Colonies of the microbe Geobacter daltonii, an iron reducer, in a test tube held up against the sky
Location of the U.S. DOE Environmental Remediation Sciences Program (ERSP) Oak Ridge Field Research Center (ORFRC), showing the former S-3 Waste Ponds during neutralization and denitrification just prior to closure in 1988 and the S-3 Ponds closed with a multilayer cap and paved at present.
Conceptual model of subsurface contaminant transport at the Oak Ridge Field Research Center (i.e., former S-3 Waste Disposal Ponds) showing association of microbial diversity in groundwater with pH and contaminant levels.

Bioremediation is broadly defined as using biology to clean up or remove contaminants from the environment. Since microbes catalyze so many geochemical reactions, bioremediation potential is most often dictated by the physiological requirements of microbial growth and metabolism. During natural attenuation, contamination is left in the environment to be degraded without interference. Through biostimulation, humans may also accelerate microbial contaminant removal by adding nutrients or other growth substrates such as oxygen. In short, the ability to clean up or remediate a site is often determined by microbial ecology (the abundance, distribution, diversity of microbes present).

One of the most important examples of bioremediation is the microbial removal of nitrogen pollution from the environment. The nitrogen cycle has now been altered by humans to a greater extent than any other biogeochemically-active element. In large portions of the U.S. and Europe, reactive nitrogen inputs are now an order of magnitude above those occurring prior to the 20th century. The relative increase in anthropogenic nitrogen fixation over the past 50 years has been at least five times greater than that observed in atmospheric CO2. The release of excess nitrogen into aquatic and marine ecosystems causes a suite of negative environmental and human health problems. Therefore, in order to effectively manage critical ecosystems such as aquifers that provide a source of drinking water, the factors controlling the microbially catalyzed removal of nitrogen need to be better understood.

Another great example is the degradation of petroleum hydrocarbons by microbes. Similar to the breakdown of natural organic matter, biodegradation mediated by microbes is the ultimate fate of the majority of spilled oil that is released into environment. An understanding of the controls and pathways of biodegradation will help to improve response strategies to major oil spills.

Thus, bioremediation research in the Kostka Lab has the following objectives:

  1. To identify, isolate, and characterize microorganisms or microbial groups with a high metabolic potential to catalyze bioremediation
  2. To quantify the distribution of these microbes in the subsurface, and
  3. To determine the mechanisms controlling their metabolism.

Recent Publications

Brooks, G. R., Larson, R. A., Schwing, P. T., Romero, I., Moore, C., Reichart, G-J., Jilbert, T., Chanton, J.P., Hastings, D.W, Overholt, W.A., Marks, K.P., Kostka, J.E., Holmes, C.W., Hollander, D. 2015. Sedimentation Pulse in the NE Gulf of Mexico Following the 2010 DWH Blowout. PLOS One (in press).

Rodriguez-R, L.M., W.A. Overholt, C. Hagan, M. Huettel, J. E Kostka, and K.T.Konstantinidis. 2015. Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill. ISME Journal doi: 10.1038/ismej.2015.5

King, G.M., J.E. Kostka, T. Hazen, and P. Sobecky. 2015. Microbial Responses to the Deepwater Horizon Oil Spill: From Coastal Wetlands to the Deep Sea. Annual Review of Marine Science 7: 377-401.

Kostka, J.E., A.P.Teske, S. B. Joye and Ian M. Head. 2014. The metabolic pathways and environmental controls of hydrocarbon biodegradation in marine ecosystems. Frontiers in Microbiology 5: 471. doi: 10.3389/fmicb.2014.00471

Joye, S.B, A.P. Teske, and J.E. Kostka. 2014. Microbial Dynamics Following the Macondo Oil Well Blowout across Gulf of Mexico Environments. BioScience. 64 (9): 766-777. doi: 10.1093/biosci/biu121

Ruddy B.M., M. Huettel, J.E. Kostka, V.V. Lobodin, B.J. Bythell, A. M. McKenna, C. Aeppli, C.M. Reddy, R. K. Nelson, A. G. Marshall, and R. P. Rodgers. 2014. Targeted Petroleomics: Analytical Investigation of Macondo Well Oil Oxidation Products from Pensacola Beach. Energy Fuels 28: 4043-4050.

P. Jasrotia, S. J. Green, A. Canion, W. A. Overholt, O. Prakash, D. Wafula, D. Hubbard, D. B. Watson, C. W. Schadt, S. C. Brooks and J. E. Kostka. 2014. Watershed scale fungal community characterization along a pH gradient in a subsurface environment co-contaminated with uranium and nitrate. Applied and Environmental Microbiology 80: 1810-1820.

R. Venkatramanan, O. Prakash, T. Woyke, P. Chain, L. Goodwin, D. Watson, S. Brooks, J.E. Kostka, and S. Green. 2013. Genome sequences for three denitrifying bacterial strains isolated from a uranium- and nitrate-contaminated subsurface environment. Genome Announcements doi: 10.1128/genomeA.00449-13 Genome Announc. 1: e00449-13

W. A. Overholt, S. J. Green, K. P. Marks, R. Venkatramanan, O. Prakash, and J. E. Kostka. 2013. Draft Genome Sequences for Oil-Degrading Bacterial Strains from Beach Sands Impacted by the Deepwater Horizon Oil Spill. Genome Announcements doi: 10.1128/genomeA.01015-13 Genome Announc. 1: e01015-13.

Green S., Rishishwar L., Prakash O., Jordan I., Kostka J.E. 2013. Insights into environmental microbial denitrification from integrated metagenomic, cultivation and genomic analyses. In: Nelson K. (Ed.) Encyclopedia of Metagenomics: SpringerReference ( Springer-Verlag Berlin Heidelberg. DOI: 10.1007/SpringerReference_359242 2013-07-18 17:38:52 UTC

Salome, K.R., S. J. Green, M. J. Beazley, S. M. Webb, J. E. Kostka, and M. Taillefert. 2013. The role of anaerobic respiration in the immobilization of uranium through biomineralization of phosphate minerals. Geochimica Cosmochimica Acta 106: 344-363.