Joel Kostka, Professor
Degree Information: Ph.D., Marine Science, University of Delaware, 1993
Office: Cherry Emerson 225
Microbial ecology, biogeochemistry, oceanography, climate change, bioremediation, bioenergy
The Kostka Laboratory combines cutting-edge microbiology/molecular biology with biogeochemistry to explore the ecosystem services provided by microorganisms that keep planet Earth habitable for human beings. These ecosystem services include the recycling of organic matter and nutrients, the production of gases that make up Earth's atmosphere, and the microbially mediated clean up of harmful pollutants that result from human activities. The lab is interested in how physical or geochemical parameters such as temperature or pH impact the functional diversity of microbial communities, thereby limiting microbial processes which are key to ecosystem functioning. Using a combination of cultivation-based and cultivation-independent molecular techniques, we investigate the physiological ecology of microorganisms, often based on hypotheses generated from genome and metagenomic sequence information. Our research is heavily field oriented and spans from coastal marine ecosystems to the terrestrial subsurface.
Microbes and Oil Spills
Similar to the microbially-mediated breakdown of natural organic matter, biodegradation mediated by indigenous microbial communities is the ultimate fate of the majority of oil hydrocarbon that enters the marine environment. An understanding of the impacts of oil on indigenous microbial communities and identification of oil-degrading microbial groups is prerequisite for directing the management and cleanup of oil-contaminated ecosystems. Our team was part of the quick response to the Deepwater Horizon oil spill that devastated the Gulf of Mexico. We have tracked the fate and transport of oil on the Gulf coast, especially in beaches that are critical to the economy of the region. A bloom of hydrocarbon-degrading bacteria was observed in Gulf beach sands in the summer and fall of 2010. Major groups of oil-degraders were identified by high throughput gene sequencing methods and isolated into pure culture. Isolates of hydrocarbon-degraders are studied in the laboratory to better understand the physiological controls and mechanisms of oil degradation.
Bioremediation of Nuclear Legacy Waste
Clean-up of nuclear waste is projected to cost hundreds of billions of dollars and last many decades in areas surrounding sites where metal radionuclides were extracted and processed for weapons production during the Cold War era. 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 within the nuclear weapons complex managed by the U.S. Department of Energy. This research seeks to: 1) identify, isolate, and characterize microorganisms or microbial groups with a high metabolic potential to catalyze bioremediation, 2.) quantify the distribution of these microbes in the subsurface, and determine the mechanisms controlling their metabolism.
Carbon Storage in Peatlands
Peatlands sequester one-third of all soil carbon and currently act as major sinks of atmospheric CO2. The ability to predict or to simulate the fate of stored carbon in response to climatic disruption remains hampered by our limited understanding of the controls of C turnover and the composition and functioning of peatland microbial communities. Given their global extent and uncertain fate with climatic change, boreal forests are considered a high priority for climate change research. The overall goal of this project is to investigate the reactivity of soil organic matter and the composition of decomposer microbial communities in response to the climatic forcing of environmental processes that determine carbon storage and sequestration in peatlands. The proposed project will be conducted at the Marcell Experimental Forest (MEF) where the U.S. Department of Energy, Oak Ridge National Laboratory, and the USDA Forest Service have established a Climate Change Response Scientific Focus Area known as Spruce and Peatland Response Under Climatic and Environmental Change (SPRUCE).
The warming of shallow seas as a result of climate change is likely to have a dramatic effect on the biogeochemical cycling of matter, nutrients and carbon. Nearly all of the major reactions of the global nitrogen cycle are catalyzed by microorganisms. Thus, a primary interest of our group is to understand the role of temperature in controlling the microbially-mediated rates and pathways of benthic nitrogen cycling in permanently cold sediments. Rate measurements of nitrogen loss through nitrate respiration (denitrification and anammox) are determined using a combination of stable nitrogen isotope tracers and mass spectrometry. We investigate the ecology of psychrophilic or cold-loving denitrifying bacteria using a combination of culture-based and molecular biology techniques.
Kostka, J.E. and S. J. Green. 2011. Microorganisms and processes linked to uranium reduction and immobilization. Chapter 7, pp. 117-138, In: Microbial Metal and Metalloid Metabolism: Advances and Applications, Edited by J. F. Stolz and R. S. Oremland, ASM Press, Washington, DC.
S. B. Joye, I. Leifer, I. R. MacDonald, J. P. Chanton, C. D. Meile, A. P. Teske, J. E. Kostka, L. Chistoserdova, R. Coffin, D. Hollander, M. Kastner, J. P. Montoya, G. Rehder, E. Solomon, T. Treude and T. A. Villareal. 2011. Technical Comment on "A Persistent Oxygen Anomaly Reveals the Fate of Spilled Methane in the Deep Gulf of Mexico" by Kessler et al. Science 332: 1033.
T.M. Gihring, G. Lavik, M. Kuypers, and J.E. Kostka. 2010. Direct determination of nitrogen cycling rates and pathways in Arctic fjord sediments (Svalbard, Norway). Limnology and Oceanography 55: 740-752.
S. J. Green, O. Prakash, T. M. Gihring, D. M. Akob, P. Jasrotia, P. M. Jardine, D. B. Watson, S. D. Brown, A. V. Palumbo, and J. E. Kostka. 2010. Denitrifying bacteria isolated from terrestrial subsurface sediments exposed to mixed-waste contamination. Applied and Environmental Microbiology 76: 3244-3254.
T. M. Gihring, M. Humphrys, H. J. Mills , M. Huettel, and J. E. Kostka. 2009. Identification of phytodetritus degrading microbial communities in sublittoral Gulf of Mexico sands. Limnology and Oceanography 54: 1073-1083.