Jammed Emulsion Matrices as Transparent Porous Media for Studying Bacteria Under Confinement

Across diverse environments, bacteria inhabit structurally complex niches such as soil, tissues, sediment beds, and aquifers where they encounter confined, internally disordered, microporous 3D architectures that significantly alter their growth, motility and chemotaxis. While past efforts have interrogated bacteria in porous media using jammed packings of optically transparent hydrogels or refractive index-matched bead suspensions, these cannot capture key elements of their natural arenas. Critically, active fluid advection through a transport-confined granular matrix-a ubiquitous feature in environments such as aquifers and sediment beds-is yet to be effectively realized using existing experimental platforms. We bridge this gap by engineering an optically transparent, 3D transport-confined granular matrix using jammed packings of oil-in-water emulsion droplets where the refractive index of the oil matches that of bacterial nutrient broth. Using this platform, we interrogate bacterial growth and motility with single-cell resolution, as well as collective chemotaxis of bacterial cells inside the matrix. To demonstrate the flow-through capabilities, we deposit bacterial cells throughout the ensemble 3D matrix using a controlled flow system. Together, our work introduces a versatile and broadly adaptable experimental platform for investigating bacterial growth, motility, chemotaxis, and transport within an optically transparent, flow-through, transport-confined 3D granular medium.