| My studies focus on the ribosomal RNA (rRNA) phylogenetic tree of life, how this framework organizes biological diversity and the application of this new perspective. Bacterial diversity is extensive and poorly understood in both extent and distribution. However, rRNA information has dramatically altered our view of this diversity. In addition to bacteria known from historical culture-based techniques, vast bacterial diversity is now evident from rRNA environmental gene surveys.; The rRNA phylogenetic tree is not reflected in all phylogenetic studies, however, and with the availability of complete genome sequences the utility of the rRNA tree was questioned. In Chapter 1, the utility of rRNA as a phylogenetic marker is examined in the context of complete genome sequences. To do this, genes present in all completely sequenced genomes were identified and sequence alignments were generated to construct phylogenetic trees, which were then compared to the rRNA phylogenetic tree. The majority of trees obtained matched the rRNA phylogenetic tree, and no consistent alternative tree was recovered. The results identify the genes that constitute the genetic core of extant genomes and justify the use of rRNA as a phylogenetic marker. The remaining chapters address the scope and distribution of bacterial diversity using rRNA as a phylogenetic marker.; The rRNA phylogenetic tree is a quantitative map of biological diversity. One attribute of this map is the ability to draw the search for new diversity to regions of the tree that are poorly sampled. Chapter 2 describes one such endeavor to expand specifically our understanding of the scope and distribution of a phylogenetic lineage of Bacteria currently known only from environmental gene surveys, although representatives of the group are conspicuously abundant in nature. The results highlight issues of phylogenetic reconstructions based on limited sampling and provide evidence for additional unexpected diversity. The results also demonstrate the incomplete nature of the current sequence databases, and raises questions as to the utility of specific sequence-based assays for microorganisms without documentation of the specificity in environmental samples.; The final chapter describes the application of ribosomal RNA-based technology to the microbiology of a specific problem in human health, cystic fibrosis. The focus of this work is to characterize the bacterial constituents of the human airway in health and disease. The complexity of bacterial communities recovered from the lung was relatively simple, and contain sequences from organisms that were unexpected in the human lung, including potential pathogens. |
