Genomic and small subunit sequence evaluations of members of the bacterial domain: Implication for microbial evolution and taxonomic assignment

Four aspects of molecular sequence analysis of the Bacterial domain are presented. In the first project, 16S rDNA from 10 marine Bacillus isolates were sequenced and analyzed. Three of the isolates appear to be terrestrial contaminants, three may be terrestrial contaminants with adaptations and the remaining four appear to be likely candidates of true marine Bacillus. The second study involved the 16S rDNA sequencing of five round spore forming Bacillus species. The sequences and subsequent analysis were used to suggest a workable bacterial taxonomy based on natural phylogeny that extends beyond genus level of the heterogenous Family Bacillaceae. This is an important step in bacterial nomenclature as the exploration of the diversity of (eu)Bacteria continues and expands. The third work introduces the concept of phylogenetic mapping. In this study, a classical morphological description was mapped onto a small subunit rRNA sequence analysis of phylogeny to determine the nature of the last common ancestor to the (eu)Bacteria and to provide insight into the phylogenetic meaning of bacterial morphological evolution. A startling pattern emerged. The coccus form of bacteria appeared to represent persistent end states of the evolution of (eu)Bacteria and have evolved independently and repeatedly. This is counter to current thinking and represents a major change in our understanding of the morphology of prokaryotes. This is only one application of the power of phylogenetic mapping, and its possible relevance to the field of biological evolution is obvious. The fourth study involves genome comparisons of six publicly available prokaryotic species and the conservation of gene order shared by them. The results indicate 19 clusters whose order remains the same among the four (eu)Bacterial genomes and reflect conserved elements of coordinated gene expression that require gene proximity. Seven clusters are preserved in the Archaea as well. Many of the clusters are regulated at the RNA level suggesting that this type of regulation may have arisen very early when there may have been entities with an RNA genome.