Thesis (Ph. D.)--Washington State University, December 2007. / Includes bibliographical references (p. 127-140).

Enzymes play an important role in the environment, they breakdown natural-occurring and anthropogenic molecules so that they can be transported into cells and utilized. Enzyme assays are routinely used in soil science and oceanography to measure the activities of specific processes and to serve as general indicators of microbial activity. Conventional enzyme assays are conducted as batch incubation of sediment and water samples. During these assays the concentration of product is measured and enzyme activity is then determined as the rate of product formation. Few studies have measured enzyme activities of groundwater. This work investigates the use of β-glucosidase and phosphatase assays for quantifying in situ enzyme activities in groundwater. Improvements to conventional enzyme assays using p-nitrophenyl substituted compounds were made by developing a high performance liquid chromatography method to improve quantitation limits of the product and to quantify concentrations of both the substrate and the product. An in situ single-well push pull test was then conducted to measure β-glucosidase activity in situ and to estimate the Michaelis constant (K[subscript m]) and the maximum reaction velocity (V[subscript max]) in petroleum-contaminated groundwater at a field site near Newberg, Oregon. An important feature of the single-well push pull test is the nonlinear drop in pore water velocity that the test solution experiences as it moves out from the injection point. The nonlinear drop in pore water velocity is of particular interest because enzyme-mediated reactions are very fast and changes in the hydraulic properties during the test may give rise to mass-transport limitations. Fast reactions lead to the simultaneous depletion of substrate and accumulation of product at the site of the reaction so substrate and product concentrations near the enzyme can be different then the concentrations in bulk solution. And the rates obtained from a single-well push pull tests may be a combination of the rates at which substrate diffuses to the microorganism and at which the reaction occurs. Laboratory experiments with sediment-packed columns were conducted with a range of pore water velocities typically achieved in the subsurface during as push-pull test as a means for examining the potential effects of inhibition and diffusion on phosphatase enzyme kinetics. In this set of column experiments rates of phosphatase-mediated reactions were investigated instead of β-glucosidase, which is an inducible enzyme. Numerical investigations were then conducted to examine the importance of diffusion limitations for describing the influence of transport processes on the observed rates of reaction. The theoretical investigation was conducted by formally upscaling the proposed sub-pore-scale processes to develop a macroscale (or Darcy scale) description of the transport of the substrate. These results indicate that mass-transfer limitations due to the diffusion of the substrate to the enzyme cause an increase in the apparent K[subscript m] but have no effect on V[subscript max]. In this study an analytical method was developed to measure rates of enzyme-mediated reaction in situ so that the measured rates reflected actual rates of microorganism in their natural environment. More carefully controlled laboratory experiments demonstrated that rates of enzyme-mediated reactions measured at low substrate concentrations depended on the flow properties of the test solution. / Graduation date: 2006

Thesis (M.S.)--Indiana University, 2007. / Title from screen (viewed on Apr. 27, 2007) Department of Earth Science, Indiana University-Purdue University Indianapolis (IUPUI) Includes vita. Includes bibliographical references.

Thesis (M.S.)--University of Wisconsin--Madison, 1982. / Typescript. Title from title screen (viewed Mar. 21, 2007). Includes bibliographical references (leaves 162-165). Online version of the print original.

Thesis (Ph. D.)--University of Rhode Island, 2005. / Typescript. Includes bibliographical references (leaves 130-159).

Ph.D. / Environmental Science and Engineering / In the past decade, permeable reactive barriers containing zero-valent iron metal (FePRBs) have emerged as the most significant new technology for the treatment of groundwaters contaminated with chlorinated organic compounds and, more recently, other organic contaminants such as 2,4,6-trinitrotoluene (TNT). Principle issues relating to the design, implementation, and monitoring of FePRBs include the rates of contaminant transformation, the resulting distribution of products, and the potential changes in FePRB performance due to aging of the iron material. Each of these issues is, at its root, a problem of chemical kinetics. In this thesis, commonly observed kinetic expressions for contaminant transformation are derived. Analyses of the simplifications involved in these derivations indicate that the forms of the rate laws are correct (either exactly or approximately) over a wider range of conditions than previously expected and that reaction rates may respond in unexpected fashion to changes in concentrations of reacting species or iron loading. These theoretical developments are applied to experimental investigations of product distribution and FePRB longevity for the treatment of TNT contaminated groundwaters.

As an intern with URS Corporation, I participated in several remediation and wastewater treatment projects during the year 2004. A groundwater remediation project was selected to present in this record of study for my Doctor of Engineering degree not only because I spent more time on it than any other project, but also because it represents the broadness and depth of a typical URS remediation project. In this report, findings from previous environmental investigations were summarized and used for computer modeling and remediation strategy evaluation. Computer models were used to simulate site conditions and assist in remedy design for the site. Current pump-and-treat systems were evaluated by the model under various scenarios. Recommendations were made for the pump-and-treat system to control the contaminant plume. Various remediation technologies were evaluated and compared for their applicability at the site. A combination of on-site remediation and downgradient plume control was chosen as the site remediation strategy. Treatability studies and additional modeling work are needed for the remediation system design and optimization.

Investigation into the effects of beaver dams on hyporheic exchange in peat dominated mountainous streams is needed to better understand stream-floodplain connections and improve our overall conceptual model of water storage and flow through riverine valleys. The objective of this study was to determine the influence of instream beaver dams on vertical and lateral hyporheic exchanges. Hyporheic interactions were examined using hydrometric methods to determine both flow pathways and water fluxes for a second-order stream draining a Canadian Rocky Mountain peatland. Investigation was conducted on two instream beaver dams and an undammed reference section for the ice free periods of summers 2006 and 2007 at the Sibbald Reseach Basin located in Kananaskis Country, Alberta, Canada. Lateral hyporheic fluxes dominated over vertical hyporheic fluxes, due to a layer with low saturated hydraulic conductivity (K &sim 10⁻⁷ 10⁻⁹ m/s) just below the streambed throughout most of the study reach. The lateral flow around the north dam (> 0.6 m high) resulted in fluxes that ranged from 0.002 to 0.015 L/s in the near bank environment. These results confirm that hydraulic properties of the substrata are an important factor in the development of hyporheic exchange in stream systems draining peatlands. Results also demonstrate the ability of beaver to connect valley floors to their streams, which maintains seasonally stable water tables and wetland conditions in the riparian zone.

Anaerobic ammonium-oxidizing (anammox) bacteria perform an important step in the global nitrogen cycle: oxidizing ammonium and reducing nitrite to form dinitrogen gas in the absence of oxygen. Anammox bacteria from the Planctomycetes phylum have been identified in a variety of natural environments but their role in groundwater ammonium oxidation has been unclear. Recent isotope studies have suggested that anammox bacteria are likely active in ammonium attenuation at contaminated groundwater sites; however, only limited biomarker-based data confirmed their presence prior to this study. I used complimentary molecular and isotope-based methods to assess the communities of anammox performing organisms at three ammonium contaminated groundwater sites in Canada: quantitative real-time PCR (qPCR), denaturing gradient gel electrophoresis (DGGE), DNA sequencing of 16S rRNA genes (with both Sanger and Illumina technologies), and ¹⁵N-tracer incubations. DNA sequencing and qPCR results demonstrated that anammox performing organisms were present at all three contaminated sites, and that they were among the dominant bacterial community members for at least one particular site (Zorra, Ontario). In addition, anammox bacterial diversity was variable. One site possessed four of five known genera of anammox performing organisms although the dominant anammox bacteria at all sites belonged to the Candidatus Brocadia genus. Isotope data from two groundwater sites showed that denitrification and anammox occurred jointly and although denitrification was the dominant process, anammox was responsible for maxima of 18 and 36% of N₂ production at these sites. By combining molecular and isotopic results I have demonstrated the diversity, abundance and activity of these anaerobic chemolithoautotrophic bacteria; these results provide strong evidence for their important biogeochemical role in attenuating groundwater ammonium contamination.

Investigation into the effects of beaver dams on hyporheic exchange in peat dominated mountainous streams is needed to better understand stream-floodplain connections and improve our overall conceptual model of water storage and flow through riverine valleys. The objective of this study was to determine the influence of instream beaver dams on vertical and lateral hyporheic exchanges. Hyporheic interactions were examined using hydrometric methods to determine both flow pathways and water fluxes for a second-order stream draining a Canadian Rocky Mountain peatland. Investigation was conducted on two instream beaver dams and an undammed reference section for the ice free periods of summers 2006 and 2007 at the Sibbald Reseach Basin located in Kananaskis Country, Alberta, Canada. Lateral hyporheic fluxes dominated over vertical hyporheic fluxes, due to a layer with low saturated hydraulic conductivity (K &sim 10⁻⁷ 10⁻⁹ m/s) just below the streambed throughout most of the study reach. The lateral flow around the north dam (> 0.6 m high) resulted in fluxes that ranged from 0.002 to 0.015 L/s in the near bank environment. These results confirm that hydraulic properties of the substrata are an important factor in the development of hyporheic exchange in stream systems draining peatlands. Results also demonstrate the ability of beaver to connect valley floors to their streams, which maintains seasonally stable water tables and wetland conditions in the riparian zone.