Bacteria can transfer DNA from one cell to another, even if they are distantly related. This is called horizontal gene transfer, and it helps bacteria adapt to new contaminants and environmental conditions. It also facilitates the spread of traits such as antibiotic resistance. In the soil, one mechanism of horizontal gene transfer can occur when bacteria contact DNA adsorbed to soil surfaces. Soil surfaces provide places for the DNA to sorb so that they can interact/"infect" with groundwater transported microbial cells. It is important to understand this process because it contributes to the development and spread of both positive (degrading contaminants) and negative (antibiotic resistance) bacterial traits.
Cell movement, or motility, affects how often cells associate with surfaces, and therefore is likely to affect the frequency of interaction between the cells and adsorbed DNA. This project investigates the relationships among cell motility, cell attachment and transport, and gene transfer by DNA adsorbed to soil. The research goal is to identify what controls how fast bacteria are transformed; this is expected to depend on how long they reside on the surface. Cells are expected to transform only when they are actually stuck on the soil surface, not when they are trapped near, but not on, soil surfaces. Thus transformation rates of both motile and non-motile cells will depend on their residence-time on surfaces coated with DNA. The ability of motile cells to swim allows them to approach surfaces independent of the chemistry of surface interactions. Consequently motile cells should exhibit greater frequency of transformation than non-motile cells. These hypotheses will be tested through specific experimental and modeling objectives involving determination of attachment mechanisms in a radial stagnation point flow (RSPF) system, of residence time distributions and spatial distribution in a micromodel system, and of attachment-detachment and gene transfer kinetics in batch and column systems. The experiments will involve both motile and non-motile bacterial strains and will use surfaces coated with DNA. Results will be used in the development and testing of models of bacterial transport and horizontal gene transfer in the soil environment. As groundwater is a major source of drinking water and irrigation water, its vulnerability to biological and chemical contaminants is a major public health concern. The research results will help risk assessment of groundwater contamination, as related processes of microbial transport and microbial evolution are studied together. Graduate and undergraduate students participating in this proposed project will receive an interdisciplinary education, including experience in outreach. The investigators will continue their commitment to recruit women and minorities and to train undergraduate students through Engineers without Borders (EWB) at U of I and at UC Davis and Women Engineering Link at UC Davis.
During the course of the project we have we have made three major contributions in the area of horizontal gene transfer in porous media and understanding flagella-mediated bacterial movement. Horizontal Gene Transfer Kinetics through Transformation Horizontal gene transfer is transfer of genetic information through contact between same of different species of bacteria or a bacteria and an abandoned DNA molecule. It particularly has a significant implication in understanding the spread of antibiotic resistance among bacteria in different environments. On this topic, we have studied the kinetics of gene transfer through transformation (i.e. cell-DNA contact) using a series of experiments in order to understand the effect recipient cell abundance, DNA abundance and time as well as presence of absence of bacterial flagella on the dynamics of transfer of tetracycline-resistance genes. In the experiments we found that at the bacteria and DNA concentration level we studied the frequency of transformation is most sensitive to the DNA concentration and less to cell concentrations. This was unexpected because the number concentration of DNA used in the experiments were several orders of magnitude larger than recipient cells. Also the decline with time of the transfer frequencies showed that some controlling factors is used up during the course of transformation. We hypothesized that only a small fraction of transformations in which the DNA is absorbed by bacteria results in the transfer of tetracycline resistant genes. Based on this hypothesis we developed a mathematical model and applied it to the entirety of data collected during the course of the study. The model successfully reproduced all of the data under different conditions for both bacterial species studied in a consistent way. The model therefore supports hypothesis. The model can be used to upscale the result of the small scale batch experiment to natural systems and to identify the bottlenecks in the process. Flagella-Mediated Bacterial Movement The other front that we have made contribution on is studying flagella mediated motility of bacteria. We have analyzed tens of movie clips collected using microscopes from the movement of motile and non-motile bacteria under a range of conditions including static and several different hydro-dynamic flow fields. We have developed tools to extract trajectories of bacterial motility and have developed methods to perform statistical analysis and identify the major features of bacterial motility. We have identified three distinct modes of bacteria swimming behavior based on a rigorous statistical analysis of swimming trajectories. Based on these findings we have developed a new mathematical motility model that can reproduce these distinct movement modes. These models can be used to predict the behavior of bacteria in natural environments such sub-surface in larger scales where other factors such as flow, adhesion and interactions with solid surfaces also affecting bacterial movement. These models expand our understanding of bacterial transport mechanisms in the subsurface environment and can help designing more effective bio-remediation strategies, perform risk assessment on pathogenic bacterial contamination of water resources and help us understand the extent of anti-biotic resistance spread in natural systems.
