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The blowout of the Macondo 252 well following the explosion of the Deepwater Horizon drilling unit resulted in the release to the environment of approximately 4.2 million barrels of oil and 1.7 x 107 g natural gases into the Gulf of Mexico over an 83 day time period from April to July 2010. This complex mixture of hydrocarbons was released at a depth of 1500m and subject to physical and chemical partitioning as it moved through the water column. We identified subsurface hydrocarbon intrusions forming at around 1000-1300m below the surface. This has been referred to as a deep-sea oil plume and consisted of dissolved gases and soluble components of oil such as mono-aromatics and monocyclic alkanes. These intrusions also reportedly contained small, neutrally buoyant oil droplets that retained some insoluble hydrocarbon fractions at depth. Using a systems biology approach we tracked the microbial community composition to determine the relationships between microbial dynamics, and hydrocarbon and dissolved-oxygen concentrations. A shift in microbial community structure corresponded with a succession of dominant hydrocarbon degrading bacteria consuming distinctive fractions of the released oil. Ongoing work seeks to identify the distribution of specific classes of hydrocarbon degrading organisms over a wider scale.