Browsing by Author "Sobecky, Patricia A."
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Item Complete Genome Sequence of Rahnella sp Strain Y9602, a Gammaproteobacterium Isolate from Metal- and Radionuclide-Contaminated Soil(American Society of Microbiology, 2012) Martinez, Robert J.; Bruce, David; Detter, Chris; Goodwin, Lynne A.; Han, James; Han, Cliff S.; Held, Brittany; Land, Miriam L.; Mikhailova, Natalia; Nolan, Matt; Pennacchio, Len; Pitluck, Sam; Tapia, Roxanne; Woyke, Tanja; Sobecky, Patricia A.; University of Alabama Tuscaloosa; United States Department of Energy (DOE); Los Alamos National Laboratory; Oak Ridge National LaboratoryRahnella sp. strain Y9602 is a gammaproteobacterium isolated from contaminated subsurface soils that is capable of promoting uranium phosphate mineralization as a result of constitutive phosphatase activity. Here we report the first complete genome sequence of an isolate belonging to the genus Rahnella.Item Deepwater Horizon oil spill: using microcosms to study effects of crude oil in coastal sediments(University of Alabama Libraries, 2013) Rentschler, Erika Kristine; Donahoe, Rona Jean; University of Alabama TuscaloosaApproximately 4.9 million gallons of crude oil traveled with ocean currents to reach the Gulf coast after the Deepwater Horizon oil drilling rig explosion. Microcosm experiments were conducted to determine how oil contamination affects the concentration and distribution (between solid and aqueous phases) of trace elements in a salt marsh environment. Sediment and seawater from a salt marsh at Bayou La Batre, Alabama, were measured into jars and spiked with 500 ppm MC-252 oil. The solid phase and aqueous samples were analyzed by ICP-OES, ICP-MS, and IC. A second experiment was conducted using various concentrations (0 ppm, 10 ppm, 100 ppm, 500 ppm, 1000 ppm, 2500 ppm) of MC252 oil. ICP-OES data show variations in aqueous elemental concentrations occurred over the 14 day experiment. The pH for the water in the experiments ranged from 6.93 to 8.06. Significant positive correlations (r>0.75) were found in the solid phase samples between iron and the following elements: aluminum, cobalt, chromium, and nickel. Aqueous iron concentrations were highly correlated (r>0.75) with solution pH. The presence of iron oxide and clays in the salt marsh sediment indicates potential for adsorption of trace elements sourced from the environment and from crude oil contamination. The release of aqueous Fe (II) observed between two and 14 days is likely caused by reductive dissolution of iron-bearing clays or iron oxide. All the samples that contained oil behaved in similar ways with respect to time, but the controls showed almost no changes in the concentrations of the trace elements. Although the levels of some trace elements in the solid phase changed during the experiments, their final concentrations were at the same levels as the control samples. With the exception of nickel, the 14 day samples contained lower trace metal concentrations than the sterile control which contained no oil. The reason for this is likely attributable to the in situ oil-degrading bacteria, which were found to be present in the sediment. The oil-degrading bacterial community increased in the presence of oil and decreased as the oil concentration decreased. Oil-degrading bacteria are capable of inducing reductive dissolution in Fe (III) minerals.Item Establishing cost effective methods to analyze a wide range of pharmaceutical compounds through laboratory scale experiments aimed at assessing fate and transport mechanisms in groundwater(University of Alabama Libraries, 2015) Salome, Patrick Anthony; Tick, Geoffrey R.; University of Alabama TuscaloosaPharmaceutical and organic wastewater contaminants have been increasingly detected in drinking water and groundwater supplies. A stepwise approach was used to determine a simple and cost effective method for testing various classes of pharmaceutical compounds. A robust, accurate method was developed and validated using two commonly detected pharmaceuticals in water resources; sulfamethoxazole (SMX) and carbamazepine (CMP). Tandem solid-phase extraction in conjunction with high performance liquid chromatography (HPLC) analysis was effective for quantifying concentrations of analytes under environmentally relevant laboratory-scale scenarios. Using predetermined standards and known concentrations, an average recovery percentage of 96.25% was achieved in validation efforts. Batch tests consisting of streambed sediment and known concentrations of the study analytes were conducted over a 96-hour period to determine Freundlich adsorption isotherm coefficients (KF) and retardation factors (R). The results of these tests demonstrate that CMP had a greater affinity to adsorb to the sediment (K_F=8.79) compared to SMX (K_F=4.22) with corresponding retardation factors (R) of 49.3 and 20.7, respectively. In addition to the development of a promising cost-effective analytical method to quantify different types of pharmaceutical compounds in groundwater, this work also demonstrates that SMX (compared to CMP) may pose higher risk for entering drinking water supplies, as natural retention processes will be less under most conditions. Limits of detection using the SPE/SPE HPLC-UV method was 0.48 μg/L for SMX and 0.60 μg/L for CMP.Item Investigating the presence and distribution of organic components in bacterial magnetite(University of Alabama Libraries, 2013) Spry, Jacob; Perez-Huerta, Alberto; University of Alabama TuscaloosaThe formation of magnetites within magnetosomes is subjected to highly controlled biomineralization processes by bacteria. Similar biominerals have been observed to contain occluded ("intra-crystalline") organics, revealing significant information about such processes. The size of magnetite particles produced by bacteria (< 100 nm) and limitations in analytical instrumentation have hindered a better understanding of whether organics are located within these nanoparticles. In this study, bright field TEM images, STEM images, and EDS chemical data have been collected for magnetite particles produced by Magnetospirillum gryphiswaldense in order to investigate the potential presence and distribution of organic components. Results reveal low atomic number features in STEM images, suggesting presence of an organic matrix near the edges of nanoparticles. Additionally, STEM-EDS analysis indicates presence of phosphorous within the magnetosome nanoparticles. The mean P/Fe ratio for the outer half of the magnetsome nanoparticles was significantly higher than the mean ratio for the inner "core", suggesting that phosphorus is present with greater magnitude in the "rim" in a co-location with STEM features. Phosphorus is not accounted for in any known mineral constituent of the samples and it is a vital organic element, present in certain types of lipids, which have been associated to the formation of magnetosomes. Overall results contribute to a better knowledge of these highly controlled biomagnetite particles, with significant implications for the recognition of biomarkers and their potential applications in nanotechnology and medicine.Item Microbial Community Analysis of a Coastal Salt Marsh Affected by the Deepwater Horizon Oil Spill(PLOS, 2012) Beazley, Melanie J.; Martinez, Robert J.; Rajan, Suja; Powell, Jessica; Piceno, Yvette M.; Tom, Lauren M.; Andersen, Gary L.; Hazen, Terry C.; Van Nostrand, Joy D.; Zhou, Jizhong; Mortazavi, Behzad; Sobecky, Patricia A.; University of Alabama Tuscaloosa; United States Department of Energy (DOE); Lawrence Berkeley National Laboratory; University of California Berkeley; University of Tennessee Knoxville; University of Oklahoma - Norman; Dauphin Island Sea LabCoastal salt marshes are highly sensitive wetland ecosystems that can sustain long-term impacts from anthropogenic events such as oil spills. In this study, we examined the microbial communities of a Gulf of Mexico coastal salt marsh during and after the influx of petroleum hydrocarbons following the Deepwater Horizon oil spill. Total hydrocarbon concentrations in salt marsh sediments were highest in June and July 2010 and decreased in September 2010. Coupled PhyloChip and GeoChip microarray analyses demonstrated that the microbial community structure and function of the extant salt marsh hydrocarbon-degrading microbial populations changed significantly during the study. The relative richness and abundance of phyla containing previously described hydrocarbon-degrading bacteria (Proteobacteria, Bacteroidetes, and Actinobacteria) increased in hydrocarbon-contaminated sediments and then decreased once hydrocarbons were below detection. Firmicutes, however, continued to increase in relative richness and abundance after hydrocarbon concentrations were below detection. Functional genes involved in hydrocarbon degradation were enriched in hydrocarbon-contaminated sediments then declined significantly (p<0.05) once hydrocarbon concentrations decreased. A greater decrease in hydrocarbon concentrations among marsh grass sediments compared to inlet sediments (lacking marsh grass) suggests that the marsh rhizosphere microbial communities could also be contributing to hydrocarbon degradation. The results of this study provide a comprehensive view of microbial community structural and functional dynamics within perturbed salt marsh ecosystems.Item Microbial Community Responses to Organophosphate Substrate Additions in Contaminated Subsurface Sediments(PLOS, 2014) Martinez, Robert J.; Wu, Cindy H.; Beazley, Melanie J.; Andersen, Gary L.; Conrad, Mark E.; Hazen, Terry C.; Taillefert, Martial; Sobecky, Patricia A.; University of Alabama Tuscaloosa; University of California Berkeley; United States Department of Energy (DOE); Lawrence Berkeley National Laboratory; University of Tennessee Knoxville; Georgia Institute of TechnologyBackground: Radionuclide-and heavy metal-contaminated subsurface sediments remain a legacy of Cold War nuclear weapons research and recent nuclear power plant failures. Within such contaminated sediments, remediation activities are necessary to mitigate groundwater contamination. A promising approach makes use of extant microbial communities capable of hydrolyzing organophosphate substrates to promote mineralization of soluble contaminants within deep subsurface environments. Methodology/Principal Findings: Uranium-contaminated sediments from the U. S. Department of Energy Oak Ridge Field Research Center (ORFRC) Area 2 site were used in slurry experiments to identify microbial communities involved in hydrolysis of 10 mM organophosphate amendments [i.e., glycerol-2-phosphate (G2P) or glycerol-3-phosphate (G3P)] in synthetic groundwater at pH 5.5 and pH 6.8. Following 36 day (G2P) and 20 day (G3P) amended treatments, maximum phosphate (PO43-) concentrations of 4.8 mM and 8.9 mM were measured, respectively. Use of the PhyloChip 16S rRNA microarray identified 2,120 archaeal and bacterial taxa representing 46 phyla, 66 classes, 110 orders, and 186 families among all treatments. Measures of archaeal and bacterial richness were lowest under G2P (pH 5.5) treatments and greatest with G3P (pH 6.8) treatments. Members of the phyla Crenarchaeota, Euryarchaeota, Bacteroidetes, and Proteobacteria demonstrated the greatest enrichment in response to organophosphate amendments and the OTUs that increased in relative abundance by 2-fold or greater accounted for 9%-50% and 3%-17% of total detected Archaea and Bacteria, respectively. Conclusions/Significance: This work provided a characterization of the distinct ORFRC subsurface microbial communities that contributed to increased concentrations of extracellular phosphate via hydrolysis of organophosphate substrate amendments. Within subsurface environments that are not ideal for reductive precipitation of uranium, strategies that harness microbial phosphate metabolism to promote uranium phosphate precipitation could offer an alternative approach for in situ sequestration.