Thesis (Ph. D.)--University of Wisconsin--Madison, 1981. / Typescript. Vita. Includes bibliographical references (leaves 235-255).

Thesis (Ph. D.)--Civil & Environmental Engineering, Georgia Institute of Technology, 2006. / Pennell, Kurt, Committee Chair ; Lawrence Bottomley, Committee Member ; James Mulholland, Committee Member ; Carolyn Ruppel, Committee Member ; D. Webster, Committee Member. Includes bibliographical references.

Thesis (Ph. D.)--University of Toronto, 2004. / Includes bibliographical references.

Graduation date: 2000

Thesis (M. Sc.), Memorial University of Newfoundland, 1998. / Bibliography: leaves p.88-92.

Graduation date: 2005

The goal of this research was to mathematically simulate the ability of bioaugmented microorganisms to aerobically cometabolize a mixture of chlorinated aliphatic hydrocarbon (CAH) compounds during in-situ treatment. Parameter values measured from laboratory experiments were applied to the transport model with biotransformation processes included. In laboratory microcosm studies, a butane-grown, enriched culture was inoculated in soil and groundwater microcosms and exposed to butane and several repeated additions of 1,1,1-trichloroethane (TCA), 1,1-dichioroethylene (DCE), and 1,1-dichloroethane (DCA) at aqueous concentrations of 200 ��g/L, 100 ��g/L, and 200 ��g/L, respectively. Microcosms containing the bioaugmented culture showed 1,1-DCE to be rapidly transformed, followed by slower transformation of 1,1-DCA and 1,1,1-TCA. After most of the butane had been consumed, transformation of these latter CAHs increased, indicating strong inhibition by butane. With repeat biostimulations, butane utilization and CAH transformation accelerated, showing the increase in cell mass. These trends occurred in two sets of microcosm triplicates. No stimulation was observed in controls containing only the microorganisms indigenous to Moffett Field, confirming that activity seen in the bioaugmented microcosms was a result of the introduced culture's activity. Batch reactor results were simulated using differential equations accounting for Michaelis-Menten kinetics, transformation product toxicity, substrate inhibition, butane utilization, and CAH transformation. The equations were solved simultaneously by Runge-Kutta numerical integration with parameter values adjusted to match the microcosm data. Having defined the parameter values from laboratory studies, the biotransformation model was combined with 1-D advective-dispersive transport to simulate behavior of the culture and the substrates within an aquifer. The model was used to simulate the results of field studies where the butane-utilizing culture was injected into a 7 m subsurface test site and exposed to alternating pulses of oxygen and butane, along with the contaminant mixture studied in the microcosms. Monitoring wells spaced at 1 m, 2.2 m, and 4 m from the injection well allowed temporal and spatial changes in substrate concentrations to be determined. Model simulations of the field demonstration were performed to determine how well the biotransformation/solute transport model predicted actual field observations. To model the influences of solute transport, simulations were run and compared to breakthrough test data (prior to bioaugmentation) to determine the values for advection, dispersion, and sorption. The simulations showed that flow ranged from 1.0 to 1.5 m��/day (average linear velocity of 2.0 m/day). Dispersion was estimated as 0.31 m��/day. Sediment sorption partitioning coefficients for 1,1-DCE, 1,1-DCA, and 1,1,1-TCA were determined to be approximately 0.69, 0.50, and 0.50 L/kg, respectively. It was more difficult to determine an appropriate value of the mass transfer rate coefficient for non-equilibrium sorption, so simulations were run to compare equilibrium and non-equilibrium cases. Results indicated that non-equilibrium (with mass transfer rate coefficient of approximately 0.2 day�����) better simulated the field data. Using these transport parameters and the biotransformation values determined from the laboratory experiments, simulations of the field data showed that the model was capable of simulating the effects of transformation rates, butane inhibition, and 1,1-DCE product toxicity. Simulations for varying pulsing cycles and durations provided possible improvements for future field demonstrations. Overall, this work proved that there is good potential in extrapolating laboratory based kinetics to simulate biotransformation at a field scale. Although the complexity of such systems makes modeling difficult, such simulations are useful in understanding and interpreting field data. / Graduation date: 2003

DDT, an extremely widely used organochlorine pesticide, was banned in most developed countries more than 30 years ago. However, DDT residues, including 1,1-dichloro-2,2-bis(4-chlorophenyl)ethylene (DDE), still persist in the environment and have been identified as priority pollutants due to their toxicity and their ability to bioaccumulate and biomagnify in the food chain. In particular, DDE was long believed to be &quotenon-biodegradable&quote, however some microorganisms have now been isolated that are able to metabolise DDE in pure culture. Terrabacter sp. strain DDE-1 was enriched from a DDT-contaminated agricultural soil from the Canterbury plains and is able to metabolise DDE to 4-chlorobenzoic acid when induced with biphenyl. The primary objective of this study was to identify the gene(s) responsible for Terrabacter sp. strain DDE-1�s ability to metabolise DDE and, in particular, to investigate the hypothesis that DDE-1 degrades DDE cometabolically via a biphenyl degradation pathway. Catabolism of biphenyl by strain DDE-1 was demonstrated, and a biphenyl degradation (bph) gene cluster containing bphDA1A2A3A4BCST genes was identified. The bphDA1A2A3A4BC genes are predicted to encode a biphenyl degradation upper pathway for the degradation of biphenyl to benzoate and cis-2-hydroxypenta-2,4-dienoate and the bphST genes are predicted to encode a two-component signal transduction system involved in regulation of biphenyl catabolism. The bph gene cluster was found to be located on a linear plasmid, designated pBPH1. A plasmid-cured strain (MJ-2) was unable to catabolise both biphenyl and DDE, supporting the hypothesis that strain DDE-1 degrades DDE cometabolically via the biphenyl degradation pathway. Furthermore, preliminary evidence from DDE overlayer agar plate assays suggested that Pseudomonas aeruginosa carrying the strain DDE-1 bphA1A2A3A4BC genes is able to catabolise DDE when grown in the presence of biphenyl. A second objective of this study was to characterise pBPH1. The complete 84,054-bp sequence of the plasmid was determined. Annotation of the DNA sequence data revealed seventy-six ORFs predicted to encode proteins, four pseudogenes, and ten gene fragments. Putative functions were assigned to forty-two of the ORF and pseudogenes. Besides biphenyl catabolism, the major functional classes of the predicted proteins were transposition, regulation, heavy metal transport/resistance, and plasmid maintenance and replication. It was shown that pBPH1 has the terminal structural features of an actinomycete invertron, including terminal proteins and terminal inverted repeats (TIRs). This is the first report detailing the nucleotide sequence and characterisation of a (linear) plasmid from the genus Terrabacter.

This study evaluated the potential of the aerobic Mycobacterium strain JS6O to grow on a variety of organic acid substrates, and the possible effects an organic acid would have on the degradation rate of vinyl chloride (VC). A series of batch growth tests were designed to determine the time it took to consume the substrate and the overall increase in biomass. Strain JS6O was found capable of growth on acetate, propionate, and butyrate, but could not grow on formate or lactate. Acetate was chosen for further study because strain JS6O consumed acetate the most rapidly of all the organic acids tested, and acetate is a common product of fermentation reactions in the subsurface. Strain JS6O was confirmed to grow on both ethylene and vinyl chloride as the sole carbon and energy source. Comparatively, strain JS6O's rate of growth on VC is much slower than that of ethylene. With acetate as an augmenting growth substrate, ethylene and VC utilization rates increased by 30% and 48%, respectively. Since acetate and VC are often found together in contaminated chlorinated ethene plumes, this makes a strong case for natural attenuation of VC by strain JS6O. A series of kinetic tests were implemented to determine the K[subscript s] and k[subscript max] of strain JS6O for ethylene, VC, and c-DCE. The K[subscript s] and k[subscript max] for ethylene determined through NLSR methods was similar to the values published in Coleman et al. (2002), supporting the maintenance of a pure culture throughout the experimental work. When strain JS6O was exposed to the isomers of DCE (trans-1,2-dichloroethylene (t-DCE), cis-1,2-dichloroethylene (c-DCE), and 1,1-dichloroethylene (1,1-DCE)) the cells were unable to grow on these compounds. However, when growing on acetate, strain JS6O cometabolized c-DCE and t-DCE, but not 1,1-DCE, with c-DCE transformed more rapidly than t-DCE. Transformation of c-DCE was also observed with growth on VC and ethylene. The presence of c-DCE was shown to partially inhibit VC degradation, but had no effect on ethylene degradation. The cometabolism results with acetate further indicate that strain JS6O is a good candidate for natural attenuation of multiple chlorinated ethenes in the subsurface. / Graduation date: 2006

DDT, an extremely widely used organochlorine pesticide, was banned in most developed countries more than 30 years ago. However, DDT residues, including 1,1-dichloro-2,2-bis(4-chlorophenyl)ethylene (DDE), still persist in the environment and have been identified as priority pollutants due to their toxicity and their ability to bioaccumulate and biomagnify in the food chain. In particular, DDE was long believed to be &quotenon-biodegradable&quote, however some microorganisms have now been isolated that are able to metabolise DDE in pure culture. Terrabacter sp. strain DDE-1 was enriched from a DDT-contaminated agricultural soil from the Canterbury plains and is able to metabolise DDE to 4-chlorobenzoic acid when induced with biphenyl. The primary objective of this study was to identify the gene(s) responsible for Terrabacter sp. strain DDE-1�s ability to metabolise DDE and, in particular, to investigate the hypothesis that DDE-1 degrades DDE cometabolically via a biphenyl degradation pathway. Catabolism of biphenyl by strain DDE-1 was demonstrated, and a biphenyl degradation (bph) gene cluster containing bphDA1A2A3A4BCST genes was identified. The bphDA1A2A3A4BC genes are predicted to encode a biphenyl degradation upper pathway for the degradation of biphenyl to benzoate and cis-2-hydroxypenta-2,4-dienoate and the bphST genes are predicted to encode a two-component signal transduction system involved in regulation of biphenyl catabolism. The bph gene cluster was found to be located on a linear plasmid, designated pBPH1. A plasmid-cured strain (MJ-2) was unable to catabolise both biphenyl and DDE, supporting the hypothesis that strain DDE-1 degrades DDE cometabolically via the biphenyl degradation pathway. Furthermore, preliminary evidence from DDE overlayer agar plate assays suggested that Pseudomonas aeruginosa carrying the strain DDE-1 bphA1A2A3A4BC genes is able to catabolise DDE when grown in the presence of biphenyl. A second objective of this study was to characterise pBPH1. The complete 84,054-bp sequence of the plasmid was determined. Annotation of the DNA sequence data revealed seventy-six ORFs predicted to encode proteins, four pseudogenes, and ten gene fragments. Putative functions were assigned to forty-two of the ORF and pseudogenes. Besides biphenyl catabolism, the major functional classes of the predicted proteins were transposition, regulation, heavy metal transport/resistance, and plasmid maintenance and replication. It was shown that pBPH1 has the terminal structural features of an actinomycete invertron, including terminal proteins and terminal inverted repeats (TIRs). This is the first report detailing the nucleotide sequence and characterisation of a (linear) plasmid from the genus Terrabacter.