Browsing by Author "Pruden, Amy, advisor"
Now showing 1 - 4 of 4
Results Per Page
Sort Options
Item Open Access Development and application of functional gene profiling and quantification of microbial communities remediating mine drainage(Colorado State University. Libraries, 2009) Pereyra, Luciana Paula, author; Pruden, Amy, advisor; Reardon, Kenneth F., advisorMine drainage (MD) is the product of the oxidation of sulfide minerals. It is characterized by elevated concentrations of heavy metals and sulfate and acidic to near-neutral pH. Sulfate-reducing permeable reactive zones (SR-PRZs) represent a common passive treatment approach for MD. Although SR-PRZs are microbially catalyzed, little is known about their microbiology and ecology. In this research, several aspects of the SR-PRZ microbial community were explored at laboratory and pilot scales with established as well as newly developed biomolecular methods. A study using microcosm column experiments demonstrated that the type of inoculum plays an important role in the bioremediation of MD. The effect of the type of substrate on the microbial community was also investigated in pilot-scale SR-PRZs treating the MD. Lignocellulose-based SR-PRZs contained a more diverse microbial community and higher bacterial density than ethanol-fed SR-PRZs, as determined by 16S rRNA gene cloning and quantitative polymerase chain reaction (Q-PCR). A new biomolecular approach was developed to target genetic markers of the functions of interest (functional genes): cellulose degradation, fermentation, sulfate reduction, and methanogenesis. This approach provided a more efficient and direct means of studying microbial functions. The functional gene-based approach was adapted to denaturing gradient gel electrophoresis and Q-PCR and applied to study the microbial communities in laboratory columns simulating SR-PRZs during the initial and pseudo-steady-state operation. Although the microbial communities in the different treatments were different during pseudo-steady-state operation, performance of the columns was comparable in terms of sulfate and metal removal and pH neutralization. This suggests that various microbial compositions can lead to successful MD remediation. The studies presented in this dissertation provide significant insight in the microbial communities involved in MD remediation at laboratory and pilot scale. In addition, a variety of biomolecular methods are presented that can be applied to explore different aspects of the microbial community not only in SR-PRZs and but also in other systems with complex microbial communities. Integration of biomolecular and performance data will provide a more complete understanding of SR-PRZ function that could be used to improve SR-PRZ performance and reliability.Item Open Access Development and application of microbial community profiling techniques for mine drainage bioremediation(Colorado State University. Libraries, 2008) Hiibel, Sage Royal, author; Reardon, Kenneth F., advisor; Pruden, Amy, advisorAcid mine drainage (AMD), characterized by elevated levels of sulfate, acidity, and metals, is produced by the oxidation of mining-exposed minerals and is a major environmental issue. Sulfate-reducing bioreactors (SRBRs) are an attractive AMD treatment option. SRBRs contain an organic material, usually wood chips or compost, which provides a slow-release carbon substrate to support a complex anaerobic microbial community. A relationship between the microbial inoculum and bioremediation performance was established in laboratory experiments. The use of 16S rDNA-based profiling techniques established a correlation between SRBRs that performed well and the presence of three key functional groups: cellulose degraders, fermenters, and sulfate-reducing bacteria (SRB). Subsequent analyses of pilot- and field-scale SRBRs targeted the 16S gene and apsA functional gene, which is found in all SRB. Although multivariate statistical analyses of the 16S sequences of the communities did not reveal obvious differences, the apsA sequences of each SRBR were significantly different. The apsA sequences also revealed that Thiobacillus spp., which are capable of sulfur oxidation, were prevalent at the poorly performing SRBR. A novel, high throughput, biomolecular method called active community profiling (ACP) was developed and validated using model systems. ACP identifies the active members of mixed communities through the ratio of rRNA to rDNA, which is proportional to growth rate. When coupled with physiochemical analysis, ACP offers a powerful new tool to help understand microbial community dynamics. The effects of bioaugmentation and biostimulation on the community structure of AMD treatment systems were studied. Although all columns remediated AMD to a similar level, ACP analysis revealed that the active members of their communities were distinctive. It was determined that biostimulation or bioaugmentation at the top of the microbial carbon chain increased the active community diversity. This dissertation emphasizes the role of the microbial community associated with AMD remediation. Characterization of these communities with biomolecular tools at several scales has significantly advanced the understanding of the community's structure, function, and activity. The research approaches and methodologies developed have wide application, and provide unique and valuable contributions to the scientific knowledge of AMD treatment specifically, and to microbial ecology and bioremediation in general.Item Open Access Differential gene expression in Escherichia coli following exposure to non-thermal atmospheric-pressure plasma(Colorado State University. Libraries, 2008) Sharma, Ashish, author; Collins, George, advisor; Pruden, Amy, advisorPlasma decontamination provides a low temperature and non-toxic means of treating objects where heating and exposure to poisonous compounds is not acceptable especially in applications relating to medical devices and food packaging. The effects of various plasma constituents (UV photons, reactive species, charged particles etc.) acting independently and/or synergistically on bacteria at the biomolecular level is not well understood. High-density oligonucleotide microarrays were used to explore the differential gene expression of the entire genome of E. coli following plasma treatment. The results indicate a significant induction of genes involved in DNA repair and recombination suggesting that plasma exposure caused substantial DNA damage in the cell. There was also evidence of oxidative stress and suppression of genes involved in housekeeping functions of energy metabolism and ion transport. Experiments were also carried out to optimize plasma operating parameters to achieve a higher rate of inactivation of microbes. Overall, the results of this study will help to further optimize non-thermal plasma applications for bacterial inactivation.Item Open Access Remediation of arsenic and persistent organic contaminants using enhanced in-situ methods(Colorado State University. Libraries, 2008) Sullivan, Mary Elizabeth, author; Carlson, Kenneth, advisor; Pruden, Amy, advisorThe demand for inexpensive and reliable water treatment technologies continues to increase as the number of contaminants grows and their associated fate and transport mechanisms become more complex. Advances in public health have contributed to the implementation of more stringent drinking water standards for compounds such as arsenic. Furthermore, advances in analytical chemistry have contributed to the detection of previously immeasurable compounds including endocrine-disrupting compounds (EDCs), pharmaceuticals and personal care products (PPCPs), and other bioactive chemicals in wastewater effluents and surface waters around the world. This research examined the use of enhanced in-situ methods for the remediation of arsenic and several persistent organic contaminants. Unamended and amended electrokinetic remediation (ER) column studies conducted to determine the impact on arsenic revealed arsenic removal from the soil column due to the electrolysis of water and electromigration of the charged species. Column studies also examined the impact of amended aquifer recharge and recovery (ARR) treatment on persistent organic compounds. Water treatment residual-amended ARR columns were utilized to promote an environment capable of reducing flame retardants. The results indicated that the presence of water treatment residuals created a reducing environment and provided ideal adsorption sites and sources of organic matter in the form of leached carbon. Unamended and amended ER column studies were completed to examine the impact on two pharmaceuticals (sulfamethoxazole and carbamazepine) and three organophosphorus flame retardants (tris-(2-chloroethyl) phosphate, tris-(2-chloro-, 1-methylethyl)phosphate, and tris-(2-chloro-, 1-chloromethyl-ethylphophate). Results indicated that the highest removal results occurred in the significant redox zones of the ER column. Oxidizing conditions at the anode and reducing conditions at the cathode had significant impacts on the compounds' concentrations in the column's pore water. Lastly, critical characterization of the compounds' affinity for aqueous, colloidal, and solid phases was determined for the five organic compounds. These results, as well as sources of flame retardant contamination in the experimental design, was useful (and necessary) in interpreting the treatment results from the amended ARR and electrokinetic column studies.