Thesis defense of Antoine Hubert

Influence of flow on the growth dynamics of microorganisms - microfluidic imaging and modeling

Abstract

In subsurface environments, a large number of biogeochemical reactions have a kinetics controlled mainly by bacteria. In these environments, nutrient fluxes and solute concentrations can be highly variable over space and time. These variations can generate bio-geochemical reaction kinetics that differ significantly from the cases measured in homogeneous environmental models. The general objective of this work is, using microfluidic experiments and based only on physical descriptors, to quantify the couplings between flow heterogeneity, solute transport/mixing, reactions and biological activity. Our experiments are coupled with numerical modeling and demonstrate the coupling of nutrient transport with bacterial growth on surfaces. Observations at the scale of bacterial cells and at high acquisition rates show the effect of velocity gradients on the patterns of surface colonization by bacteria in the early stages of development of a population subjected to laminar flow. We also reveal a dependence of the properties of bacterial attachment to surfaces on the imposed shear forces. This bacterial adaptation influences their growth rate. Finally, we develop an analytical study framework describing the improvement of reaction kinetics through mixing processes.

Keywords
bacteria, flow, mixing, biogeochemical reactions, microfluidics, modeling

Supervisor : Tanguy Le Borgne & Yves Méheust