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<p>This study explores the seasonal dynamics of soil CO₂ efflux (Rs) in a temperate pine plantation forest located in Southern Ontario, Canada. Rs was continuously measured from June 15, 2008 to December 31, 2010 at this site using an automated soil CO₂ chamber system. Component analysis of Rs conducted by making continuous measurements in a trenched plot where live roots were excised indicated that heterotrophic respiration (Rh) contributed approximately 72 and 80% (895 and 920 g C m^-2 year^-1) of annual Rs in 2009 and 2010, respectively. Similarly, continuous Rs measurement in a litterless plot where the surface litter layer was removed contributed 65 and 57% (800 and 655 g C m^-2 year^-1) of annual Rs in 2009 and 2010, respectively. Results of this study suggested that overall soil temperature was the dominant control on Rs in this forest, except during the severe dry conditions.</p> <p>In order to explore the impact of soil water limitations on Rs a through-fall exclusion experiment conducted from April 1 to July 3, 2009 - the spring and early summer season. Through-fall exclusion caused a large reduction in daily Rs. This experiment further suggested that Rs became less sensitive to temperature and increasingly more sensitive to water as soil water content depleted due to the through-fall exclusion. This study helps to better understand the seasonal dynamics of Rs, and its components and controls in temperate conifer forests in Eastern North America. These forests are considered a large sink of carbon, and changes in Rs dynamics in this region may have implications for the global carbon cycle.</p> / Master of Science (MSc)

Municipal water suppliers are increasingly faced with implementing programs to address temporary water shortages in the United States. Having reliable estimates for the effectiveness of these programs will help in water supply planning. This dissertation estimates the reductions in residential water-use for voluntary and mandatory water-use restrictions used in Virginia during the 2002 drought. These restrictions were evaluated using both a conventional approach (single-dummy variable for each) and non-conventional approach where program intensity was accounted for. Program intensity was measured by information dissemination for voluntary restrictions, and by information dissemination and enforcement efforts for mandatory restrictions. An unbalanced panel with data from 21 municipal water suppliers was used in the analysis. Under the conventional approach, voluntary restrictions had no significant effect on water-use and mandatory restrictions showed a small to moderate effect. However, program intensity was found to have a significant influence on the magnitude of the water-use reductions in the non-conventional approach. These reductions ranged from 0-7% for voluntary restrictions, and from 0-22% for mandatory restrictions. Moreover, these reductions followed a pattern of increasing program effectiveness with higher levels of information and enforcement. This result indicates that water supply planners need to give considerable attention to the manner in which drought management programs are implemented. Price was also found to have an important effect on residential water-use. A moderate price increase of $3 per 1000 gallons would be expected to reduce water-use by almost 15%. Thus combining mandatory restrictions (implemented at high intensity) with a moderate to high price increase could result in water-use savings approaching 40% based on estimates from this analysis. Other important findings included: a) consumers were responding to a mix of pure marginal price and fixed fees/previous block rates, b) apartment accounts were found to be included in most of the localities residential data and had a significant impact on water-use, and c) the income parameter was measuring more than a pure income effect. / Ph. D.

Mark-recapture studies sample unevenly over distance and generate biased or distance-weighted movement data, where short distances are sampled more frequently than long distances. I examined how study design affects the degree of distance-weighted sampling and observed movement distributions of stream fish. A modeling study illustrated how distance-weighting increases with the number of mark sites and decreases with the length of stream sampled during recapture. Sub-sampled empirical data sets indicated that longer movements can be detected by increasing the length of the recapture section and that a substantial proportion of fish may move long distances outside of study areas. I also examined factors that were associated with movement in a network of streams. The probability of emigrating from a site was positively related to intermittency and body size and negatively related to distance from the mainstem creek and habitat complexity. Movement rates, measured as the number of fish moving upstream through a trap per day, were positively related to increases in flow, daylength, and water temperature. Distance moved was greater for fish that were initially marked within intermittent reaches. Overall, some species moved in association with several of these factors but others did not respond to any factors. Finally, I identified species-level attributes that were associated with colonization rates after experimental defaunation. Movement rate and abundance explained the most interspecific variation in colonization rates when compared to competing predictors (spatial distribution, body size, and family). Recovery occurred slowly and several species had not restored more than half of their pre-defaunation abundance within a year. Despite slow recovery for some species, defaunation had only a short-term (i.e., < 3 months) effect on relative abundance patterns. This study has important implications for conservation. Improvements in study design will allow detection of longer movements that may be a key component of species invasions, demographic rescue, and colonization. Species that move in association with multiple factors may be better colonists than species that do not. Finally, species that are rare and less-mobile will recover their populations slowly and will be vulnerable to extirpation in systems impacted by frequent pulse disturbances. / Ph. D.

The focus of the work has been on computational approaches to solving biological problems. First, microarray analysis was used to study the role of PLDα1 in drought stress in Arabidopsis. Second, a tool for designing and in-silico testing of primers for PCR-based pathogen detection will be discussed. Phospholipase D (PLD) has been implicated in a variety of stresses including osmotic stress and wounding. PLDα 1-derived phosphatidic acid interacts with ABI1 phosphatase 2C and promotes abscisic acid signaling. Plants with abrogated PLDα 1 show insensitivity to ABA and impaired stomatal conductance. My goal is to identify PLDα-mediated downstream events in response to progressive drought stress in Arabidopsis. <i>Arabidopsis thaliana</i> (Col-0) and antisense-PLDα 1 (Anti-PLDα) were drought stressed by withholding water. Anti-PLDα experienced severe water stress at the same time period that Col-0 experienced less water stress. Diurnal leaf water potential (LWP) measurements showed that Anti-PLDα had lower LWP than Col-0 under drought stress conditions. qRT-PCR revealed up to 18-fold lower values for PLDα transcripts in stressed Anti-PLDα plants when compared to stressed Col-0. Microarray expression profiles revealed distinct gene expression patterns in Col-0 and Anti-PLDα. ROP8, PLDδ and lipid transfer proteins were among the differentially expressed genes between the two genotypes. Different microarray analyses methods (TM4 and Expresso) were also compared on two different data sets. The results obtained from Expresso analysis were more accurate when compared with quantitative RT-PCR data. Rapid diagnosis of disease-causing agents is extremely important since delayed diagnosis can result in disease spread and delayed prophylaxis. It is even more important in an era where disease-causing agents are used as bioterrorism agents. Rapid advances in sequencing technology have resulted in the sequencing of thousands of microorganisms in recent years. Availability of genomic sequences has made it possible to identify and characterize microorganisms at the molecular level. PCR-based detection is powerful for pathogen diagnostics since it is rapid and sensitive. We have developed a tool, PathPrime, that can design primers, computationally test them against target genes, and potential contaminant sequences, and identify a minimum set of primers that can unambiguously detect a given list of sequences. / Ph. D.

Reptile populations are in decline worldwide, with turtle species showing some of the largest drops in population. The bog turtle (Glyptemys muhlenbergii) is considered one of the rarest North American turtle species, and this rarity is made more severe by anthropogenic factors. The wetland habitats that are used by bog turtles contain seepage areas and soil saturation that are characteristic of specific types of wetlands, suggesting that bog turtle rarity may in part be attributed to narrow habitat requirements. In this dissertation, I have sought to spatially and temporally characterize the hydrology and soils of wetlands that are used by bog turtles in an effort to determine how these factors are related to the species' habitat requirements, movement, and activity. In Chapter 1, I evaluated hydrology over a continuous 28-month period using shallow groundwater wells in six wetland fens known to be used by bog turtles for breeding and six apparently similar, but unused, wetlands. The saturated surface area near wells was measured and correlated with depth to the water table. Overall, water tables remained high, with mean monthly depth to the water table for all 12 wetlands remaining > -35 cm (depth below surface datum is negative). Bog turtle breeding wetlands had significantly higher mean water tables and surface saturation than wetlands where no turtles were encountered, particularly during and after the two-year drought occurring in 2007 and 2008. Findings of Chapter 1 suggest that relatively small differences in water table hydrology can affect bog turtle biology and use of wetlands. Bog turtles access soils and move through them to thermoregulate, find cover, and hibernate. Most wetlands used by bog turtles are also grazed by livestock that can modify soil strength. In Chapter 2, I identified dominant soil series and sampled surface soils from wetlands used by bog turtles and similar, but unused, wetlands. Samples were analyzed for organic carbon content and particle size distribution. Organic carbon content was greater in areas that were always wet (10%) than temporarily wet areas (5%). Somewhat higher organic carbon contents were present in wetlands that were used by bog turtles (8.8%) than wetlands where turtles were never encountered (5.7%). Soil textures were sandy loams and silt loams on all the study wetlands. Based on measurements of soil strength made with a static cone penetrometer, bog turtles selected wetland locations with low-strength soils. The mean and variability of soil strength were no different between grazed and ungrazed areas. The physical qualities of surface soils in bog turtle wetlands are dependent on consistently high water tables. In Chapter 3, I described three field studies in which I deployed temperature loggers to measure and contrast ambient air and soil temperatures to turtle carapace temperatures during activity and hibernation. I used temperature signatures to evaluate the timing and cues of spring emergence and to recognize thermoregulatory activities during periods of turtle activity. Mean daily turtle temperatures (n=16 turtles) during the coldest portion of two winters ranged between 1.3°C and 6.1°C, with one turtle experiencing 14 continuous days at temperatures between -1°C and 0°C when ambient temperatures dipped below -10°C. Water tables remained within 10 cm below the soil surface throughout the winter, preventing freezing temperatures for shallow hibernating turtles. Soil temperatures at 10 cm depth were a primary cue for spring emergence. Daily mean summer turtle temperature (n=8) was 20.8°C. My findings indicated that the presence of water near the surface and the ability for turtles to submerge themselves in mud are important for thermoregulation. In Chapter 4, I used radio telemetry to evaluate bog turtle activity (distance moved / hour), linear range, and the pathways used for dispersal. I also investigated bog turtle activity during sampling periods with either wet or dry hydrology. Mixed model analysis indicated that turtles were much less active between 18:30 and 09:30 relative to the daytime and that turtles were most active during times when hydrology was categorized as wet during 2008 when moderate to severe drought was the dominant condition. Sex was not a factor in turtle activity. Bog turtle paths during large movements (≥ 80 m) were mostly contained to areas within 80 m of USGS 7.5â quadrangle mapped streams. Turtles made large movements more frequently during dry conditions. Results suggested that drying conditions can stimulate bog turtles to either remain inactive in sparsely available saturation or to move long distances to find wetter conditions. Future conservation efforts should focus on allowing safe dispersal among habitats by reducing obstructions and risks to travel near streams. I n chapter 5, I used GIS-derived data to compare land cover, stream order, topographic wetness index inverse, presence of hydric soils, and presence of National Wetland Indicator (NWI) wetlands on bog turtle occupied wetlands (n=50) to the same variables on apparently unoccupied (n=48) wetlands or random areas (n=74) along streams. Occupied areas differed from random areas in having near zero values of the topographic wetness index inverse (indicating areas with low slopes and large upstream drainage areas that are more prevalent in wet portions of the landscape), the presence of > 50% low vegetation typical of non-forested agricultural areas, and presence of 3rd order streams. I used significant regression coefficients to create a GIS layer of high quality bog turtle habitat over the landscape, and tested this layer with bog turtle field survey data collected in 2009 independently of model building data. The resulting model has the potential to quickly rule out large portions of the landscape as potential bog turtle habitat. Finally, in Chapter 6, I provided general recommendations for managing bog turtle habitats in Southwestern Virginia. Managing bog turtle wetlands must emphasize the maintenance of high water tables, while avoiding inundation. Maintaining connectivity among wetlands used by bog turtles is an important aspect to consider when developing bog turtle conservations plans associated with development and other land use changes. Educating landowners and enforcing existing wetland laws are imperative for effective bog turtle management in Southwestern Virginia. / Ph. D.