Metagenomics of the Riftia pachyptila symbiont

Despite the organisms' relative inaccessibility relative to most biological systems, much has been learned regarding the physiology of the Riftia pachyptila tubeworm and its chemolithoautotrophic symbiont since its discovery a quarter century ago, but many questions regarding the physiology of this association remain unanswered. Since the symbiont is unculturable and all experiments are performed with dying preparations, one molecular option to approach these queries is metagenomics. Metagenomics is inherently difficult, as sequences are derived from an environmental sample rather than a pure monoclonal culture, and the methods used to create the Riftia symbiont metagenome were not optimal for genome closure. However, the symbionts' metagenome provides a wealth of information regarding its physiology. Investigations in this thesis support the theory that trophosome contains a single species, and genomic heterogeneity is very low within the symbiont populations at 9°N. Though sequence fractionation is a problem with the symbiont metagenome, much information has been gathered from it regarding the symbionts' metabolic capabilities. It has been discovered that the symbionts can use the reverse TCA cycle for carbon fixation in addition to the Calvin-Benson Cycle, which explains the discrepancy in the hosts' carbon isotope ratios. The symbionts can also function heterotrophically and have a large suite of signal transduction mechanisms to respond to various environments. It appears as though the host can supply both inorganic and organic carbon to the mixotrophic symbionts, which contain various enzymes to break down host cells. These are the most significant of several new insights the symbiont metagenome has provided us, and a large number of new hypotheses have been proposed as a result.