Biogenic bubbles enable microbial escape from physical confinement

Abstract

Immotile microbes inhabit nearly every environment on Earth, from soils and sediments to food matrices -- yet how they disperse through these physically confining environments is poorly understood. Here, we show that immotile microbial colonies confined in a model transparent yield-stress matrix can achieve long-range dispersal by harnessing their own metabolism. Using yeast as a model organism, we find that fermentation drives dissolved CO$_2$ to supersaturation, nucleating biogenic bubbles that grow, yield the matrix, and rise, hydrodynamically entraining cells vertically in their wake. Sequential bubble nucleation sculpts persistent columnar colonies extending far beyond what growth alone permits. Multiple colonies interact via their fermentation byproducts, merging and mixing genetically as they collectively sculpt self-sustaining conduit networks. Our findings reveal a third mode of microbial dispersal, distinct from the canonical mechanisms of motility and growth, with implications for ecology, environmental science, and biotechnology. More broadly, they exemplify a previously unrecognized class of active behavior -- Metabolically Driven Active Matter -- in which metabolic byproducts reshape the physical landscape of confinement to drive population-scale motion.