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A systems approach to improve predictions of biodegradation and ecosystem recovery in coastal marine sediments impacted by oil spills.

Markus Huettel, Florida State University

Kostas Konstantinidis, Joel Kostka, Georgia Institute of Technology

Funded by the Gulf of Mexico Rese


About 22,000 t of the Deepwater Horizon oil slick reached the shorelines of the northern Gulf of Mexico eventually contaminating approximately 900 km of sandy beaches. Oil was deposited on the dry sand, in the intertidal zone, and in submerged sediment near Gulf beaches (Fig. 1). Surface residue balls (SRBs), typically 0.5–5 cm in diameter and containing 5% to 10% hydrocarbons by weight are still washed up today, re-contaminating tourist beaches. Sedimentary microbes are central for the degradation of oil buried in shoreline or beach sediments. Studies of the microbial community response to oil contamination recognize shifts in composition, including an increase in the relative abundance of members of the Gammaproteobacteria, a prevalence of known hydrocarbon-degrading populations, and the enriched abundance and expression of genes related to hydrocarbon degradation. However, beyond this descriptive understanding of the effects of oil on the indigenous microbial communities, very little quantitative information exists on the exact pathways and metabolites employed by microorganisms to break down oil, and how the environmental conditions affect the biodegradation rates. 

This study, funded by the Gulf of Mexico Research Initiative (RFP V) addresses these knowledge gaps with the following working hypotheses:

1) microbial oil degradation in permeable coastal sands is a function of oxygen and nutrient transport and a limited set of environmental parameters, and

2) supra-, inter-, and subtidal shore sands substantially differ with respect to oil degradation kinetics due to differences in key environmental variables and microbial community interaction networks.

Oil on Pensacola Beach  

Fig. 1 Oil washed onto Pensacola beach 6/30/2010


To test our hypotheses, we perform laboratory incubations with inocula from water saturated, temporally saturated and unsaturated beach sands, using state-of-the-art mesocosms that can simulate in-situ conditions. The mesocosms are treated with Macondo crude oil, and the fate of oil will be followed over time and under different conditions of oxygen and nutrient supply rates. Genomic (who is there?) and the transcriptomic (who and what genes are active?) information will be linked to different environmental settings, transport regimes and degradation rates of oil constituents (Fig.2). Laboratory findings are compared to results and samples from the field as well as pure bacterial isolates recovered from our previous work. Taxonomic, genetic and functional data are integrated into advanced dynamic models that will represent the responses of whole microbial communities and allow predictions of their activities under different levels of oxygen and nutrients; thereby, providing practical tools for modeling and predicting the fate of oil spills.


Fig. 2.

Project concept

  Schematic Fig. 2


Research objectives guiding the project:

Determine the structures and successions of the microbial communities developing after petroleum hydrocarbon burial in dry, periodically flushed and water saturated coastal sand.

Assess gene expression and microbial crude oil degradation rates modulated by supply rates of electron acceptors and nutrients to the buried oil.

Produce quantitative information on microbial activities that can be used to predict decomposition rates of buried petroleum hydrocarbons in coastal sands.

Identify microbial indicators suitable for the prediction of the degradation process of buried crude oil.

Develop a model using a systems approach that incorporates microbiological, genomics, biogeochemical and transport data to predict in situ decomposition rates of buried oil in sub-, inter- and supratidal beach sands.


Foam on Beach Intertidal oil sublittoral tar

Fig. 3 Oil buried in supralittoral sand, intertidal sand, and sublittoral tar balls.


This research will integrate taxonomic, genetic and process/degradation rate data into advanced dynamic models that will represent responses of whole microbial communities (Fig. 4). The models will be applied to available data from long-term monitoring sites in Florida beach sands to provide system-level insights into how communities respond to the combined effect of multiple environmental factors (oxygen and nutrient levels, temperature) during crude oil biodegradation and to test for differences and similarities between the these important coastal ecosystems.


Conceptual model

Fig. 4

 Conceptual overview of the modeling analysis of shore sand microbial communities.


The project produces information on microbial indicators and models of oil degradation that can help to plan for responses to future oil spills in coastal zones. Buried oil may persist for decades in anaerobic sedimentary environments and thus may be a long-term source of potentially harmful hydrocarbons that can seep out of the sediment. Gulf beaches, intertidal zones and inner shelf areas are not only a prime tourist destination and of great economical value, they are also important coastal ecosystems for many organisms, some of which are rare or endangered (e.g. beaches as nesting grounds for sea turtles). Investigating and modeling the fate of buried oil thus is central for risk assessment associated with these hydrocarbons for environmental and human health, coastal food sources, and economic impacts.







Fig. 5

Oil sheen on nearshore Gulf water




Further information on oil degradation and oil in marine sediments

Bernabeu, A. M. and others 2006. Beach morphodynamics forcements in oiled shorelines: Coupled physical and chemical processes during and after fuel burial. Marine Pollution Bulletin 52: 1156-1168.
Da Silva, A. C., F. J. S. De Oliveira, D. S. Bernardes, and F. P. De Franca. 2009. Bioremediation of Marine Sediments Impacted by Petroleum. Applied Biochemistry and Biotechnology 153: 58-66.
Del'arco, J. P., and F. P. De Franca. 2001. Influence of oil contamination levels on hydrocarbon biodegradation in sandy sediment. Environmental Pollution 112: 515-519.
Gonzalez, M., R. Medina, A. M. Bernabeu, and X. Novoa. 2009. Influence of Beach Morphodynamics in the Deep Burial of Fuel in Beaches. Journal of Coastal Research 25: 799-818.
Head, I. M., D. M. Jones, and W. F. M. Roling. 2006. Marine microorganisms make a meal of oil. Nature Reviews Microbiology 4: 173-182.
Peterson, C. H. and others 2003. Long-term ecosystem response to the Exxon Valdez oil spill. Science 302: 2082-2086.
Wrenn, B., K. L. Sarnecki, E. S. Kohar, K. Lee, and A. D. Venosa. 2006. Effects of nutrient source and supply on crude oil biodegradation, in continuous-flow beach microcosms. Journal of Environmental Engineering-Asce 132: 75-84.