The balance between prokaryotic autotrophy and heterotrophy in the oceans

Abstract

Bacteria play in integral role in the marine carbon cycle by mediating crucial transformations of organic and inorganic matter. Within the organic carbon pool, heterotrophic bacteria control the flux of labile and recalcitrant organic compounds, which has significant impacts on the marine food web and nutrient cycling. In this dissertation, I used a suite of culture-dependent and culture-independent techniques to investigate the functional roles and distributions of key microorganisms in the marine carbon cycle. The SUP05 clade of marine gammaproteobacteria is an abundant group of closely related sulfur-oxidizing bacteria. Members of the SUP05 clade have the genetic potential for autotrophic, heterotrophic, and mixotrophic growth. SUP05 is widely distributed throughout the world’s oceans including oligotrophic gyres, eutrophic estuaries, hydrothermal vent plumes, and oxygen minimum zones. In chapter one, we used laboratory techniques including physiological growth experi- ments, proteomic surveys, and genomic reconstructions to find that a potentially mixotrophic strain of SUP05 predominantly functions as a heterotroph under oligotrophic and copiotrophic conditions. In chapter two, I sequenced the complete genome of a third isolate from the SUP05 clade and compared its genomic content to other complete and incomplete SUP05 genomes. While the SUP05 strains were all very similar at the 16S rDNA level, striking differences in metabolic potential exist in the SUP05 clade. Notably, the newly sequenced genome does not contain the metabolic potential for carbon fixation, which was previously thought to be a defining characteristic of the SUP05 clade. Finally, in chapter three I expand my exploration of key carbon and energy-cycling microbes beyond the SUP05 clade to explore the heterogeneous distribution of microbes across fresh lava from a deep-sea volcanic eruption. Collectively, the results from this research show that closely related microorganisms may differ wildly in their role in the marine carbon and energy cycles. Further, fine-scale disturbances in geochemical parameters have the potential to alter the composition of microbial communities, potentially impacting the overall community function.