Habitat geometry in artificial microstructure affects bacterial and fungal growth, interactions, and substrate degradation

Microhabitat conditions determine the magnitude and speed of microbial processes but have been challenging to investigate. In this study we used microfluidic devices to determine the effect of the spatial distortion of a pore space on fungal and bacterial growth, interactions, and substrate degradation. The devices contained channels differing in bending angles and order. Sharper angles reduced fungal and bacterial biomass, especially when angles were repeated in the same direction. Substrate degradation was only decreased by sharper angles when fungi and bacteria were grown together. Investigation at the cellular scale suggests that this was caused by fungal habitat modification, since hyphae branched in sharp and repeated turns, blocking the dispersal of bacteria and the substrate. Our results demonstrate how the geometry of microstructures can influence microbial activity. This can be transferable to soil pore spaces, where spatial occlusion and microbial feedback on microstructures is thought to explain organic matter stabilization. Arellano Caicedo et al. use microfluidic devices to determine how spatial distortion of pore spaces in soil organic matter affects bacterial and fungal growth and substrate degradation. Their newly conceptualized chip design allows the quantification of bacterial and fungal biomass, and ecosystem function organic matter cycling with help of fluorescent markers in different microstructures.