Evolutionary Genomics of Dominant Bacterial and Archaeal Lineages in the Ocean

The ocean plays essential roles in Earth's biochemistry. Most of the nutrient transformations that fuel trophic webs in the ocean are mediated by microorganisms. The extent of phylogenetic and metabolic diversity of key culture and uncultured marine microbial clades started to be revealed due to progress in sequencing technologies, however we still lack a comprehensive understanding of the evolutionary processes that led to the microbial diversity we see in the ocean today. In this dissertation, I apply phylogenomic and comparative genomic methods to explore the evolutionary genomics of bacterial and archaeal clades that are relevant due to their abundance and biogeochemical activities in the ocean. In Chapter 1, I review relevant literature regarding the evolutionary genomics of marine bacteria and archaea, with emphasis on the origins of marine microbial diversity and the evolution of genome architecture. In Chapter 2, I use a comparative framework to get insights into the evolutionary forces driving genome streamlining in the Ca. Marinimicrobia, a clade widely distributed in the ocean. This project shows that differences in the environmental conditions found along the water column led to contrasting mechanisms of evolution and ultimately genome architectures. In Chapter 3, I assess the phylogenetic signal and congruence of marker genes commonly used for phylogenetic studies of bacteria and archaea and propose a pipeline and a set of genes that provide a robust phylogenetic signal for the reconstruction of multi-domain phylogenies. In Chapter 4, I apply a phylogeny-based statistical approach to evaluate how tightly genome size in bacteria and archaea is linked to evolutionary ii history, including marine clades. I present evidence suggesting that phylogenetic history and environmental complexity are strong drivers of genome size in prokaryotes. Lastly, in Chapter 5, I estimate the emergence time of marine bacterial and archaeal clades in the context of the Prokaryotic Tree of Life and demonstrate that the diversification of these groups is linked to the three main oxygenation periods occurring throughout Earth's history. I also identify the metabolic novelties that likely led to the colonization of marine realms. Here I present methodological frameworks in the fields of comparative genomics and phylogenomics to study the evolution of marine microbial diversity and show evidence suggesting that the main evolutionary processes leading to the extant diversity seen in the ocean today are intimately linked to geological and biological innovations occurring throughout Earth's history.