Visualization and modeling of soil bacteria under confinement*

Bradyrhizobium diazoefficiens is a soil bacterium that fixes atmospheric N₂ in symbiosis with soybean, used as biofertilizer in sustainable agronomy. It has two different flagellar systems, a thick subpolar flagellum, and several thin lateral flagella. The motility parameters (average speed, characteristic reorientation time and angle) were measured for two B. diazoefficiens strains, the wild type with both flagellar systems, and a mutant with only the subpolar flagellum. Confinement effects on their swimming behavior were studied using microfluidics devices designed to imitate the soil intricated structure. Realistic models were proposed for each strain and simulated, using the same experimental geometries and measured swimming parameters, with Langevin equations of motion. The diffusion properties of B. diazoefficiens populations were investigated, for each strain motility parameters as well as for multiple soil porosities. Our contributions and methods from physics hope to bring light to long searched improvements of bioproducts used for soybean crops for more than 20 years, which are yet far from being efficient.