| Summary: | 2013 Spring. Includes illustrations (some color). Includes bibliographical references (pages 126-148). Oceans cover two-thirds of the planet's surface and the subsurface biosphere that resides therein extends at least 1600 meters below the seafloor. The microorganisms living in this habitat are estimated to represent up to one-third of the world's living biomass and are consequently crucial participants of global biogeochemical cycling. This thesis focuses on the global carbon cycle, which has received increased scrutiny since the acknowledgment of global warming. As the planet warms, so do ocean waters. As a result, primary productivity, and fluxes of organic matter (OM) to the seafloor are expected to increase. Reactions mediated by subsurface bacterial communities have been recognized as the primary mechanisms responsible for OM diagenesis and remineralization in marine sediments. While the general steps of OM diagenesis have been established, few studies investigate how OM quality and quantity affect microbial abundances and phylogenic diversity in the subsurface. Furthermore, it is unclear how different microbial communities degrade, remineralize and preserve the sedimenting OM. The intent of this thesis is to characterize the microbial communities and metabolic pathways occurring at three contrasting deep-sea Antarctic environments: (1) the oxic sediments beneath the Ross Sea ice shelf; (2) the deep-sea sediments of the Wilkes Land continental margin; and (3) the anoxic sediments of the Adelie Basin. These studies integrate structural and stable carbon isotope analyses of phospholipid fatty acids, SSU rRNA gene sequencing, porewater and sedimentary geochemistry as well as measurements of labile amino acids to describe the viable microbial communities and their degradation of OM. Collectively, the sampled sites reveal that microbial abundances and diversity decrease with sediment depth. Relative proportions of archaea were ~ 2% within the oxic sediments of the Ross Sea and the Adelie Basin. This finding was unexpected at the Adelie Basin since large volumes of methane and 13C values of dissolved inorganic carbon suggest archaeal methanogenesis within the basin, and imply that molecular techniques, including SSU rRNA sequencing, failed to amplify genes from all archaeal organisms. These studies also demonstrate that greater volumes of sedimented OM support larger bacterial populations, the majority of which are heterotrophs including Bacteroidetes, Chloroflexi, Actinobacteria, and [gamma]-Proteobacteria, as evident by [delta]13C PLFA values and SSU rRNA gene sequencing. Despite abundant populations of heterotrophic bacteria in the Adelie Basin, large amounts of labile amino acids and DNA from chloroplast and aerobic organisms indicate that high phytodetritus fluxes can result in the burial of labile OM.
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