Modeling the physics behind soil bacteria motility

M. L. CORDERO; M. PIRES MONTEIRO; V. I. MARCONI; S. MONTAGNA; A. R. LODEIRO

Viña del Mar

Workshop; Physics of Active Matter; 2019

Núcleo Milenio Física de la Materia Activa

Bradyrhizobium diazoefficiens is a soil bacteria used as biofertilizer for fixing nitrogen in symbiosis with soybean. Bacteria should move close to the roots for infection. Therefore, it is crucial to understand the motility properties of this active system in soil. We work interdisciplinarily on bacteria diffusion in porous media, with numerical and experimental approaches, to mimic the complex and intricate soil medium with artificial micro-fluidic devices. With transparent and easy to manipulate devices, we aim to master the transport properties of the system for further realistic applications.In this work we present a phenomenological model and numerical predictions of free and confined soil bacteria behaviour. We use Langevin dynamics to solve the equations of motion and the key ingredient in our method is to use only realistic parameters for the motility parameters of the simulated bacteria dynamics. We make remarkable efforts in finding the parameters as accurate as possible. To obtain them, it is necessary to count with good microscopy videos analysis tools. Tracking, automatic detection of change of directions and classification of trajectory shapes help to improve the statistical analysis. Manually, it is possible to analyze hundreds of tracks in a reasonable time, however the use of our software [3,4,5] for a direct automatic analysis allow us to analyze from 1000 to 10000 trajectories in total.Bacteria dynamics was studied in bulk and under a broad spectrum of micro-confinement environments, i. e. in different networks of micro-channels. The channel width scale is similar or larger than the characteristic scale of its swimming strategies (run and reverse, run, reverse and flick, etc). We compare experiments and simulations finding a good agreement.Our results help to understand the diffusion properties of B. diazoefficiens as a function of its two flagellar systems (different motilities) and micro-confinement conditions. These contributions hopefully will be useful for further developments in susta