Evolutionary studies through Sulfolobus islandicus genomics: Ancient relationships and modern dynamics

It is rare for microbes to leave fossils, and thus we must study microbial evolution by comparing existing organisms and their constituent biomolecules. The past two decades have seen dramatic increases in the power of DNA sequencing technology to affordably record, catalog, and study the biodiversity of life on Earth. As a result, the tree of life has undergone radical transformations from root to tip. The evolutionary hypotheses generated by sequencing data, however, require experimental systems in which to test them to understand the functional consequences of evolutionary change. After decades of environmental sampling and laboratory manipulation, Sulfolobus islandicus is one of few model systems in which molecular and population-level data can be studied simultaneously. It is a hyperthermoacidophile of the domain Archaea found in geographically isolated hot springs throughout the Northern Hemisphere. As a member of the Crenarchaeota, its evolutionary lineage is crucial to investigations probing the relationship between Archaea and Eukaryotes. Its biogeographic distribution and extensive library of sequenced isolates also enable comparison of evolutionary forces in different conditions. This thesis examines both the ancient and contemporary evolution of Sulfolobus. Chapter 1, the introduction, gives background on the state of knowledge in this field before and during these studies. Chapter 2 details the genome-wide mutagenesis and sequencing of S. islandicus M.16.04, an isolate from Kamchatka, Russia. The resulting essential genome is interrogated for several surprising insights into Sulfolobus cell biology, such as the non-essentiality of the surface layer, but also into the shared molecular machinery that differentiates Archaea from Eukaryotes and Bacteria. Chapter 3 contains preliminary analyses on one such piece of molecular machinery that is highly conserved and differentiates Archaea/Eukaryotes from Bacteria but remains uncharacterized in Archaea. Chapter 4 examines the population biology of S. islandicus and its effect on genome organization. Through comparison of 82 sequenced isolates, I find that strains from Yellowstone National Park experience different levels of selection compared to those from Kamchatka, resulting in genomic instability similar to that observed in recently host-associated bacteria. These results are the first to show that free-living microbes undergoing changes in their population structure display similar trends in genome restructuring compared to pathogens. Together, this thesis elucidates new aspects of ancient and contemporary evolution through the lens of archaeal microbiology.U of I OnlyAuthor requested U of Illinois access only (OA after 2yrs) in Vireo ETD syste