Morphology and size of bacterial colonies control anoxic microenvironment formation in porous media

TL;DR

This study demonstrates how bacterial colony morphology and size influence the formation of anoxic microenvironments in porous media, using innovative microfluidic and optical sensing techniques to observe microscale processes.

Contribution

It introduces a novel experimental approach combining microfluidics and optical sensors to directly observe microscale oxygen and biomass distributions in porous media.

Findings

Bacterial colony morphology controls anoxic microenvironment formation.

A Damkohler number predicts the extent of anoxic zones.

Microenvironment dynamics can be scaled to 3D porous systems.

Abstract

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.