Patricia Sobecky

Professor and Chair

Phone (205) 348-1807

Email: psobecky@bama.ua.edu

Patricia Sobecky received a Ph.D. in Microbiology from the University of Georgia in 1993 and completed her postdoctoral research at the University of California at San Diego. Prior to joining the Department of Biological Sciences as Professor and Chair in 2009, she was a faculty member at Georgia Institute of Technology.

Research Interests
Bioremediation of Subsurface Soils Contaminated with Radionuclide and Heavy Metals

Scanning electron micrograph of Rahnella sp. Y9602.

Genome map of Rahnella sp. Y9602.

The treatment of hazardous mixed waste sites, particularly those contaminated with heavy metals and radionuclides, remains one of the most costly environmental challenges currently faced by the U.S. and other countries. Our research examines microbial mechanisms necessary for cell survival and  how to apply them to bioremediation strategies. Specifically, we are interested in heavy metal efflux systems, low molecular weight phosphatases, microbial community dynamics, and the influence of horizontal gene transfer in acidic soils contaminated with nitrate, toxic metals, and radionuclides.  Our work utilizes both culture-dependent and culture-independent approaches to understand the influences of acid and oxidant stress on natural subsurface microbial communities with constitutive phosphatase activity.  Our ongoing experiments are designed to address microbial and geochemical mechanisms that promote phosphate biomineralization of metals and radionuclides for long-term sequestration within subsurface soil and groundwater systems. Genomic studies of two constitutive phosphatase expressing strains are underway as the Joint Genome Institute recently completed genome sequencing of our Rahnella sp. Y9602 and Rahnella aquatilis. This work is funded by the Department of Energy’s Subsurface Biogeochemical Research Program.

Vibrio Parahaemolyticus Survival and Adaptation

The incidence of gastrointestinal illnesses, wound infections, and septicemia caused by species of the genus Vibrio is rising dramatically. Among the ubiquitous Vibrio species occurring in coastal marine and estuarine environments is Vibrio parahaemolyticus , an opportunistic human pathogen. V. parahaemolyticus presently accounts for the majority of Vibrio infections in the United States. The emergence of the serotype O3:K6 in 1996 is now the first documented V. parahaemolyticus serotype to cause global, pandemic disease. Increases in V. parahaemolyticus -associated outbreaks may be due to the emergence and evolution of novel genotypes that promote the organism’s expansion to new niches, host populations or enhance its ability to cause disease. Our studies are addressing the molecular mechanisms and associated mobile genetic elements facilitating the emergence of V. parahaemolyticus pathogens to better understand the threat of this emerging pathogen. Understanding molecular processes that promote rapid genome evolution will yield insights into the evolution of V. parahaemolyticus pathogenicity and the emergence of new serotypes of this opportunistic pathogen.

Long-term Impact of Deepwater Horizon Oil spill on the Alabama Coast

Beginning in June 2010, a collaboration between our research group, Behzad Mortazavi’s group at the Dauphin Island Sea Lab, and researchers at the Lawrence Berkeley National Laboratory was initiated to study the long-term impact of the Deepwater Horizon oil spill.  The two major goals of this interdisciplinary study are to identify biogeochemical changes, in Alabama salt marsh sites, that are a result of the oil spill and develop strategies to remediate contaminated sites.  Monthly sampling of sediments and water undergo geochemical, culture-dependent, and culture independent (PhyloChip) microbiological analyses to track temporal changes in the salt marsh geochemistry and  microbial community  structure.  Additionally, we are examining the influence of horizontal gene transfer to understand the genomic potential for indigenous microbial populations to promote the mineralization of aliphatic and aromatic hydrocarbons. This work is funded by the National Science Foundation RAPID Program.

Coastal Alabama salt marsh site involved in long-term impact of Deepwater Horizon oil spill.

Life in Extreme Environments

Johnson-Sea-Link submersible used for Gulf of Mexico sea-floor sampling.

The northern continental slope of the Gulf of Mexico, a hydrocarbon seep region, contains vast reservoirs of oil and gas deposits, areas of active gas venting and gas hydrate mounds occurring as seafloor outcroppings and in the shallow subsurface. The ice-like gas hydrate, composed of water and hydrocarbon gas molecules (predominately methane), requires suitable gas, temperature and pressure conditions for formation and stability. Although such conditions occur globally, with gas hydrates distributed in many marine (active and passive continental margins) and terrestrial locales, focused seep locations in the shallow Gulf of Mexico basin provide a unique access to abundant gas hydrate mounds and associated sediments at the seafloor. Gas hydrates have become the subject of intense investigation owing to their potential use as an alternative energy resource, possible effect on sea-floor stability, change in climatic conditions and presence on other planets and satellites. In collaboration with researchers from Georgia Tech, the University of Georgia and Texas A&M, sediments and gas hydrate were sampled by deploying a custom-made hydrate drill from a manned research submersible at two different cold seep locations (550-575 m water depth). The objective was to characterize the sediment microbial community in direct contact with surface breaching gas hydrates. Our studies are among the first 16S rDNA gene surveys to be conducted on free-living GoM seep sediment microbial communities directly associated with surface-breaching gas hydrate mounds. Funding for this research was provided by a number of agencies including the NSF, DOE NETL and NOAA NURP.

Marine Plasmid Ecology

To investigate plasmid distribution and plasmidmediated effects on marine microbial community activities, plasmids, extrachromosomal accessory genetic elements, are obtained from marine sediment bacterial populations and characterized at the molecular level. DNA probes specific for replication regions (e.g., plasmid incompatibility-group probes) are used to characterize the distribution, diversity and persistence of these replicons in marine environments. Marine plasmids are also being sequenced to determine biological functions. The transfer dynamics of plasmids are also determined by elucidating environmental and molecular constraints likely to affect horizontal gene exchange. In addition, we have developed new molecular techniques to rapidly assess plasmid populations along spatial and temporal scales. Funding for this research effort has been provided by the Office of Naval Research.

Selected Publications

Beazley, M.J., Martinez, R.J., Webb, S.M., Taillefert, M., and Sobecky, P.A. 2010. The effect of pH and natural microbial phosphatase activity of the speciation of uranium in subsurface soils. Geochimica et Cosmochimica Acta (submitted).

Hazen, T.H., Pan, L., Gu, J., and P.A. Sobecky. 2010. The contribution of mobile genetic elements to the evolution and ecology of Vibrios. FEMS Microbiology Ecology 74(3):485-499.

Beazley, M.J., Martinez, R.J., Sobecky, P.A., Webb, S.M., and Taillefert. M. 2009. Nonreductive biomineralization of uranium(VI) phosphate via microbial phosphatase activity in anaerobic conditions. Geomicrobiology Journal 26(7):431-441.

Hazen, T.H., Kennedy, D.K., Chen, S., Yi, S.V., and P.A. Sobecky. 2009. Inactivation of mismatch repair increases diversity of Vibrio parahaemolyticus. Environmental Microbiology 11(5):1254-1266.

Giannantonio, D.J., Kurth, J.C., Kurtis, K.E., and Sobecky, P.A 2009. Effects of concrete properties and nutrients on fungal colonization and fouling. International Biodeterioration & Biodegradation 63(3):252-259.

Sobecky, P.A. and Coombs, J.A. 2009. Horizontal gene transfer in metal contaminated and radionuclide contaminated soils. In: Maria Boekels Gogarten, Johann Peter Gogarten, and Lorraine Olendzenski (Eds.).  Horizontal Gene Transfer: Genomes In Flux. pp.455-472. Humana Press. New York, NY.

Sobecky, P.A and Hazen, T.H. 2009. Horizontal gene transfer and mobile genetic elements in marine systems. In: Maria Boekels Gogarten, Johann Peter Gogarten, and Lorraine Olendzenski (Eds.).  Horizontal Gene Transfer: Genomes In Flux. pp.435-453. Humana Press. New York, NY.

Giannantonio, D.J., Kurth, J.C., Kurtis, K.E. and P.A. Sobecky. 2009. Molecular characterizations of microbial communities fouling painted and unpainted concrete structures. International Biodeterioration & Biodegradation 63(1):30-40.

Hazen, T.H., Wu, D. Eisen, J.A., and P.A. Sobecky. 2007. Sequence characterization and comparative analysis of three plasmids isolated from environmental Vibrio spp. Applied and Environmental Microbiology 73(23):7703-7710.

Criminger, J.D., Hazen, T.H., Sobecky, P.A. and C.R. Lovell. 2007. Nitrogen fixation by Vibrio parahaemolyticus and its implications for a new ecological niche. Applied and Environmental Microbiology 73(18):5959-5961.

Martinez, R.J., Beazley, M.J., Taillefert, M. Arakaki, A.K., Skolnick, J., and P.A. Sobecky. 2007. Aerobic uranium(VI) bioprecipitation by metal resistant bacteria isolated from radionuclide- and metalcontaminated subsurface soils. Environmental Microbiology 9(12):3122-3133.

Beazley, M.J., Martinez, R.J., Sobecky, P.A., Webb, S.M., and Taillefert, M. 2007. Uranium biomineralization as a result of bacterial phosphatase activity: insights from bacterial isolates from a contaminated subsurface. Environmental Science and Technology 41(16):5701-5707.

Kurth, J.C., Giannantonio, D.J., Allain, J., Sobecky, P.A., and Kurtis. K.E. 2007. Mitigating Biofilm Growth through the Modification of Concrete Design and Practice. In: P. Baglioni and L. Cassar (Eds.), Proceedings of the International RILEM Symposium on Photocatalysis, Environment and Construction Material, Volume PRO50, pp. 195-202.

Sobecky, P.A. 2007. Exploring the Deep Biosphere: Probing Microbial Systems at Earth’s Extremes. Eos Trans. AGU 88(34): 336.

D’Hondt, S., Inagaki, F., Feldman, T., Jorgensen, B.B., Kato, K., Kemp, P., Sobecky, P.A., Sogin, M., and Takai, K. 2007. Exploring subseafloor life with the integrated ocean drilling program. Scientific Drilling Journal. September, No. 5, p. 26-37.

Burkepile, D.E., Parker, J.D., Woodson, C.B., Mills, H.J., Kubanek, J., Sobecky, P.A., and M.E. Hay. 2006. Chemically-mediated competition between microbes and animals: microbes as consumers in food webs. Ecology 87(11):2821-2831.

Martinez, R.J., Wang, Y., Raimondo, M.A., Coombs, J.M., Barkay, T., and P.A. Sobecky. 2006. Horizontal gene transfer of PIB-type ATPases among bacteria isolated from radionuclide- and metal-contaminated subsurface soils. Applied and Environmental Microbiology. 72(5):3111-3118.

Martinez, R.J., Mills, H.J., S. Story, P.A. Sobecky. 2006. Prokaryotic diversity and metabolically active microbial populations in sediments from an active mud volcano in the Gulf of Mexico. Environmental Microbiology 8(10):1783-1796.

Pfiffner, S.M., P.A. Sobecky, T.J. Phelps, and A.V. Palumbo. 2002. Microbiology of Atlantic Coastal Plain aquifers and other unconsolidated subsurface sediments. In Gabriel Bitton (ed.) Encyclopedia of Environmental Microbiology, Vol. 4, pp. 2028-2042. John Wiley & Son, Inc. New York, NY.