The Southern Ocean (SO) is a major site for air-sea exchange of anthropogenic carbon dioxide (CO2). It accounts for up to 40% of global annual oceanic CO2 uptake, subsequently releasing significant amounts of biologically sequestered CO2 to the ocean interior. It also dominates many other key biogeochemical nutrient cycles through microbially driven ‘biological pumps’. The efficiency of these pumps is ecologically regulated as a balance between photosynthetic CO2 fixation and remineralisation by heterotrophic bacteria and archaea. The effects of climate change on the physical oceanography of the SO may have a globally significant impact on the efficiency of the biological pumps, but the extent of this is unclear, because while considerable work has been done to estimate the possible responses of photosynthetic microbes to climate change, very little has been done for heterotrophic microbiota - the basic biogeography of these organisms is virtually unknown. Our present study aims to greatly expand the existing coverage and understanding of the distributions of SO microbes, as a step towards determining important physical, chemical and ecological factors that regulate SO microbial community structures. We have particular interest in the bottom water microbial community and roles of ocean circulation as well as Antarctic Bottom Water that radiates out to the global ocean in structuring microbial biogeography. To better understand this microbial community, we sampled seawater at multiple transects and ocean depths along the Australian and New Zealand region of the SO (71°E-170°W) and examined the bacterial, archaeal and eukaryotic community composition through high resolution 16S and 18S rRNA gene tag sequencing. This is combined with corresponding physical and biogeochemical observations to investigate potential triggers of the observed microbial community shifts. These findings will contribute significantly to filling critical gaps of knowledge on how changes in SO physical oceanography under forecasted global change scenarios leading to microbial community shifts might change the SO biological pump.