Project Metagenome

A diverse, yet phylogenetically constrained, epsilon (?) proteobacterial community is associated with the dorsal surface of Alvinella pompejana, a polychaete worm which colonizes the sides of black smoker chimneys along the East Pacific Rise. Our central hypothesis maintains that under the intense constraints imposed by the geochemical environment, the episymbiotic consortia employ a core metabolic strategy. To test this hypothesis, we generated small insert shotgun libraries of the bacterial symbiont metagenome. We designed a semi-automated annotation pipeline and have implemented a web-based MySQL relational database to access myriad data from the analyses of over 300,000 high quality sequences. Metabolic pathways and functional categories have been assigned to these sequences based on comparison to known COGs and placement in KEGG pathway maps. 16S rDNA gene analysis from a PCR library and the shotgun library revealed that the symbiont consortia is comprised almost solely of ?-proteobacterial phylotypes (>98%) based on over 450 clones with two dominant phylotypes making up over 50% of the metagenome. The data is currently being analyzed using clustering and genome assembly techniques to explore and describe the complexity of the metagenome. It does not appear that the metagenome has been saturated, revealing even more diversity than expected. Preliminary sequence analysis has identified the prevalence of nitrate reduction and reverse TCA cycle (an alternate carbon fixation pathway) genes. These data have allowed us to form a preliminary 'core' metabolic model that will be tested via gene expression and proteomic profiling of the community using samples collected during our Extreme 2003 and 2004 cruises.