Patricia Sobecky

Patricia  Sobecky

Professor | Associate Provost for Academic Affairs


  • Ph.D., Microbiology, University of Georgia, 1993
  • Postdoctoral research: University of California at San Diego

Research Interests

Bioremediation of Subsurface Soils Contaminated with Radionuclide and Heavy Metals

Scanning electron micrograph of Rahnella sp. Y9602.
Scanning electron micrograph of Rahnella sp. Y9602.

Genome map 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

V. parahaemolyticus seen under a microscope

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.
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.
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.

annotated marine bacterial plasmids

Selected Publications

(64). Zhao, X., Sobecky, P.A., Guo, X., Zhao, Lanpo, and M. Li. (2015) Chromium(VI) transport and fate in unsaturated zone and aquifer: 3D Sandbox results. (submitted; Journal of Hazardous Materials)

(63). Rajan, S., Fluornoy, N., Beazley, M., and Sobecky, P.A. (2015) Temporal metagenomic insights of a coastal Alabama saltmarsh microbial community impacted by the Deepwater Horizon oil spill. In preparation.

(62). Flournoy, N., Beazley, M., and Sobecky, P.A. (2015) Metagenomic analysis of tarballs from coastal Alabama after the Deepwater Horizon oil spill. (in revision; Frontiers in Microbiology).

(61). Salome, K.R. Beazley, M., Webb, S.M., Sobecky, P.A. and M. Taillefert. (2015) Uranium biomineralization promoted by microbially-mediated phytate hydrolysis in subsurface soils. Submitted (submitted; Environmental Science and Technology).

(60). Horel, A., Mortazavi, B., Sobecky, P.A. 2015. Input of organic matter enhances degradation of weathered diesel fuel in sub-tropical sediments. (Accepted; Science of the Total Environment)

(59). Hazen, T.H, Lafon, P.C. Garrett, N.M., Lowe, T.M., Silberger, D.J., Rowe, L.A., Frace, M., Parsons, M.B., Bopp, C.A., Rasko, D.A., and Sobecky, P.A. 2015. Insights into the environmental reservoir and emergence of pathogenic Vibrio parahaemolyticus using comparative genomics” Frontiers in Microbiology (section Food Microbiology).

(58). King, G.M., Kostka, J.E., Hazen, T.C., and Sobecky, P.A. 2015. Microbial responses to the Deepwater Horizon oil spill: from coastal wetlands to the deep sea. Annual Reviews in Marine Science 7:X–X doi: 10.1146/annurev-marine-010814-015543.

(57). Martinez, R., Beazley, M. and Sobecky, P.A. (2014). Phosphate-mediated Remediation of Metals and Radionuclides. (Advances in Ecology review article, accepted)

(56). Martinez, R.J., Wu, C.H., Beazley, M.J., Andersen, G.L., Conrad, M.E., Hazen, T.C., Taillefert, M., and Sobecky, P.A. 2014. Microbial community responses to organophosphate substrate additions in contaminated subsurface soils. PLOS ONE. (publication date June 20, 2014); Vol.: 9  Issue: 6; Article doi #: e100383

(55). Horel, A., Mortazavi, B. and Sobecky, P.A. 2014. Biostimulation of weathered Macondo 252 crude oil in northern Gulf of Mexico sandy sediments. International Biodegradation & Biodeterioration. Vol. 93:1-9.

(54). Mortazavi, B., Horel, A., Anders, J.S., Mirjafari, A., Beazley, M.J. and Sobecky, P.A. 2013. Enhancing the biodegradation of oil in sandy sediments with choline: A naturally methylated nitrogen compound. Environmental Pollution. 182:53-62.

(53). Mortazavi, B., Horel, A., Beazley, M.J., and Sobecky, P.A. 2013. Intrinsic rates of petroleum hydrocarbon biodegradation in Gulf of Mexico intertidal sandy sediments and its enhancement by organic substrates. Journal of Hazardous Materials Vol. 244 pp. 537-544.

(52).Tezel, U., Tandukar, M., Martinez, R.J., † Sobecky, P.A., and S.G. Pavlostathis. 2012. Aerobic Biotransformation of n-Tetradecylbenzyldimethylammonium chloride by an Enriched Pseudomonas spp. community. Environmental Science and Technology. Vol. 46 pp. 8714-8722 DOI: 10.1021/es300518c.

(51). Beazley, M.J., † Martinez, R.J., † Rajan, S.,* Powell, * J. Piceno, Y.M., Tom, L.M., Andersen, G.L., Hazen, T.C., Van Nostrand, J.D., Zhou, J.Z., Mortazavi, B., and P.A. Sobecky. 2012. Microbial Community Analysis of a Coastal Salt Marsh Affected by the Deepwater Horizion Oil Spill. PLOS ONE vol. 7, no.7 e41305 DOI 10.1371/journal.pone.0041305   Published: JUL 18 2012

(50). Martinez, R., † D. Bruce, C. Detter, L. Goodwin, J. Han, C. Han, B. Held, M. Land, N. Mikhailova, M. Nolan, L. Pennacchio, S. Pitluck, R. Tapia, T. Woyke, and P. Sobecky. 2012. Complete Genome Sequence of Rahnella aquatilis CIP 78.65. Journal of Bacteriology Vol. 194 pp. 3020-3021. DOI: 10.1128/JB.00380-12.

(49). Martinez, R., † D. Bruce, C. Detter, L. Goodwin, J. Han, C. Han, B. Held, M. Land, N. Mikhailova, M. Nolan, L. Pennacchio, S. Pitluck, R. Tapia, T. Woyke, and P. Sobecky. 2012. Complete Genome Sequence of Rahnella sp. Y9602, a Gammaproteobacteria Isolate from Metal and Radionuclide Contaminated Soil. Journal of Bacteriology 194(8):2113-2114. DOI: 10.1128/JB.00095-12.

(48). Horel, A., † B. Mortazavi, and Sobecky, P.A. 2012. Seasonal monitoring of hydrocarbon degraders in Alabama marine ecosystems following the Deepwater Horizon oil spill. Journal of Water, Air, and Soil Pollution Vol. 223 pp 3145-3154 DOI: 10.1007/s11270-012-1097-5

(47). Kinsella, K., † Schlyer, D.J., Fowler, J.S., Martinez, R.J., † and Sobecky, P.A. 2012. Evaluation of positron emission tomography as a method to visualize subsurface microbial processes Journal of Hazardous Waste. Vol 213 pp 498-501. DOI information: 10.1016/j.jhazmat.2012.01.037

(46). Agota, H., † B. Mortazavi, and Sobecky, P.A. 2012. Responses Of Microbial Community From Northern Gulf Of Mexico Sandy Sediments Following Exposure To Deepwater Horizon Crude Oil. Environmental Toxicology and Chemistry Journal. Vol. 31 pp 1004-1011. DOI: 10.1002/etc.1770.

(45). †Beazley, M.J., †R.J. Martinez, S.M. Webb, P.A. Sobecky and M. Taillefert. 2011. The effect of pH and natural microbial phosphatase activity on the speciation of uranium in subsurface soils. Geochimica et Cosmochimica Acta 75:5648-5663.

(44). Technical Report: FAQ: Microbes and Oil Spills. 2011. pp 16. American Academy of Microbiology. *This report was the result of a mini-colloquium held by the AAM in October 2010, and is the first in a new series of reports to provide rapid responses to emerging issues. (Sobecky was an invited participant and report contributor).

(* Denotes graduate and ** undergraduate student co-author; † Denotes post-doctoral co-author; c denotes corresponding author)