Elucidating the metabolic activities of SUP05, an abundant group of marine sulfur oxidizing gamma-proteobacteria

Thesis (Ph.D.)--University of Washington, 2015Chemoautotrophic bacteria that oxidize sulfur and reduce nitrogen in low oxygen zones carry out chemical transformations of molecules containing the key elements: carbon, nitrogen and sulfur. Members of the SUP05 clade of marine gamma-proteobacterial sulfur oxidizers (GSOs) are abundant and cosmopolitan in the oceans, consisting of metabolically diverse bacteria that have been found throughout the water column in oxic and anoxic marine environments and as symbionts in the gill tissues of deep sea clams and mussels. Environmental studies suggest that the SUP05 clade is comprised of diverse members with autotrophic, heterotrophic or mixotrophic capabilities. Although there are indications that these physiologies correspond to differing ecological niches, the lack of cultivated representatives has limited studies to elucidate patterns of metabolic diversity within the clade. In chapter one, I obtain the first isolate from the SUP05 clade (Thioglobus singularis GSO-PS1) and show that energy from sulfur oxidation enhances heterotrophic biosynthesis in controlled growth experiments. In chapter two, I demonstrate that despite having a streamlined genome, T. singularis GSO-PS1 has the genetic potential for carbon mixotrophy and confirm that autotrophic and heterotrophic functions are expressed in the environment. In chapter three, I use the complete genome sequences of two SUP05 isolates, T. singularis GSO-PS1 and T. autotrophica SUP05-EF1 (Shah et al., in prep) to identify co-occurring subclades in diverse OMZs. Results from these analyses indicate that members of the T. singularis subclade are aerobic mixotrophs with the metabolic potential to produce energy and to biosynthesize using organic and inorganic substrates, and that members of the T. autotrophica subclade are chemoautotrophic facultative anaerobes with the metabolic potential for denitrification. This suggests that T. singularis and T. autotrophica represent SUP05 subclades with distinct ecological niches and with different roles in carbon, nitrogen, and sulfur cycling