Entrainment by biogenic bubbles enables long-range microbial dispersal in yield-stress environments

Microbial communities typically inhabit spatially-constrained 3D environments, such as soils and sediments, foods, and gels and tissues in the body. While some microbes can disperse in their surroundings using motility, many are non-motile and can only grow and proliferate locally. Here, we show how even these non-motile microbes can break free of their local microenvironments and disperse over long ranges by riding bubbles they produce through metabolism. We study non-motile yeast growing in transparent 3D granular hydrogel matrices. We show that through fermentation, yeast produce carbon dioxide (CO₂), which initially dissolves in the medium. As fermentation progresses, the medium gradually reaches supersaturation, resulting in the nucleation of CO₂ bubbles. These biogenic bubbles then grow, deform the surrounding matrix, and ultimately rise, entraining yeast cells in their wake over large vertical distances. The motion of these bubbles leaves a lasting imprint in the matrix, acting as a nucleation site for subsequent bubbles. The sequential entrainment by the train of rising bubbles ultimately culminates in the formation of a conduit within the matrix, encapsulating the colony and giving rise to a distinct columnar morphology. Simulations of bubble dynamics in a viscoplastic medium underscore the critical role of sequential entrainment in shaping the columnar structure. Our study provides a quantitative insight into the entrainment process driven by biogenic bubbles and demonstrates its connection to the microbial dispersal. It highlights the pivotal role of biogenesis in the proliferation and transport of living matter within complex environments, which mirrors many biogeological processes in nature.