The comparative genomics of salinispora and the distribution and abundance of secondary metabolite genes in marine plankton

This dissertation is based on a bioinformatics approach to study microbiology, ecology, evolution, marine biology and secondary metabolites. Comparative genomics was applied to identify the similarities and differences between two marine Actinobacteria Salinispora tropica and S. arenicola. The first step in this analysis was to identify orthologous genes between the two species and create a gene-by-gene alignment of the genomes in order to identify synteny of orthologs. The second step was to identify all secondary metabolite gene clusters and mobile genetic elements followed by a thorough analysis of the evidence for horizontal gene transfer. The first two steps reveal that the main differences between these species lie on genomic islands that harbor secondary metabolites and mobile genetic elements. The Salinispora genomes were used as the basis for comparison against other Actinobacteria to identify possible marine adaptation genes. Several marine adaptation genes were identified based on two fundamental approaches, a comparative genomic approach and a study of gene annotation previously linked to marine adaptation. These two approaches, coupled with phylogenetic analyses, identified genes that show a close relationship to marine bacteria and appear to be involved in marine adaptation. During this study, a gene that encodes a mechanosensitive channel was identified as having been lost in Salinispora relative to almost all other terrestrial Actinobacteria. This gene is likely a contributing factor to the inability of Salinispora to grow when seawater based media is replaced with DI based growth media. In this dissertation, I also describe a method to identify sequence tags related to polyketide synthase and non-ribosomal peptide synthetases. I applied this method to study a metagenome of surface water collected in the California current and metatranscriptomes of a dinoflagellate bloom in surface water of the coast of California and water beneath sea ice in Antarctica. This study revealed an abundance of protist-associated secondary metabolite genes and evidence that extensive sequencing efforts will be required to detect rare functional genes such as those involved in secondary metabolis