| The abundance of bacterial and archaeal life is astonishing. These microbes comprise the majority of Earth's biodiversity and play critical roles in ecosystem functions that are vital to plant and animal existence. Understanding the evolutionary and ecological processes that generate and maintain microbial diversity is a fundamental goal of microbial ecology and is the central theme of this thesis.; The work presented herein is focused on a group of aerobic, halophilic archaea commonly known as haloarchaea. Many aspects of haloarchaea, such as their phylogenetic coherence, shared physiology, and ease of cultivation, make them a model group for investigations of microbial diversity. Throughout this thesis comparative genomics, phylogenetics, and molecular ecological methods were used to characterize members of this group.; Comparative genomics demonstrated that the evolutionary origin of aerobiosis and heterotrophy in haloarchaea involved gene acquisition from bacteria. Moreover, metabolic traits that differentiate haloarchaeal species could be explained by differences in their 'bacterial' gene content. Phylogenetics was used to examine and compare the evolutionary histories of the RNA polymerase B' subunit (rpoB') and 16S rRNA genes in haloarchaea. Both genes consistently reconstructed two groups, the clade I and clade II haloarchaea, within a collection of less well resolved lineages. However, rpoB ' and 16S rRNA trees were incongruent, perhaps as a result of lateral gene transfer (LGT) between haloarchaeal species. In combination, these two studies indicate that LGT of metabolic and core housekeeping genes has influenced the evolution of haloarchaea.; To advance our understanding of the ecological processes that govern haloarchaeal diversity, a series of studies describing the distribution of archaea in a hypersaline soil environment was performed. A 16S rRNA survey of archaea identified a highly structured community along a spatial soil salinity gradient, dominated by uncultured lineages at low salinity and haloarchaea at elevated salinity. The temporal dynamics of the haloarchaeal community were followed using the rpoB' gene as a molecular marker. In the face of significant seasonal fluctuations in soil salinity, haloarchaeal community composition remained stable over the course of several years. These environmental studies collectively indicate that ecosystem disturbance and spatial heterogeneity are critical factors regulating haloarchaeal diversity. |
