Research on Oil Biodegradation and Monitoring that Informs Spill Response

An image of a Lepidophthalmus louisianensis. These mudshrimp act as bioturbators and can help with oil degradation. (Photo by Darryl Felder)

(Click to enlarge) An image of a Lepidophthalmus louisianensis. These mudshrimp act as bioturbators and can help with oil degradation. (Photo by Darryl Felder)

The third in a three-part series of GoMRI science-for-response articles

The Deepwater Horizon oil spill and the remediation efforts that followed raised many concerns about impacts on coastal and ocean environments. Five years later as the largest coordinated research endeavor around an ocean-related event in history continues, we know more than ever before about the Gulf’s complex environment, diverse marine life, and dynamic natural processes and how they respond to stressors.

Recently, consortia directors and leads for smaller-group projects funded by the Gulf of Mexico Research Initiative (GoMRI) talked about how their science could be used to inform response if there were another oil spill. This article covers some of the science advances and tools related to oil biodegradation and monitoring. It is the third in a three-part GoMRI science-for-response article series. The first article was Research on Oil Transport that Informs Response and the second was Research on Dispersants that Informs Oil Spill Response.

SEA TO SHORE BIODEGRADATION. The Macondo blowout provided a unique opportunity for studying microbial responses to a large hydrocarbon input in habitats from deep offshore waters and sediments to coastal beaches and wetlands. This improved understanding about the Gulf’s bacterial diversity and function can inform response and remediation decisions.

GoMRI-funded scientists conducted research to understand the early distribution and concentrations of hydrocarbons and the Gulf’s microbial dynamics following the spill. Scientists with ECOGIG, GISR, and Deep-C have shown that the Gulf has naturally occurring microbial populations that were effective in degrading hydrocarbons after the oil spill, including microbes that consumed methane. At the 2015 Gulf of Mexico Oil Spill & Ecosystem Science conference, ECOGIG’s Samantha Joye suggested the potential of stimulating natural biodegradation by fertilizing the microbes as an alternate to dispersants for mitigating surface oil.

Uta Passow, also with ECOGIG, studied the role of microbes in oil-contaminated marine snow formation. Passow said that microbial-mediated marine snow may be a potentially effective mechanism contributing to surface oil removal. Other research from colleagues with C-IMAGE, Deep-C, and ECOGIG indicated potential long-term impacts resulting from oil transport to the ocean floor and geochemical changes in sediment, likely as a result of marine snow.

MOSSFA (Marine Oil Snow Sedimentation and Flocculent Accumulation), a multi-consortium working group, was founded in May 2013 to better understand microbial-induced marine snow and subsequent oil transport that led to oil accumulation on the seafloor. They organized a workshop and town hall meeting and continue to hold smaller topic-specific meetings.

Oil degradation in deep marine environments has been the focus of scientists with C-IMAGE who conducted high-pressure biodegradation experiments, simulating the extreme conditions associated with depths and temperatures. They found that high pressure inhibits growth and function of oil-degrading microbes and that pressure needs to be taken into account in biodegradation estimations under these conditions.

Several research groups studied oil degradation in coastal environments. Deep-C colleagues Joel Kostka and Markus Huettel focused on microbial oil degradation on Florida beaches using state-of-the-art metagenomics techniques to observe microbes degrading the oil for one year after it was deposited at Pensacola Beach. They related specific microbial groups to corresponding degradation rates and compounds. Kostka described how this information could inform response:

Specific microbial groups could serve as sentinels or bioindicators to tell responders whether important ecosystem services such as organic matter decomposition and nutrient regeneration are impacted by oil exposure. With an established baseline for the microbes present in beaches, we could advise environmental managers as to when the ecosystems had been restored to close to their original condition.

CWC research on coastal environments has provided insights about biodegradation for remediation decisions. Annette Engel’s research from 2010-2014 resulted in approximately 7 million DNA sequences that provided unprecedented information about microbial communities in habitats from Louisiana and Alabama coastlines. These data indicated that sand washing and tilling moved open ocean microbes to the shoreline. This microbial regime shift may have initially enhanced hydrocarbon degradation in sediment; however, longer-term studies need to assess the persistence and impact of the newly-formed microbial communities to the overall sandy beach ecosystems. Bacterial shifts also were observed in marshes with changes in bacterial diversity corresponding to alkane and polycyclic aromatic hydrocarbon (PAH) presence and composition over time and to salinity fluctuations due to fresh water. These compositional changes led to functional shifts in marsh ecosystems that affected organic matter degradation, potentially leading to diminished physical stability of a marsh system.

Paul Klerks and his group have investigated animals, such as mudshrimp, that are abundant on beaches. These animals burrow several feet deep and move water and sand around, earning them the names “bioturbators” and “ecosystem engineers.” Klerks explained their importance:

Bioturbation can lead to changes in the numbers of microbes, the types of microbes living in the sand, and their ability to break down oil. The bioturbation by the mudshrimp helps the oil disappear faster from the sand surface and to be broken down faster by microbes. Having a healthy coast with lots of bioturbators means that if there were another spill, bioturbation could play a role in oil degradation.

The above information highlights some of the processes involved with oil biodegradation and the need for continued research of the Gulf’s complex biological systems that can inform response decisions.

MONITORING. Some researchers offered suggestions for monitoring that could inform response if there were another oil spill.

Scientists’ early marsh assessments of biological responses to the oil spill indicated the importance of monitoring should there be another oiling of coastal wetlands, areas that supply critical ecosystem services: microbial communities associated with eroding marsh soils and grass; Seaside Sparrows; insects, ants, and crickets; estuarine fishes; seaweed and crustaceans; oysters; phytoplankton; and bottom-water dissolved oxygen and inorganic carbon concentrations.

CWC director Nancy Rabalais explained that understanding and monitoring the oiling impacts on marshes is complicated. Their research has provided a much improved understanding of marsh processes, and if there were another oil spill, they would be better poised to design experiments that target its effects. However, Rabalais said that because Louisiana marshes have been and continue to be affected by multiple stressors from natural and human-caused disturbances, the ecosystem is fragile:

One message we want to convey is that prevention of oil accidents is imperative. Relatively unweathered Macondo oil can still be found below the sediment surface at impacted areas of Terrebonne and Barataria bays. Research is indicating that hydrocarbons can linger for decades in marshes and oiling can accelerate shoreline erosion. Some impacts will not be readily seen. For example, the presence of above ground vegetation does not necessarily indicate recovery, especially if microbial stimulation of hydrocarbons below ground is degrading the structural roots that bind the marsh together.

Researchers monitored shorelines, many of which their economies depend on tourism. Scientists with Deep-C developed a catalog that provides measurable indicators to classify and order the microbial degradation of weathered hydrocarbons in wet and dry beach environments, providing information that may be useful in toxicity assessments. Deep-C researchers demonstrated that colorful Coquina clams (Donax variablis) could be used to detect and monitor biologically available PAHs in sandy shoreline systems where currently no biological indicators are employed. Loss rates of PAHs in clam tissues mirrored loss rates of PAHs in continental shelf sediments.

DROPPS director Edward Buskey suggested the importance of off- and near-shore atmospheric monitoring of tiny oil droplets aerosolized as a result of interactions with dispersants and physical factors such as waves and rain drops:

Droplets in the micron-size range are essentially like smoke particles and can be carried by the wind and inhaled by humans working on recovery at sea or on shorelines and by wildlife and passed through the lungs and into the blood stream.

Monitoring marine life, especially commercial and recreational species, has been a priority as well. GoMRI scientists have conducted several hundred sea expeditions, collecting tens of thousands of biological samples from hundreds of species from the coast to the deep sea. They used biomarkers, isotopic signatures, and other means to evaluate the presence and bioaccumulation rates of toxins across a wide range of species. Specific species have been the focus of several project leads, such as Joseph Neigel (blue crab), Debra Murie (red drum, sea trout and southern flounder), Edward Chesney (bay anchovy, blue crab, sea trout, and red drum), Frank Hernandez (Atlantic bumper, Spanish mackerel, and red snapper), and Dean Grubbs and Jim Gelsleichter (dogfish sharks, gulper sharks, king snake eel, deep-water hake, and tilefish).

Other GoMRI research has added to our knowledge base of Gulf biodiversity, providing better records for future environmental assessments. For example, several researchers identified and documented newly discovered marine animals or those rare to Gulf waters. Stephen Landers found sediment-dwelling microscopic animals. Darryl Felder and Suzanne Fredericq with CWC added knowledge about fauna and flora (decapod crustaceans and macroalgae) composition on northern Gulf of Mexico shelf edge banks. Grubbs and Charles Cotton with Deep-C have revised taxonomy and documented the biology, ecology, and life history for many species of hagfishes, bony fishes, skates, and sharks of the deep-sea.

For deep ocean monitoring, C-IMAGE director Steven Murawski said that research is revealing circumstances that facilitate oil transport to the seafloor. He spoke about future sediment monitoring:

We recommend sediment sampling that combines coring technology with high-frequency dating. Core samples capture the chronology of conditions before an event. The public wants an accounting for where the oil is in the environment, to know what fraction was recovered, dispersed, and sank.

Murawski suggested that pre- and post-spill contingency planning could use new research from multiple consortia about sub-surface oil transport and spatial inventories of fish and other marine populations:

Models for particular scenarios could identify populations that are potentially at risk and the downstream implications from those at-risk populations. There is now some history about benthic, mesopelagic, and surface-dwelling animals that we could use to make some of those early calls of potential severity related to where the affected areas are located. We know to look for things like skin lesions and to extract liver tissues, blood, and bile. Acoustic monitoring is an efficient and non-invasive way to monitor marine mammals such as the robust sperm whale and dolphin communities.

The above information highlights some of the monitoring priorities for Gulf ecosystem health that can inform decisions in response to various ecological stressors.

GoMRI-FUNDED SCIENTISTS ARE CONDUCTING RESEARCH to improve society’s ability to understand, respond to, and mitigate the impacts of petroleum pollution and related stressors on marine and coastal ecosystems. Communication and collaboration are critical for getting science to the right people at the right time during a response, and the GoMRI research community is seeing many signs of progress in these working relationships.

To learn more about GoMRI research mentioned above, refer to the following information:

C-IMAGE: the Center for Integrated Modeling and Analysis of Gulf Ecosystems consortium, Director Steven Murawski, University of South Florida College of Marine Science. C-IMAGE publications and website.

CWC: the Coastal Waters Consortium, Director Nancy Rabalais, Louisiana Universities Marine Consortium (LUMCON) DeFelice Marine Center. CWC publications and website

Deep-C: the Deepsea to Coast Connectivity in the Eastern Gulf of Mexico consortium, Director Eric P. Chassignet, Florida State University Center for Ocean-Atmospheric Prediction Studies. Deep-C publications and website

DROPPS: the Dispersion Research on Oil: Physics and Plankton Studies, Director Edward J. Buskey, The University of Texas at Austin Department of Marine Science, DROPPS website

ECOGIG: the Ecosystem Impacts of Oil and Gas Inputs to the Gulf consortium, Director Charles Geoffrey Wheat, University of Mississippi, ECOGIG website

GISR: the Gulf of Mexico Integrated Spill Response consortium, Director Piers Chapman, Texas A&M University Department of Oceanography, GISR website

RFP-II Investigator grants:


This research was made possible by grants from BP/The Gulf of Mexico Research Initiative (GoMRI). The GoMRI is a 10-year independent research program established to study the effect, and the potential associated impact, of hydrocarbon releases on the environment and public health, as well as to develop improved spill mitigation, oil detection, characterization and remediation technologies. An independent and academic 20-member Research Board makes the funding and research direction decisions to ensure the intellectual quality, effectiveness and academic independence of the GoMRI research. All research data, findings and publications will be made publicly available. The program was established through a $500 million financial commitment from BP. For more information, visit

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