Linking Microbial Diversity to Bioremediation Potential at U.S. DOE Sites

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.

Metal contaminants, many of which are radioactive and/ or toxic, are concentrated in subsurface aquifers and represent a global scale threat to groundwater that is used for drinking. In the U.S. alone, the Department of Energy (DOE) currently is responsible for remediating 1.7 trillion gallons of contaminated groundwater, an amount equal to approximately four times the daily U.S. water consumption, and 40 million cubic meters of contaminated soil, enough to fill approximately 17 professional sports stadiums (U.S. DOE, 2000).

Clean-up projects are projected to cost nearly 150 billion dollars and last many decades in areas surrounding sites where metal radionuclides were extracted and processed for weapons production during the Cold War era. Within the nuclear weapons complex managed by the U. S. DOE, uranium is the most common radionuclide contaminant found in subsurface sediments and groundwaters. Nitrate is often a cocontaminant with uranium because of the use of nitric acid in the processing of uranium and uranium-bearing waste. Because of their widespread significance as groundwater contaminants in subsurface aquifers, Kostka laboratory research on metal contaminants has centered on the cleanup of uranium(VI) and nitrate.

Current subsurface remediation practices employ costly “pump and treat” or excavation methods that generally do not include in situ remediation options like bioremediation. However, laboratory and field experiments have indicated that indigenous microorganisms (dissimilatory Fe(III)-reducing and sulfate-reducing prokaryotes, in particular) could provide more cost-effective solutions for remediating mobile metal contaminants near source zones than current practices. Uranium [U(VI)] can be microbiologically or abiotically immobilized from water by its reduction to insoluble U(IV) oxide. However, for most DOE sites, there is as yet no consensus on the metabolic activity and distribution of predominant microbial groups that catalyze radionuclide immobilization in situ.

To address these data gaps, the DOE created a Microbial Communities Working Group in association with the Oak Ridge (Tennessee) Field Research Center (ORFRC), designated by the agency’s Environmental Remediation Sciences Program (ERSP) for multidisciplinary subsurface remediation and long-term stewardship science. Dr. Kostka has led the Working Group since 2003. His current research at the ORFRC, centers on metal- and nitrate-reducing microbial communities and 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.

From the Kostka Lab:



O. Prakash, S. J. Green, D. M. Akob, T. M. Gihring, P. Jardine, D. B. Watson, and J. E. Kostka. 2009. Novel denitrifying bacteria isolated from the terrestrial subsurface exposed to mixed waste contamination. Environmental Microbiology (in review).

W. Wu, J. Carley, S.J. Green, J. Luo, S. D. Kelly, K. Lowe, T. Mehlhorn, S. Carroll, B. Boonchayanant, D. Watson, K. M. Kemner, J. Zhou, P. K. Kitanidis, J.E. Kostka, P. M. Jardine, and C. S. Criddle. 2009. Impact of Nitrate on Stability of Immobilized Uranium in the Bioremediated Subsurface. Environmental Science & Technology (in review).

O. Prakash, T.M. Gihring, D.D. Dalton, K.-J. Chin, S.J. Green, D.M. Akob, G. Wanger, J.E. Kostka. 2009. Geobacter daltonii sp. nov., an iron(III)- and uranium(VI)-reducing bacterium isolated from the shallow subsurface exposed to mixed heavy metal and hydrocarbon contamination. (In press).

D. M. Akob, H. J. Mills, T. M. Gihring, L. Kerkhof, J. W. Stucki, Kuk-Jeong Chin, Kirsten Kuesel, Anthony V. Palumbo, David B. Watson, and Joel E. Kostka. 2008. Functional diversity and electron donor dependence of microbial populations capable of U(VI) reduction in radionuclide contaminated subsurface sediments. Applied and Environmental Microbiology 74: 3159-3170.

D. M. Akob, H. J. Mills, D. L. Swofford, J. E. Kostka. 2007. Metabolically-Active Microbial Communities in Uranium-Contaminated Subsurface Sediments. FEMS Microbiology Ecology 59: 95-107.

L. Edwards, K. Kuesel, H. Drake, and J.E. Kostka. 2007. Electron flow in acidic subsurface sediments cocontaminated with nitrate and uranium during nuclear weapons production. Geochimica et Cosmochimica Acta 71: 643-654.

N.N. North, S.L. Dollhopf, L. Petrie, J.D. Istok, D.L. Balkwill, and J.E. Kostka. 2004. A Change in Bacterial Community Structure During in situ Biostimulation of Subsurface Sediment Cocontaminated with Uranium and Nitrate. Applied and Environmental Microbiology 70: 4911-4920.

L. Petrie, N.N. North, S.L. Dollhopf, D.L. Balkwill, and J.E. Kostka. 2003. Enumeration and characterization of iron(III)-reducing microbial communities from acidic subsurface sediments contaminated with uranium (VI). Applied and Environmental Microbiology 69: 7467-7479.