Shifting role of chemoautotrophic SUP05 bacteria in nitrogen, sulfur and carbon cycles across oxygen gradients in marine environments

Thesis (Ph.D.)--University of Washington, 2018Microbes make up a large percentage of the biomass within marine environments and play a key role in cycling of biogeochemical cycles. Despite this, majority of important species of bacteria and archaea remain poorly understood due to lack of cultured representatives. Ecological studies have utilized macromolecules like small subunit RNA (16S) to identify and enumerate important groups of microbes in the environment. An uncultivated group of thiotrophic gamma-proteobacteria from the clade SUP05 are ubiquitous and abundant at the interface at the boundaries of marine oxygen minimum zones (OMZs). Metagenomic studies have shown that they play an important role in the cycling of nitrogen, carbon and sulfur within OMZs. In this thesis, I present the first cultivated representative from the chemoautotrophic SUP05 subclade, Candidatus Thioglobus autotrophicus along with its complete and annotated genome. SUP05 bacteria have been long suspected as important players in the nitrogen, carbon and sulfur cycles within OMZs. Particularly in processes that involve loss of fixed nitrogen in the form of gases (denitrification) and fixation of carbon. Using laboratory experiments on T.autotrophicus, I show that SUP05 bacteria produce large amounts of nitrite by carrying out dissimilatory nitrate reduction and consuming ammonia. Furthermore, I use growth experiments, cryo-electron tomography and protein expression data T. autotrophicus in aerobic and anaerobic to show that SUP05 have the potential to assimilate more carbon and store large amounts of reduced sulfur when they are exposed to oxic environments. This thesis provides a cultured representative of the chemoautotrophic SUP05 and a working model of its growth and metabolic constraints