete, alternative community-level attractors. By examining the prevalence of species across these attractors, we uncover a striking taxonomic signal: phylogenetically close relatives are significantly more likely to display reciprocal prevalence patterns--where the dominance of one relative necessitates the suppression of the other--than expected by chance. This discovery directly rejects models based on simple functional redundancy. Instead, it proves that state-dependent competitive exclusion is a primary driver of community divergence, where the identity of the "winner" is contingent on the collective state of the entire community. Our work reframes microbial community structure through the lens of discrete population states, providing a predictive framework for understanding ecosystem stability and the engineering of community functions.