Bacterial dynamics in the rhizosphere observed through transparent soil

Soil bacteria play critical roles in various ecological and agricultural processes—yet understanding their behavior in situ remains challenging due to the opacity of natural soils. To overcome this limitation, we develop a cryolite-based transparent soil mimic that allows direct visualization and quantification of bacterial dynamics at single-cell resolution. By adjusting the pore size distribution to emulate different soil types, we observe the transition of Escherichia coli from running-and-tumbling to hopping-and-trapping to eventually fully arrested motility with decreasing pore size. To further explore the impact of soil processes on microbial activity, we introduce Arabidopsis thaliana roots into the artificial soil matrix and study their ability to recruit bacteria. While root exudates can act as chemoattractants, our results indicate that soil architecture is another important factor in facilitating or impeding bacterial accumulation in the rhizosphere. These results based on direct visualization provide novel insights into the interplay between microbial motility, soil structure, and root exudation.