Rare taxa modulate the emergence of dominants in microbial communities

ABSTRACT Microbial communities typically comprise a few dominant taxa alongside numerous rare members. While dominant formation is generally attributed to species-level traits that confer adaptation to specific environments, it remains unclear how the rare biosphere influences which taxa ultimately become dominant. We constructed thousands of sub-communities from a soil microbiome using appropriate dilution to preserve the dominants but allow stochastic variation in rare assemblages. Following cultivation under an identical growth condition, dominant taxa varied substantially across replicates, which were determined to be driven primarily by species generalist competitive capacities rather than their initial relative abundances. Notably, the identity of the most abundant taxon in each sub-community was modulated by interactions with rare community members. Co-occurrence and metabolic resource overlap analyses revealed predominantly negative interactions among dominant taxa, while rare taxa exhibited variable and asymmetric interaction patterns. A refined consumer–resource model supported these observations, showing that species are first “nominated” as dominant candidates based on generalist competitive capacities, and then “voted” into the most abundant taxon in a community through collective feedback from rare taxa. The findings imply that dominant emergence in microbial communities is not solely determined by intrinsic species traits but is also critically shaped by interactions with rare taxa. The proposed “nomination–voting” model highlights a collective role of the rare biosphere in shaping community structure and offers a new framework for understanding microbial assembly. IMPORTANCE Microbial ecosystems are almost always dominated by only a few species, but their diversity resides in the rare biosphere. These rare members are usually considered passive passengers with little influence, yet our work reveals that they can collectively determine which species to become the most abundant taxon. We describe this process as a “nomination–voting” system: competitive traits nominate potential dominants, while rare taxa vote for the ultimate winner through their complex interactions. Recognizing this hidden but decisive role of rare microbes provides a new perspective on community assembly and underscores how subtle ecological interactions shape community outcomes. This assembly framework offers new opportunities for the prediction, manipulation, and stabilization of agriculture, health, and environmental microbiomes.