Marine sediments are one of the largest habitats for microbial life on earth. These microorganisms play critical roles in biogeochemical cycling both within the subsurface and between the sediment and water columns. However, microbial communities in sediments are highly heterogeneous and the factors defining microbial community structure and metabolic function are not well characterized. The goals of this dissertation were to define the physical and geochemical factors controlling microbial communities in marine sediments on regional scales and to link changes in community structure to shifts in biogeochemical potential. Microbial communities, sediment geochemistry, and sediment physical properties of sediments from the South China Sea and the US Atlantic Margin were characterized. The South China Sea exhibits differences in sedimentation rates across the basin, shifts from sulfate availability to absence with depth in the sediment column, and contains distinct sediment layers of varying sedimentological origins. Microbial community structure was found to correlate strongly with sedimentation rate and sulfate availability, but not with sedimentology. The US Atlantic Margin is characterized by widespread occurrence of methane seeps and the presence of methane in shallow sediments around areas of seepage. Microbial communities were found to be distinct
between the different sites sampled along the margin. Further analysis of sediment geochemistry demonstrated that this is due to divergence in the availability of oxygen and nitrate, the ephemerality of methane seepage, and the availability of labile organic matter along the margin. Shotgun metagenomics enabled insight into the metabolic potential of selected microbial communities on the US Atlantic Margin. These communities, which were distinct in their taxonomic composition, also hosted differing metabolic potential with respect to carbon, nitrogen, and sulfur cycling. In particular, communities in suboxic sediments hosted a much higher abundance of Gammaproteobacteria and Alphaproteobacteria, had more genetic potential for sulfur oxidation and denitrification, and had less genetic potential for nitrogen fixation compared to anaerobic communities. The results reported here will contribute to understanding how microbial communities are structured in diverse marine sediment environments and will aid in linking microbial community composition to biogeochemical potential.