Can we harness bacteria to help clean up future oil spills?

Surface oil slick from the Deepwater Horizon oil spill. Andreas Teske, University of North Carolina Chapel Hill. , Author provided

Can we harness bacteria to help clean up future oil spills?

Surface oil slick from the Deepwater Horizon oil spill. Andreas Teske, University of North Carolina Chapel Hill. , Author provided

In 2010 the Deepwater Horizon oil spill released an estimated 4.2 million barrels of oil into the Gulf of Mexico – the largest offshore spill in U.S. history. The spill caused widespread damage to marine species, fisheries and ecosystems stretching from tidal marshes to the deep ocean floor.

Emergency responders used multiple strategies to remove oil from the Gulf: They skimmed it from the water’s surface, burned it and used chemical dispersants to break it into small droplets. However, experts struggled to account for what had happened to much of the oil. This was an important question, because it was unclear how much of the released oil would break down naturally within a short time. If spilled oil persisted and sank to the ocean floor, scientists expected that it would cause more extensive harm to the environment.

Before the Deepwater Horizon spill, scientists had observed that marine bacteria were very efficient at removing oil from seawater. Therefore, many experts argued that marine microbes would consume large quantities of oil from the BP spill and help the Gulf recover.

In a recent study, we used DNA analysis to confirm that certain kinds of marine bacteria efficiently broke down some of the major chemical components of oil from the spill. We also identified the major genetic pathways these bacteria used for this process, and other genes, which they likely need to thrive in the Gulf.

Altogether, our results suggest that some bacteria can not only tolerate but also break up oil, thereby helping in the cleanup process. By understanding how to support these natural occurring microbes, we may also be able to better manage the aftermath of oil spills.

Finding the oil-eaters

Observations in the Gulf appeared to confirm that microbes broke down a large fraction of the oil released from BP’s damaged well. Before the spill, waters in the Gulf of Mexico contained a highly diverse range of bacteria from several different phyla, or large biological families. Immediately after the spill, these bacterial species became less diverse and one phylum increased substantially in numbers. This indicated that many bacteria were sensitive to high doses of oil, but a few types were able to persist.

We wanted to analyze these observations more closely by posing the following questions: Could we show that these bacteria removed oil from the spill site and thereby helped the environment recover? Could we decipher the genetic code of these bacteria? And finally, could we use this genetic information to understand their metabolisms and lifestyles?

Individual puzzle pieces of DNA making up a bacterial genome. Each color represents an individual genome and each dot depicts one piece of DNA.

To address these questions, we used new technologies that enabled us to sequence the genetic code of the active bacterial community that was present in the Gulf of Mexico’s water column, without having to grow them in the laboratory. This process was challenging because there are millions of bacteria in every drop of seawater. As an analogy, imagine looking through a large box that contains thousands of disassembled jigsaw puzzles, and trying to extract the pieces belonging to each individual puzzle and reassemble it.

We wanted to identify bacteria that could degrade two types of compounds that are the major constituents of crude oil: alkanes and aromatic hydrocarbons. Alkanes are relatively easy to degrade – even sunlight can break them down – and have low toxicity. In contrast, aromatic hydrocarbons are much harder to remove from the environment. They are generally much more harmful to living organisms, and some types cause cancer.

Microscopy image of oil-eating bacteria. Tony Gutierrez, Heriot-Watt University

We successfully identified bacteria that degraded each of these compounds, and were surprised to find that many different bacteria fed on aromatic hydrocarbons, even though these are much harder to break down. Some of these bacteria, such as Colwellia, had already been identified as factors in the degradation of oil from the Deepwater Horizon spill, but we also found many new ones.

This included Neptuniibacter, which had not previously been known as an important oil-degrader during the spill, and Alcanivorax, which had not been thought to be capable of degrading aromatic hydrocarbons. Taken together, our results indicated that many different bacteria may act together as a community to degrade complex oil mixtures.

Neptuniibacter also appears to be able to break down sulfur. This is noteworthy because responders used 1.84 million gallons of dispersants on and under the water’s surface during the Deepwater Horizon cleanup effort. Dispersants are complex chemical mixtures but mostly consist of molecules that contain carbon and sulfur.

Their long-term impacts on the environment are still largely unknown. But some studies suggest that Corexit, the main dispersant used after the Deepwater Horizon spill, can be harmful to humans and marine life. If this proves true, it would be helpful to know whether some marine microbes can break down dispersant as well as oil.

Cleaning an oiled gannet, Theodore, Alabama, June 17, 2010. Deepwater Horizon Response/Flickr, CC BY-ND

Looking more closely into these microbes’ genomes, we were able to detail the pathways that each appeared to use in order to degrade its preferred hydrocarbon in crude oil. However, no single bacterial genome appeared to possess all the genes required to completely break down the more stable aromatic hydrocarbons alone. This implies that it may require a diverse community of microbes to break down these compounds step by step.

Back into the ocean

Offshore drilling is a risky activity, and we should expect that oil spills will happen again. However, it is reassuring to see that marine ecosystems have the ability to degrade oil pollutants. While human intervention will still be required to clean up most spills, naturally occurring bacteria have the ability to remove large amounts of oil components from seawater, and can be important players in the oil cleanup process.

To maximize their role, we need to better understand how we can support them in what they do best. For example, adding dispersant changed the makeup of microbial communities in the Gulf of Mexico during the spill: the chemicals were toxic to some bacteria but beneficial for others. With a better understanding of how human intervention affects these bacteria, we may be able to support optimal bacteria populations in seawater and reap more benefit from their natural oil-degrading abilities.