Bacterial transport and horizontal gene transfer in subsurface: multiple-scale experimental studies

Horizontal gene transfer rapidly changes bacterial genetic repertoire and contributes to bacterial evolution. Natural transformation, one mechanism of horizontal gene transfer, is defined as the process by which bacterial cells successfully take up and incorporate extracellular DNA. The extracellular DNA and the bacterial cells are both exposed to various environmental conditions that may alter natural transformation. Bacterial fate and transport in the subsurface may influence bacterial transformation with adsorbed DNA on surfaces. The objectives of this thesis were to investigate the physicochemical and biological factors affecting the extracellular DNA-bacterial cell interaction and the natural transformation, with a long-term goal of modelling and assessing natural transformation in the environment. This thesis developed experimental approaches to systematically study natural transformation with the model strain Azotobacter vinelandii. The systematic experimental approaches consisted of quartz crystal microbalance with dissipation (QCM-D) and Fourier transform infrared spectroscopy (FTIR) for measuring extracellular DNA adsorption and the conformation of the attached NOM on top of adsorbed DNA layer on model soil surfaces, a multi-scale approach for understanding bacterial fate and transport including the use of radial stagnation point flow (RSPF) cells, two-dimensional micromodels, and column experiments, and transformation assays for quantifying the natural transformation. The most important findings of this research are the following: 1) adsorbed DNA transforms bacterial cells in the presence of natural organic matter; 2) flagella affect the dynamics of bacterial deposition and swimming motility reduces bacterial deposition; 3) natural transformation kinetics depend on availability of transforming DNA; 4) extracellular DNA transforms both swimming and swimming-impaired A. vinelandii cells similarly. This work provided supporting evidences in addressing the environmental significance of natural transformation and quantified the transformation rates with the model organism A.vinelandii