How Microbes Clean up Oil: Lessons From the Deepwater Horizon Oil Spill

April 19, 2020

A new joint colloquium report from the American Academy of Microbiology (AAM), the American Geophysical Union (AGU), and the Gulf of Mexico Research Initiative (GoMRI) titled “Microbial Genomics of the Global Ocean System reports on science findings in the 10 years since the Deepwater Horizon (DWH) oil spill, which dumped 4.9 million barrels of oil and 250,000 metric tons of natural gas into the Gulf of Mexico over 86 days. The spill contaminated the open ocean, deep sea and more than 1,300 miles of Gulf shoreline.  A massive, interdisciplinary and collaborative research initiative was launched a decade ago to understand the effects of the oil spill – it supported the development and use of new genomic tools that have contributed greatly to our understanding of how to mitigate the effects of oil released into our oceans. 

In the months after DWH, the government released an estimate of what happened to the oil. About half of the oil was removed from the Gulf by standard physical and chemical methods. The ultimate fate of the other half? Unknown at the time.

Formed in the aftermath of DWH, GoMRI investigated the impacts of the oil spill and cleanup on the various ecosystems of the Gulf of Mexico. “Early on, we recognized the importance of bringing together collaborative teams of researchers who could use novel tools and techniques to unravel the complex dynamics of the Gulf of Mexico and how the oil from the Deepwater Horizon was influencing the system,” said Dr. Rita Colwell, Chair of  the GoMRI Research Board, and a Fellow of the American Academy of Microbiology. 

The spill and formation of the GoMRI coincided with the arrival of genomic and bioinformatic tools like metagenomic sequencing. Because these advances removed the necessity and difficulty of culturing individual microbes, scientists were able to study the DWH spill in unprecedented detail. Many new microbial species, genes, metabolic pathways and community dynamics were discovered as outlined in the joint colloquium report, none of which would  have been possible without this important three-way partnership that brought together two societies of international (AAM and AGU) renown and the important, time relevant investment by GOMRI. “This report provides a clear and insightful understanding as to how some of the world’s smallest creatures, microbes, helped rescue the Gulf of Mexico after an environmental catastrophe,” said Dr. Ken Halanych, member of the GoMRI Research Board and Schneller Endowed Chair in the Department of Biological Sciences at Auburn University. 

The DWH tragedy was the “first time sophisticated genomics tools – namely metatranscriptomics and metagenomics – were applied to track an ecosystem’s response to perturbation, revealing signals…The ocean’s microbiome is a robust sentinel of change and continued refinement and application of genomics tools will help detect changes in ocean systems rapidly and at broad scales,” said Dr. Samantha Joye,  who co-led the colloquium, and is a distinguished professor in the Department of Marine Sciences at the University of Georgia.

Because of these large scale ‘omics studies, scientists are beginning to understand the fate of the remaining DWH oil and are better prepared to respond to future environmental disasters.

How Do Microbes Respond to Oil Spills?

Although hydrocarbon-degrading microbes seem exotic, they are found around the world in low abundance, even when crude oil is not present. In fact, GoMRI researchers discovered that many well-known types of microbes (ex: Bacteroidetes) have the potential to degrade hydrocarbons. During an oil spill, these low-abundance microbes sense hydrocarbons and move toward the source. There they flourish and reproduce. The bloom consumes hydrocarbons, sometimes transforming them into byproducts that are harder to break down. After depleting available nutrients, the bloom species die off and other organisms that degrade these byproducts dominate.

The microbial ecosystem in the Gulf of Mexico may have been primed for oil bioremediation before DWH because of persistent oil seepage in the waters from drilling. For example, genes for hydrocarbon degradation (ex: alkB) are found in uncontaminated samples from the Gulf of Mexico more commonly than in other regions around the world. After the DWH spill, hydrocarbon-degrading microbes dominated the microbial ecosystem in contaminated water, accounting for as much as 90% of the microbial community

Similar shifts were also observed in deep-sea, salt marsh and beach sand environments, with unique species and dynamics. Biodegradation occurs much more slowly in sediments at the seafloor or in salt marshes due to lack of oxygen. However, GoMRI researchers did find evidence of anaerobic hydrocarbon degradation, suggesting that even in these environments, microbes are working to break down the spilled oil.

GoMRI ‘omic studies on entire communities also demonstrated the cooperative nature of oil degradation, which would have been overlooked by examining individual species. In some cases, different microbes shuttle metabolites between one another to complete degradation processes that neither could complete alone. Importantly, developments in genomic technologies allowed researchers to take a more holistic approach of studying microbial systems with unprecedented spatial and temporal resolution, with the potential to study fine scale spatial differences on the time scale of days or hours.

"Through this effort we hope to communicate to the international community that genomics research is not just for microbiologists or for the researchers that perform this work.  Rather, we can now use the knowledge and tools gleaned from genomics research to diagnose and to provide solutions for problems threatening the world’s oceans.”  Said Joel Kostka who co-led the colloquium, and is professor in the School of Biological Sciences at Georgia Tech University.

Listen: Joel Kostka discusses microbes and oil spills, including his studies of oil’s effect on microbial communities and where microbes can best degrade oil.

How Do Microbes Respond to Cleanup Efforts?

Initial cleanup efforts following an oil spill involve the use of chemical dispersants, mixtures of emulsifiers and solvents that break oil slicks down into smaller droplets. The smaller droplets then move into the waters below, diluting the oil through a larger volume of water. The dispersant itself can be toxic to marine life, including microbes - some of which have the potential to degrade the oil itself.

Perhaps unsurprisingly, GoMRI scientists found that adding dispersants into the ocean changes microbial communities, favoring growth of microbes that “clean up the cleanup” by degrading the dispersants. DNA sequencing shows that some bacteria are capable of degrading sulfur-containing compounds in dispersants that were used in the DWH spill. 

Given that dispersants can also be harmful to key bacteria, it is important for cleanup efforts to identify microbe-friendly dispersants. For future spills, genomic studies, such as those from the GoMRI program, may inform the development of nontoxic or biologically-inert dispersants that don’t disrupt the ability of natural microbial communities to degrade hydrocarbons. 

What Happens to Oil That Reaches the Seafloor?

Oil droplets (ex: after chemical dispersal) make their way down to the seafloor by latching onto marine snow, sinking particles, organic materials and biological debris that traverse the depths of the water column. These particles are known as “marine oil snow” (MOS).

The DWH oil spill triggered the formation of copious amounts of marine oil snow. MOS, a hot spot for oil degradation, sinks rapidly and reaches the seafloor in about 10 days. In this process, hydrocarbons are removed from the water column, changing the impact of the spill on aquatic ecosystems.

However, there’s another side to the story. Once MOS reaches the seafloor where it is  ultimately deposited, it can impact organisms that live there, particularly filter-feeding fauna like bi-valves and corals, as well as sediment biogeochemistry and the small animals between sand grains.

What Does the Future Hold for the Gulf?

The Gulf of Mexico remains a complex system and that necessarily makes understanding the effects of oil difficult.  Gone is the large surface slick of oil.  Fisheries are once again open.  Some species and parts of the system have yet to recover and what the new ‘normal’ may look like for these parts of the Gulf remains unclear. 
“One legacy of GoMRI is that there is now a networked community of researchers from various disciplines, as represented by the sponsoring organizations of this report,” said Colwell.  “These teams have done a remarkable job.  Importantly, these researchers and the hundreds of students they have trained will continue to study the long-term effects of oil on the Gulf of Mexico. They are also the cadre of scientists who can deploy to study, prevent, and mitigate effects of future oil spills – wherever they may occur.”
Among the lessons learned is that microbes, though tiny, have large impacts on global problems.   As genomic technologies continue to develop, we will be able to simultaneously monitor thousands of microbial species on the time scale of minutes and hours to understand and predict how microbes control and enhance ecosystem dynamic in the face of nature and human-induced insults.  The wealth and diversity of microbes in the oceans undoubtedly contributed to ecosystem recovery after DWH, and our ability to capture and study those processes will help provide data-driven solutions to future environmental challenges.

Author: Jennifer Tsang, Ph.D.

Jennifer Tsang, Ph.D.
Dr. Jennifer Tsang works in science communications and marketing and writes her own microbiology blog called "The Microbial Menagerie." She completed a Ph.D. in microbiology studying bacterial motility.