  Anaerobic processes (e.g., methanogenesis and fermentation) largely
contribute to element cycling and natural contaminant attenuation/mobilization,
even in well-oxygenated porous environments, such as shallow aquifers. This
paradox is commonly explained by the occurrence of small-scale anoxic
microenvironments generated by the coupling of bacterial respiration and the
heterogeneous oxygen (O2) transport by porewater. Such microenvironments allow
facultatively and obligately anaerobic bacteria to proliferate in oxic
environments. Microenvironment dynamics are still poorly understood due to the
challenge of directly observing biomass and O2 distributions at the microscale
within an opaque sediment and soil matrix. To overcome these limitations, we
integrated a microfluidic device with transparent O2 planar optical sensors to
measure the temporal behavior of dissolved O2 concentrations and biomass
distributions with time-lapse video-microscopy. Our results reveal that
bacterial colony morphology, which is highly variable in flowing porous
systems, controls the formation of anoxic microenvironments. We rationalize our
observations through a colony-scale Damkohler number comparing dissolved O2
diffusion and bacterial O2 uptake rate. Our Damkholer number enables predicting
the pore space occupied by anoxic microenvironments in our system, and, given
the bacterial organization, it can be applied to 3D porous systems.
