Evolution of genomic diversity in natural microbial populations

Abstract

Life on Earth is immensely diverse. The largest fraction of genomic diversity is encoded in the uncultivated and understudied microbial populations that inhabit every corner of the planet. Because of the elusive nature of uncultivated microbes, the evolutionary processes that govern the generation and maintenance of genomic diversity in their genomes remain poorly characterized, despite these processes being foundational to the diversification of the tree of life. This thesis examines the evolutionary processes that result in genomic diversity of natural microbial populations to address the central question of “how stochastic or deterministic is the evolution of genomic diversity?” I address this question by placing genome evolution in organismal context. The three chapters of my thesis explore how environmental, ecological and intra-genomic contexts, respectively, shape genomic diversity of natural microbial populations. In Chapter 1, I examine how environmental contexts shape the evolutionary strategies of a marine archaeal population across ocean basins. In Chapter 2, I characterize how the ecological context of syntrophy and viral predation in chemosynthetic microbial mats result in genomic information transfer across large phylogenetic distances. In Chapter 3, I develop a machine learning method to model relationships between a gene and its genomic context, and thereby derive functionally meaningful representations. Through these three investigations across temporal and spatial scales, I conclude that interactions inherent to organismal context underpin many of the evolutionary processes critical to genome diversification.