The statistical structure of alternative stable states in microbial communities

An ecological community assembled from the same pool of species can lead to very different compositions, corresponding to alternative stable states. Using experiments where microbes from single or multiple inocula are grown on simple substrates, we investigate community equilibrium and taxonomic variability from ASV to family level. We find that ASV-level variability can be separated into two sources: rapid abundance fluctuations around typical levels, weakly correlated across species, and strongly correlated variation in these typical abundances. The former source of variation can be explained by a simple model taking into account growth limitation and environmental stochasticity. The latter variation corresponds to a small number of alternative stable states. These fine-grained stable states only partially map to family-level variability but exhibit a non-trivial phylogenetic signal. We discuss how these findings inform our understanding of microbial communities and align with common theoretical models.