(415h) Direct Imaging of Root-Bacteria Interactions in Soil Microcosms

The thin soil layer surrounding plant roots, i.e., the rhizosphere, is a dynamic microenvironment where microbial activity, chemical gradients, and root processes converge to influence plant health and nutrient cycling. Yet, visualizing how microbial communities spatially organize around roots in real soil remains a major challenge due to the medium's opacity. Here, we present a transparent soil microcosm that enables in situ imaging of bacterial dynamics near live Arabidopsis thaliana roots at high spatiotemporal resolution. Using this platform, we track the real-time migration of fluorescent Escherichia coli in response to root-derived chemical cues while systematically varying the pore structure to mimic different soil textures. We find that root-bacteria interactions are not governed by chemotaxis alone: the geometry and connectivity of the pore network fundamentally alter how bacteria approach, accumulate, and organize around the root. In loosely packed media, bacteria travel directionally toward the root tip, while in more confined environments, accumulation becomes patchy and temporally fluctuating. We connect these observations with the measurable transition from run-and-tumble to hopping-and-trapping dynamics revealing how soil architecture modulates root-bacteria interactions. These observations reveal early signatures of rhizosphere self-organization that emerge from the coupling between microbial motility, porous confinement, and root signaling. By directly visualizing these interactions, our system provides a powerful experimental foundation for understanding the biophysical principles that underlie root microbiome assembly which is an area of growing importance for sustainable agriculture, synthetic ecology, and engineered living materials.