Comparative and evolutionary genomics of chemosynthetic symbionts

Chemosynthetic symbioses are metabolically based associations between sulfur- or methane-oxidizing bacteria and marine eukaryotes. In these interactions, the hosts provide the symbionts with access to the substrates needed for their chemosynthetic metabolism (such as reduced sulfur and oxygen) while the symbionts provide the hosts with most, if not all, of their nutrition. It is perhaps because of the intimacy of this association that the bacteria] partners have yet to be cultured in the lab and so little is known about their metabolism in situ. This thesis presents the first genomics-based analysis of the biology of these enigmatic bacteria. Although other chemosynthetic symbionts are discussed, the Vesicomyid (Mollusca: Bivalvia) symbionts are the focus of this work. These symbionts are predominantly maternally transmitted and their hosts are distributed around the globe at hydrothermal vents and cold seeps. The genome of the hydrothermal vent clam ( Calyptogena magnifica ) symbiont Ruthia magnifica is presented. This first genome sequence of a vent chemosynthetic symbiont, and subsequent comparative genomics using heterologous microarray hybridizations and sequence analyses, support the hypothesis that these symbionts are providing their hosts with all of their nutrition. The symbionts are metabolically capable chemoautotrophs and retain pathways for the biosynthesis of 19 amino acids, 9 vitamins and cofactors, as well as carbon fixation, sulfur oxidation, and nitrogen assimilation pathways. Supporting evidence for host-level selection on symbiont function is presented in the form of an analysis of evolutionary rates. Finally, the comparative genomics approach yielded a possible functional difference between the symbionts (a dissimilatory nitrate reductase), investigated here through enzymatic and sequence analyses. In conclusion, the use of genomics in this group of "unculturable" bacterial symbionts has provided valuable insights: (i) the Vesicomyid chemosyntetic symbionts are completely capable autotrophs (ii) and their hosts likely depend on them for all of their nutrition. (iii) The transmission strategy utilized by a symbiont affects their rate of genomic evolution and (iv) a possible functional difference between these symbionts is the use of a dissimilatory nitrate reductase, (vi)expressed, although at low levels, in a vesicomyid symbiont and (vii) found in other chemosynthetic symbioses.