A blanket of oil: the role of bacteria in cleaning up after Deepwater Horizon


Handley KM, Piceno YM, Hu P, Tom LM, Mason OU, Andersen GL, Jansson JK, Gilbert JA. 2017. Metabolic and spatio-taxonomic response of uncultivated seafloor bacteria following the Deepwater Horizon oil spill. ISME Journal 11:2569-83. doi:10.1038/ismej.2017.110


The impacts of the Deepwater Horizon oil spill didn’t end with the capping of the Macondo well in 2010. While ships were able to use booms to trap and collect oil that slicked on the Gulf of Mexico’s surface, nearly a quarter of the spilled oil – about one million barrels’ worth – remained deep in the water column more than 3,000 feet below the surface. That oil didn’t just disappear. It drifted in a plume as far as 35 miles from the well site, slowly sinking towards the seafloor. The question for scientists was, what would happen to it after it settled there?


The answer to that question depended entirely on how microorganisms living in the seafloor would respond to being covered in a layer of oil. In every handful of seafloor mud, hundreds of millions of bacteria and related microorganisms make a living by eating detritus – the remains of dead fish and algae – that rains down onto the seafloor. But oil is vastly different than detritus to a bacteria’s stomach, and it remained unclear what types of bacteria, if any, could eat away at the blanket of oil.

Map of the extent of the surface oil spill following the Deepwater Horizon. Image courtesy of NOAA.

To find out, Kim Handley and colleagues sailed out to the Deepwater Horizon site only two months after the well had been capped. By this time, other researchers working to trace the sinking plume of oil had confirmed the swath of seafloor that had been coated in oil so that Handley was able to target areas of both high and low oil contamination. The team used a device known as a mega corer to collect sediments, which lands on the seafloor gently enough to leave the surface relatively undisturbed, but with enough force to collect mud into the core barrel.


Back on shore, the team went to the lab to extract all of the DNA from the thousands of different species of microorganisms living in the mud they collected and then sequenced it. The result was a tangle of millions of gene sequences – some of which encoded proteins that played a role in oil degradation, but most of which were simply genes that every bacteria species shares. The goal, however, was to find out which species those oil degradation genes came from. So the researchers took that tangle of sequences and tried to piece them together one-by-one by finding areas where the DNA sequences of two snippets overlapped – an impossible task by hand, but something that recent advances in computational biology have made readily possible.


Using this approach, Handley’s team was able to recover 57 distinct genomes belonging to bacteria that have the genes necessary to consume oil – a huge number of completed puzzles from the original pile of millions of DNA pieces. This analysis first of all pointed to the identities of these bacteria and clearly showed that they came from several different types of bacteria that are about as evolutionarily related as humans and fish.

Satellite image of the surface oil plume. Nearly one-quarter of the oil spilled from the Deepwater Horizon remained deep in the water column before sinking onto the seafloor. Image courtesy of NASA.

But even more important, examining the sites close to and far from the Deepwater Horizon well site revealed that almost all of these different bacteria were present everywhere the team sampled – including sites that saw very little oil contamination. That means that these oil-consuming bacteria likely didn’t spring up overnight with the appearance of oil or get transported across the Gulf of Mexico by the oil plume itself, but rather that they are native to the seafloor mud across the Gulf.


That makes sense given that simple hydrocarbons with some similarities to oil, like methane and butane, are found throughout the Gulf of Mexico seeping naturally out of the seafloor. However, this finding also has important implications for how we think about the role of microorganisms in cleaning up after oil spills. The microbial response to oil settling onto the seafloor in the Gulf of Mexico depended on microorganisms that were native because of the Gulf’s already frequent exposure to hydrocarbons. But if oil were spilled in an area where these bacteria are not present, for example in the case of an oil tanker spill, microorganisms in the seafloor may not be able to consume the oil.


While the Deepwater Horizon spill was an environmental catastrophe, it did provide scientists with a natural laboratory to learn more about how microorganisms respond to oil spills on the seafloor. And while in an ideal world another spill would never happen, the results of Handley and her team are a starting point for understanding whether we can count on bacteria to clean up the seafloor in the event of a spill.


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