The Southern Ocean (SO) is a major site for the sequestration of global anthropogenic carbon dioxide (CO2), responsible for up to 40% of annual oceanic CO2 uptake. Within harsh low temperature and high salinity environments of the SO, microbes dominate and support carbon sequestration and critical nutrient cycling processes. Carbon sequestration occurs mainly through a microbial-driven CO2 fixation biological pump. The effects of climate change on the physical oceanography of the SO may have a globally significant impact on the microbial ecology and therefore the efficiency of this biological pump. The extent of this impact is unclear, because the diversity and functional capacity of the microbial assemblages inhabiting the SO is still not well understood. Water masses within the SO also have distinct physicochemical properties and are likely to harbor varying microbial communities. Additionally, the key environmental parameters controlling these microbial community variations are still poorly deciphered. To better understand this microbial community, we sampled seawater at multiple ocean depths from 4 different transects along the Australian and New Zealand region of the Southern Ocean (71°E-170°W). Sampling interval was every 0.5 – 1 degree from 42 - 66°S. This study will not only advance the depth and breadth of the SO’s bacterial, archaeal and eukaryotic community composition through high vertical and spatial resolution metagenomics profiling using 16S and 18S rRNA gene tag sequencing, but combine this with physicochemical observations to investigate the potential triggers of the observed microbial community shifts. Preliminary bacterial 16S Operational Taxonomic Unit (OTU) data have shown community shifts before and after crossing major SO fronts, indicating the SO bacterial community to be endemic to hydrographically distinct water masses. Shifts were also at observed at depths between 200 and 1000m. These findings will contribute significantly to filling critical gaps of knowledge on how changes in Southern Ocean physical oceanography under forecasted global change scenarios might change the CO2 uptake and biological pump in the Southern Ocean.