Genome Evolution and Competitiveness in Bacteria

Bacteria are essential components of both agricultural and natural ecosystems. They perform functions that may be either beneficial or harmful, depending on the species and ecological context. Many bacteria, including plant pathogens and food-borne pathogens such as Escherichia coli, have short generation times and large population sizes, enablingthem to rapidly evolve. Such rapid evolution often limits efforts to control harmful species, as exemplified by the emergence of pathogenic bacteria that are resistant to antibiotics. The overarching goals of this project are to quantify and characterize changes in the genome sequences, competitive fitness, and antibiotic-resistance profiles in bacteria that have evolved under defined and controlled conditions. The project will address the following specific objectives: (i) We will analyze metagenomic samples obtained at multiple time points from 12 replicate E. coli populations that have been propagated under the same conditions for over 60,000 generations, providing insights into bacterial genome evolution including rates of change, types of mutations, and extent of genetic diversity within and between populations. (ii) We will quantify the dynamics of competitive fitness over time from one population and compare the resulting trajectory with the metagenomic dynamics obtained above, providing insights into the coupling of genome evolution and competitive fitness. (iii) We will examine the effects of horizontal gene transfer on genome structure by analyzing E. coli isolates from an experiment in which donor strains carrying plasmids were mixed with recipients, providing insights into the effects of gene transfer and its interplay with selection. (iv) We will examine how the antibiotic-resistance profiles of bacteria have changed over the course of long periods without exposure to antibiotics, providing insights into the tension between antibiotic resistance and bacterial competitiveness.