The eco-evolutionary dynamics of microbial populations

Abstract

Microbes have adapted to life in complex microbial communities in a large variety of ways, and they are continually evolving to better compete in their changing environments. But identifying the conditions that a particular microbe thrives under, and how they have become adapted to those condition can be exceedingly difficult. For instance, Clostridium difficile became widely known for being the world's leading cause of hospital associated diarrhea, but people can also have C. difficile in their gut without developing diarrhea. Although these asymptomatic carriers are now thought to be the largest source of infection, we know very little about how these people become colonized. In the first chapter of my thesis I use publicly available microbiome survey data and a mouse model of colonization to show that C. difficile colonizes people immediately after diarrheal illnesses, suggesting C. difficile is a disturbance adapted opportunist.

However, the differences between very recently diverged microbial populations that are adapted for growth in different conditions can be very difficult to detect. To address this limitation, I developed a method of identifying regions that have undergone recent selective sweeps in these populations as a means of distinguishing them, and specifically quantifying their abundance in complex environments. But part of what makes microbial evolution so difficult to interpret is the vast diversity of genes that are only shared by a fraction of all the members in a population. To better understand how these flexible regions are structured, I systematically extracted all contiguous flexible regions in nine marine Vibrio populations and compared their organization and evolutionary histories.

I found that horizontal gene transfer and social interactions have led to the evolution of modular gene clusters that mediate forms of social cooperation, metabolic tradeoffs, and make up a substantial portion of these flexible genomic regions. The observations made in these studies help us understand how microbes are organized into socially and ecologically cohesive groups, and how they have evolved to interact with complex and changing environments.