EXPLORATION OF ECOLOGICAL AND EVOLUTIONARY MECHANISMS UNDERLYING MICROBIAL BIOGEOGRAPHY AND ADAPTATION

Abstract

256 pagesAs the most abundant and diverse organisms on Earth, microorganisms perform multiple vital ecological functions in our environments. Unveiling the geographic distribution and structure of microbial populations and communities and elucidating the interaction between microorganisms and environments are fundamental goals in the field of microbial ecology and evolution. There has been growing evidence showing that microorganisms including bacteria display biogeographic patterns and have the ability to endure various stresses and adapt to the environments. However, our mechanistic understanding of the distribution patterns and adaptive traits of bacteria, particularly foodborne pathogens, is still limited largely due to the intertwined effects of eco-evolutionary dynamics and a dearth of data from large-scale investigations and from specific environment. In the studies presented here, we used Listeria including the foodborne pathogen L. monocytogenes, Salmonella enterica (a foodborne pathogen), and Escherichia coli (an enteric bacterium) as three model organisms to understand what ecological and evolutionary mechanisms underpin microbial biogeography and adaptation. We approached this question from a variety of angles including by analyzing sequence data of bacteria isolated from different environments (e.g., natural, food-associated, and host) and at different scales (nationwide, regional, and local), and by focusing on different ecological processes (e.g., environmental selection and dispersal) and evolutionary processes (e.g., positive selection and horizontal gene transfer). We found that the niche breadth, host range, and source of closely related bacteria are strongly associated with the genome variations mediated by horizontal gene transfer and transposition. Positive selection mainly targets cell surface proteins (e.g., porins and transporters), and is a key for bacteria to achieve ecological success in nature. Notably, we showed that genes involved in cell motility (e.g., flagella assembly) and metabolism (e.g., amino acid metabolism) under strong positive selection appear to allow motile and non-motile bacteria to occupy a broad niche at a nationwide scale, respectively. In addition, we found evidence that local and regional factors impact the distribution and genetic divergence of bacteria in combination. Regional factors such as landscape appear to shape the distribution of bacteria via influencing the frequency of dispersal and the strength of environmental selection. Overall, this dissertation provides valuable insights on a number of genetic, ecological, and evolutionary bases of microbial biogeography and adaptation. These insights not only shed light on the biological strategies that bacteria may employ to colonize, survive, and persist in the environments with diverse stressors, but also could benefit the control and traceback investigation of disease outbreaks and contamination events caused by foodborne pathogens.2022-08-2