Thesis (Ph. D.)--Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2001. / "February, 2001." "Funding was provided by a grant from the National Science Foundation (OCE-9618729), the National Science Foundation Coastal Traineeship (DGE-9454129), and by an Environmental Protection Agency STAR Graduate Fellowship (U-914966-01-0)." Includes bibliographical references.

Thesis (M.S.)--Oregon State University, 2001. / Typescript (photocopy). Includes bibliographical references (leaves 53-57). Also available on the World Wide Web.

Thesis (M. Sc.)--York University, 1998. Graduate Programme in Geography. / Typescript. Includes bibliographical references (leaves 223-234). Also available on the Internet. MODE OF ACCESS via web browser by entering the following URL: http://wwwlib.umi.com/cr/yorku/fullcit?pMQ39210.

Thesis (Ph. D.)--Oregon State University, 2002. / Typescript (photocopy). Includes bibliographical references. Also available on the World Wide Web.

Bioremediation is currently one of the most popular methods for remediating soil and groundwater contaminated by organic compounds. However, it has been found that the availability of the target contaminant to the microbial populations capable of degrading the compound may serve as a limiting factor in many systems. Thus, there is interest in the use of solubilization agents for enhancing bioavailability of organic contaminants. The impact of hydroxypropyl-β-cyclodextrin (HPCD) on the biodegradation of polycyclic aromatic hydrocarbons (PAHs) was investigated in a batch study. Results showed that HPCD can significantly increase the apparent solubility of phenanthrene, which had a major impact on the biodegradation rate of phenanthrene. For example, in the presence of 10⁵ mg L⁻¹ HPCD, the substrate utilization rate increased 5.5 times and only 0.3% of the phenanthrene remained at the end of a 48-hour incubation. It strongly suggests that HPCD can significantly increase the bioavailability, and thereby enhance the biodegradation, of phenanthrene. Biodegradation is often of great importance for the transport, fate, and remediation of organic contaminants in the subsurface. When modeling biodegradation processes, it is usually assumed that the microbial population responsible for biodegradation is composed of a single species. However, this is unlikely to be true for many, if not most, field situations. The effect of multiple species of degraders on phenanthrene biodegradation and transport in a saturated soil (with a high phenanthrene sorption capacity) was evaluated with a series of miscible-displacement experiments. Breakthrough curves obtained for the non-sterile column experiment exhibited oscillations in microbial populations as well as in oxygen and phenanthrene concentrations during the 6 months of continuous injection of a constant-concentration phenanthrene solution. This behavior is due to the response of the heterogeneous bacterial population (24 species) to substrates and oxygen availability, wherein population dynamics is hypothesized to be mediated by competition and other multi-species interactions. The dynamics of heterogeneous microbial populations, especially under growth conditions, should be considered when evaluating contaminant biodegradation and transport in natural subsurface systems.

Since industrialization atmospheric CO₂ concentrations have increased from 280 to 365 ppmv and δ¹³Cₐᵢᵣ has decreased from -6.5 to -8.2‰. These two trends have consequences for plant physiology. I examine δ¹³C plant and physiological parameters in herbarium specimens of Atriplex confertifolia, Atriplex canescens, Ephedra viridis, Pinus edulis, Pinus flexilis , Juniperus scopulorum, and Quercus turbinella. For all species, I found relatively high and unsystematic variability. δ¹³C values for A. confertifolia and A. canescens varied by up to 7.9 and 9.5‰ respectively; δ¹³C values of these C₄ shrubs are unsuitable for reconstructing δ¹³Cₐᵢᵣ, as previously claimed. δ¹³C(plant) generally becomes more depleted except in P. edulis. Other calculated parameters such as Δ, Cᵢ/Cₐ, Cᵢ, and A/g have varying responses even among similar functional groups. Because much of the isotopic variability caused by interplant, intertree, intersite, and interannual differences is implicit, herbarium specimens are inadequate for precise detection of direct CO₂ effects on plant physiology.

Trichloroethylene (TCE) contamination of soil and groundwater is extensive in Canada and the U.S. Under saturated soil conditions, TCE partitions with the organic fraction of soil and under anaerobic conditions is subject to biodegradation to dichloroethylene (DCE) isomers and vinyl chloride (VC). However, biodegradation is slow, and TCE often persists with accumulation of the DCE isomers and VC. The objective of the present study was to determine the effect of soil organic matter (SOM) on the fate of TCE in a saturated soil environment under anaerobic conditions. In natural soil, the presence of inorganic minerals as well as indigenous microorganisms greatly complicates the study of the concurrent processes of sorption and anaerobic biodegradation. To overcome such difficulties, a surrogate soil organic matter (SSOM) was used in conjunction with the pure strain Desulfomonile tiedjei to determine the effects of sorption and desorption on the anaerobic biodegradation of TCE. Composted sphagnum moss, sterilized so as to eliminate indigenous microbial activity, was implemented as a SSOM since it is representative of natural SOM. Desulfomonile tiedjei was utilized as a model of anaerobic consortia that exist in soil since it is a well studied microorganism. Results of the present study indicate that as the initial contact time ( i.e. aging) between the TCE and SSOM increases, TCE becomes increasingly resistant to biodegradation. The extent of biodegradation declined by 75% when the SSOM was aged with TCE for 30 d. This decline was attributed to TCE partitioning with SSOM and possibly due to complexation with dissolved organic matter (DOM). Results of this study indicate that soils contaminated with TCE for prolonged time periods may be less amenable to bioremediation efforts. Resistance of TCE to biodegradation was not paralleled by resistance to desorption for the 30 d aging that was studied. Results of longer term biodegradation tests (i.e. incubation times of up t

<p> In this study, the Weather Research and Forecasting Model (WRF) is coupled with the Advanced Canopy-Atmosphere-Soil Algorithm (ACASA), a high complexity land surface model (LSM). Although WRF is a state-of-the-art regional atmospheric model with high spatial and temporal resolutions, the land surface schemes available in WRF are simple and lack the capability to simulate carbon dioxide, for example, the popular NOAH LSM. ACASA is a complex multilayer land surface model with interactive canopy physiology and full surface hydrological processes. It allows microenvironmental variables such as air and surface temperatures, wind speed, humidity, and carbon dioxide concentration to vary vertically. </p><p> Simulations of surface conditions as well as reference and actual evapotranspiration from WRF-ACASA and WRF-NOAH are compared with surface observations for year 2005 and 2006. Results show that the increase in complexity in the WRF-ACASA model not only maintains model accuracy, it also properly accounts for the dominant biological and physical processes describing ecosystem-atmosphere interactions that are scientifically valuable. The different complexities of physical and physiological processes in the WRF-ACASA and WRF-NOAH models also highlight the impacts of different land surface and model components on atmospheric and surface conditions. </p><p> Lastly, unlike the simple big-leaf WRF-NOAH model with no carbon dioxide simulation, the high complexity WRF-ACASA model is used to quantify the carbon dioxide exchange between the biosphere and atmosphere and to examine the importance of atmospheric carbon dioxide concentration on surface processes on a regional scale. A new carbon dioxide (COCO₂) tracer is introduced into the WRF-ACASA coupled model to allow atmospheric CO₂ concentration to vary spatially and temporally according to surface plant physiological processes. The comparison between the two model simulations with and without a COCO₂ tracer shows that the impact of atmospheric COCO₂ concentration and transportation are important, and therefore these should not be neglected when simulating COCO₂ flux at regional scales. Overall, this study shows that the high complexity WRF-ACASA model is robust and able to simulate the surface conditions and COCO₂ fluxes well across the region, particularly when given accurate surface representations. </p>

Redox measurements were used to study whether different mitigation options affect methane emission and production by altering the electrochemical environment in rice paddy soil. These mitigation options include field drainage, use of different cultivars, and changing soil texture. Results indicate that the redox potential (Eh) is an accurate indicator of whether or not methane is produced. Also, the timing of methane production and emission was found to be dependent upon the reduction of iron and subsequent increase of the ferrous ion concentration. Field drainage is a mitigation option that successfully lowers methane emission rates by increasing the Eh. By studying the other mitigation options, it was found that once sufficiently negative Eh values are reached, different non-redox parameters control the actual amount of methane emitted.

Exocytosis in Saccharomyces cerevisiae requires the specific interaction between the plasma membrane t-SNARE complex (Sso1/2p;Sec9p) and a vesicular v-SNARE (Snc1/2p). While SNARE proteins drive membrane fusion in the secretory pathway, many aspects of SNARE assembly and regulation are ill defined. I examined the yeast regulatory protein, Sec1p, and its function in exocytosis. I show that the majority of Sec1p localizes to the plasma membrane, even though it is predicted to be a soluble protein. Furthermore, a significant portion of Sec1p colocalizes with Sso1, but is enriched in the bud neck. Sec1p binds to the t-SNARE complex and directly stimulates membrane fusion in vitro. I have also examined several defined structural regions of the yeast plasma membrane t-SNARE component Sso1p for their effect on membrane fusion in vivo and in vitro. To analyze the role of the N-terminal regulatory domain in Sso1p, I generated a chimeric protein that physically links the two separate proteins of the yeast plasma membrane t-SNARE complex, namely a truncated Sec9p and Sso1p. With this chimera, I have shown that the required function of the N-terminal regulatory domain Sso1p can be circumvented when t-SNARE complex formation is made intramolecular, suggesting the N-terminal regulatory domain is required for efficient t-SNARE complex formation and does not recruit necessary scaffolding factors. Next, I used targeted sequence modification, including insertions and replacements, in a conserved, highly charged juxtamembrane region between the transmembrane helix and the core coiled-coil domain of Sso1p. The effects of the modifications were examined both in vitro and in vivo. I found that mutant Sso1 proteins with insertions or duplications show limited function in vivo, whereas replacement of as few as three amino acids preceding the transmembrane domain results in a non-functional SNARE in vivo. Viability is also maintained when two proline residues are inserted in the juxtamembrane of Sso1p, suggesting helical continuity between the transmembrane domain and the core coiled-coil domain is not essential. Analysis of these mutations in vitro utilizing a reconstituted fusion assay illustrate that the mutant Sso1 proteins are only moderately impaired in fusion. These results suggest that the sequence of the juxtamembrane region of Sso1p is vital for function in vivo, independent of the ability of these proteins to direct membrane fusion.