Fig. 1.

Conceptual view of a model pore network. Aerobes (blue) and anaerobes (red) spatially segregate in a natural soil aggregate due to anoxic conditions at the core (illustrating a central carbon source and oxygen diffusing from the aggregate outer surface). Glass-etched micrometric 2-D pore networks mimicking an idealized cross-section in a soil aggregate were used in the experiments. Chemical boundary conditions similar to those postulated for saturated soil aggregates within an unsaturated soil were imposed via 5 ports allowing access to an otherwise sealed pore network. The pore network geometry allows nutrient diffusion through saturated pores and ample space for bacterial flagellated motility. The emerging spatial self-organization of the two microbial species due to opposing nutrient sources and locally modified gradients can be directly visualized and quantified using fluorescence microscopy through the transparent glass walls