Biostimulation is the use of in-situ microorganisms and added reagents in order to biosequester, precipitate, or absorb contaminants from contaminated groundwater and sediment. To test the effectiveness of this remediation approach at a particular site, small scale experiments, such as miscible-displacement, batch, or microcosm experiments, should be performed before a large-scale in-situ biosequestration electron donor injection. In this study, electron donor solutions containing contaminated groundwater and ethanol, acetate, benzoate, or glucose were injected into aquifer sediments collected from a UMTRCA Title 1 Site in Monument Valley, AZ. These experiments showed that ethanol, acetate, and glucose were effective electron donors for the stimulation of microbial activity in order to sequester uranium and reduce nitrate and sulfate concentrations. Conversely, benzoate was not effective at sequestering or reducing the contaminants. After electron-donor deficient groundwater was injected into the columns, a rebound of nitrate, sulfate, and uranium concentrations was observed. Due to this rebound, it was inferred that the mechanism of sequestration of uranium and hence reduction of nitrate and sulfate was due to the creation of reducing conditions via microbial activity. The insoluble reduced uranium was hypothesized to have precipitated or adsorbed to surrounding sediments. Incoming groundwater contained dissolved oxygen and therefore oxidized the reduced contaminants, consequently returning them into solution. It was hypothesized that a similar rebound would occur if ethanol, acetate, or glucose were to be injected in-situ due to sustained groundwater flow through the aquifer sediments on site.

This study evaluates the effects of nitrogen and phosphorus response in young (two- and three-year-old), non-bearing,'Western Schley' and 'Wichita' varieties of pecan (Carya illinoinensis (Wangenh.) C. Koch) grown in two orchards in San Simon, AZ. Using tree trunk diameter and rates of photosynthesis, transpiration, stomatal conductance, and transpiration as proxies for tree growth and positive response, and by analyzing foliar elemental concentrations of N and P, preliminary results suggest that 'Wichita' responds better than 'Western' to N and P fertilizer with respect to tree growth. Additions of nitrogen ranging from 5.6 kg N·ha⁻¹ to 35.9 kg N·ha⁻¹ increased foliar N concentration in 'Wichita', although there was no response to photosynthesis, stomatal conductance, intracellular CO₂, or transpiration. Additions of phosphorus fertilizer up to 112 kg·ha⁻¹ improved tree growth; and growth increased with increasing foliar P concentration.

Irrigation agriculture is the largest use of water (~80%) in the United States ('Irrigation and Water Use', 2016) A combination of irrigation and precipitation infiltrates through the Earth's subsurface and represents the primary inputs to an agricultural field's groundwater system. This water propagates down from the surface, with some of it recharging the underlying groundwater storage as return flow. The difference between the amount of irrigation water applied and the return flow to the aquifer, represents the consumptive use of the system. The alterations in the quality and distribution of water from groundwater pumping and irrigation places greater emphasis on the need to understand the connection between agricultural consumption and subsurface groundwater flux. Temperature fluctuations in the Earth's shallow subsurface are mainly governed by spatial and temporal variations in temperature at the ground surface (Hatch et al., 2006). These temperature signals at depth are primarily controlled by advection, dispersion, and thermal conduction. It has been shown for streambeds that when temperature propagates through the subsurface, it is a nonlinear function of fluid velocity, the frequency of the surface temperature variations, and the sediment and fluid thermal properties (Stallman, 1965). This information has been useful for understanding fluxes for saturated conditions such as in stream systems, but has not yet been applied to understand consumptive use in unsaturated conditions such as in agricultural systems. Temperature propagation in unsaturated conditions is different than saturated conditions due to changes in soil and thermal properties. Previous models have had difficulty estimating groundwater fluxes for some unsaturated conditions. This study experiments with the possibility of using a combination of MATLAB and HYDRUS 1D to infer unsaturated groundwater fluxes, saturated hydraulic conductivity, and saturated water content. One application of this type of flux estimation could be the inference of root water uptake and the consumptive use of an agricultural system. The method is designed to calculate root water uptake under steady-state conditions; and therefore might have limitations for quantifying consumptive use in field applications.It is beneficial to research the consumptive use in agricultural systems in order to gain understanding of the effects of irrigation on the total flux in groundwater storage. Other applications of consumptive use include: site specific farm efficiency and crop use parameters, nonpoint source pollution to estimate nutrient fluxes, irrigation efficiency, soil salinization, waste isolation, and slope stability.

The Nogales International Wastewater Treatment Plant releases treated wastewater from both Nogales, Arizona and Nogales, Sonora, Mexico into the Santa Cruz River. In recent years, the discharged effluent has contained high levels of cadmium and nickel, which exceed the plant's permit standards. Due to the industrial demographic of the region, outdated infrastructure, and differences in sampling schedules of multiple organizations, the treatment facility and the treated effluent is an important area of study. To understand how the treated effluent is affecting the river, data were compiled from existing water quality databases and flow reports from 2008 to 2015. To address how flow quantity has changed during drought periods, effluent flows were compared to historical flood data produced by the USGS. To evaluate water quality issues, water quality reports produced by the International Boundary and Water Commission were examined for past exceedances of constituents. According to flow volumes reported at the U.S.-Mexico border, the majority of the effluent was produced in Nogales, Sonora. Results showed that spikes in effluent flow corresponded with rainfall events. Results also show that rainfall influences the flow volumes from Nogales, Arizona, but there is little impact to flow volumes from Mexico. Although the quality of the effluent generally meets the permitted standards, exceedances did occur. The potential impact of such exceedances on stream water quality was evaluated using measured and simulated data. Although outreach to stakeholders across the border and updated infrastructure has improved the quality of water in the river, there are still many areas to improve upon, including sampling and monitoring schedules. To identify opportunities for improvement, further studies should examine the specific fate of each contaminant present in the effluent.

Canal maintenance, involving mechanical removal of sediments and algal growth from canal basins, is necessary for sustaining the viability of the irrigation water delivery system in the Imperial Valley of California. Maintenance activities, however, disturb canal sediments laden with bacteria and can negatively impact water quality downstream. Our work quantified fecal indicator bacteria (Escherichia coli) and pathogens (Salmonella) in canal water prior to, during, and post-maintenance events. The goal of this study was to construct a post-maintenance time matrix that will allow growers downstream to estimate when canal water once again meets water quality guidelines. In addition, we assessed the water quality impacts of lining canals with concrete, which is a costly endeavor in the short term, but may be beneficial in the long term as lined canals do not require routine dredging to maintain canal integrity. During eight maintenance events from March 2013 through August 2014, 22% of 396 water samples collected exceeded the irrigation water quality guidelines (<126 MPN E. coli 100 mL-1) during canal maintenance. During summer months (July and August 2013-2014), E. coli concentrations in water samples commonly reached maximum values (>2419.6 MPN E. coli 100 mL-1), and these samples were more readily collected from unlined canal sampling sites. During winter and spring months, 80.8% of E. coli exceedances for unlined canals met guideline standards in less than 22 hours, while 19.2% of exceedances took longer (up to 48 hours) to return to acceptable levels; in lined sites, 63.6% and 36.4% met guidelines in less than 22 hours and 48 hours, respectively. Summer months showed a different trend: in unlined canal sites, 56.3% of E. coli exceedances met standards within 22 hours and 43.7% within 48 hours; in lined sites, 100% of water samples met standards in less than 22 hours. Unlined sites averaged higher temperatures overall compared to lined sites, and canal water in July (2013) was extremely warm (averaging 32.8°C) and reached human body temperature (37°C) at several unlined sites, a temperature at which enteric bacteria are known to thrive. Culturable Salmonella were detected in water samples collected in summer, with 22.2% of Salmonella-positive samples within 1°C of human body temperature. E. coli concentrations were significantly correlated with temperature and pH in unlined canals only. Unlined canals showed 15.2% of water samples were Salmonella-positive during summer maintenance whereas 1.7% of lined canals were positive. Salmonella significantly correlated with pH in lined canals. Fecal indicators (E. coli) did not predict pathogen (Salmonella) presence. Molecular methods (qPCR) suggested far higher levels of Salmonella when compared to cultural methods, with molecular markers for Salmonella exceeding culturing by more than 600%. The results of this work suggest that growers should exercise caution when irrigating after canal maintenance events, and to be completely certain of acceptable irrigation water quality, should wait for 48 hours following the onset of maintenance (typically 24 hours following the re-introduction of water to the channels) prior to irrigating crops. Further, irrigation district guidelines may consider: 1) disposing of the“first flush”of canal water following maintenance into nearby open areas, rather than sending poor-quality water into the irrigation canal system; 2) collect sediments and algae deposited on canal banks and transport to a secondary location to prevent precipitation runoff and re-introduction of bacteria-laden sediments to canals, and 3) consider the long-term costs and benefits of canal lining.

The health of natural vegetation communities is of concern due to observed changes in the climatic-hydrological regime and land cover changes particularly in arid and semiarid regions. Monitoring vegetation at multi temporal and spatial scales can be the most informative approach for detecting change and inferring causal agents of change and remediation strategies. Riparian communities are tightly linked to annual stream hydrology, ground water elevations and sediment transport. These processes are subject to varying magnitudes of disturbance overtime and are candidates for multi-scale monitoring. My first research objective focused on the response of vegetation in the Upper San Pedro River, Arizona, to reduced base flows and climate change. I addressed the correlation between riparian vegetation and hydro-climate variables during the last three decades in one of the remaining undammed rivers in the southwestern U.S. Its riparian forest is threatened by the diminishing base flows, attributed by different studies either to increases in evapotranspiration (ET) due to conversion of grasslands to mesquite shrublands in the adjacent uplands, or to increased regional groundwater pumping to serve growing populations in surrounding urban areas and or to some interactions of those causes. Landsat 5 imagery was acquired for pre- monsoon period, when riparian trees had leafed out but before the arrival of summer monsoon rains in July. The result has showed Normalized Difference Vegetation Index (NDVI) values from both Landsat and Moderate Resolution Imaging Spectrometer (MODIS) had significant decreases which positively correlated to river flows, which decreased over the study period, and negatively correlated with air temperatures, which have increased by about 1.4°C from 1904 to the present. The predictions from other studies that decreased river flows could negatively impact the riparian forest were supported by this study. The pre-monsoon Normalized Different Vegetation Index (NDVI) average values in the adjacent uplands also decreased over thirty years and were correlated with the previous year's annual precipitation. Hence an increase in ET in the uplands did not appear to be responsible for the decrease in river flows in this study, leaving increased regional groundwater pumping as a feasible alternative explanation for decreased flows and deterioration of the riparian forest. The second research objective was to develop a new method of classification using very high-resolution aerial photo to map riparian vegetation at the species level in the Colorado River Ecosystem, Grand Canyon area, Arizona. Ground surveys have showed an obvious trend in which non-native saltcedar (Tamarix spp.) has replaced native vegetation over time. Our goal was to develop a quantitative mapping procedure to detect changes in vegetation as the ecosystem continues to respond to hydrological and climate changes. Vegetation mapping for the Colorado River Ecosystem needed an updated database map of the area covered by riparian vegetation and an indicator of species composition in the river corridor. The objective of this research was to generate a new riparian vegetation map at species level using a supervised image classification technique for the purpose of patch and landscape change detection. A new classification approach using multispectral images allowed us to successfully identify and map riparian species coverage the over whole Colorado River Ecosystem, Grand Canyon area. The new map was an improvement over the initial 2002 map since it reduced fragmentation from mixed riparian vegetation areas. The most dominant tree species in the study areas is saltcedar (Tamarix spp.). The overall accuracy is 93.48% and the kappa coefficient is 0.88. The reference initial inventory map was created using 2002 images to compare and detect changes through 2009. The third objective of my research focused on using multiplatform of remote sensing and ground calibration to estimate the effects of vegetation, land use patterns and water cycles. Climate change, hydrological and human uses are also leading to riparian, upland, grassland and crop vegetation changes at a variety of temporal and spatial scales, particularly in the arid and semi-arid ecosystems, which are more sensitive to changes in water availability than humid ecosystems. The objectives of these studies from the last three articles were to evaluate the effect of water balance on vegetation indices in different plant communities based on relevant spatial and temporal scales. The new methodology of estimating water requirements using remote sensing data and ground calibration with flux tower data has been successfully tested at a variety sites, a sparse desert shrub environment as well as mixed riparian and cropland systems and upland vegetation in the arid and semi-arid regions. The main finding form these studies is that vegetation-index methods have to be calibrated with ground data for each new ecosystem but once calibrated they can accurately scale ET over wide areas and long time spans.

Western riparian zones have undergone significant landscape changes over the past several decades, with introduced saltcedar (Tamarix spp.) as a crucial component of this transformation. Saltcedar, now a dominating presence along many western rivers, due to its high tolerance to drought, salinity and stress, is considered to be a high-water-use plant that can desiccate disturbed river systems. Where native and saltcedar plant communities occur together, it is important to understand water use patterns and the physiological responses of each species to environmental stress factors, as a way to project an eventual course of succession processes and management options at a given site. Stress and disturbance in the form of reduced stream flows and land use changes may influence these interactions. Understanding the conditions that allow for saltcedar dominance is critical in determining riparian water budgets, and developing effective management strategies. Sap flux sensors were used to measure the physiological response of co-occurring communities of saltcedar and native trees to these environmental stress factors during the pre-monsoon period in early summer, a time of maximum stress for riparian vegetation. The results suggest that native trees are still competitive with salt cedar so that a mixed plant community is likely to continue on the San Pedro River on the condition that current groundwater levels and river flows are maintained. If base flows and depth to groundwater continue to decline, this competitive balance between saltcedar and native trees likely could change.

Extensive coastal sabkhas in the northern Gulf of California in North America are colonized by Distichlis palmeri, an endemic perennial grass that produces a grain that was harvested as a staple food by native Cocopah people. Previous short-term trials have shown good vegetative growth but low grain yields. During outdoor trials under anaerobic saline soil conditions of paddy-style irrigation, D. palmeri exhibited high salt tolerance, grain and biomass production. Reproductive maturity was reached four years after initial establishment of plants from seed and a 1:3 mixture of male and female plants produced 231-310 g m⁻² of grain, with nutritional content similar to domesticated grains, confirming the feasibility of developing D. palmeri as a perennial grain and biomass crop for salinized soils and water supplies. Salicornia bigelovii Torr., a cosmopolitan annual coastal marsh succulent, produces seed with high oil content and has been suggested as a potential cash crop for fuel production from saline irrigation but its domestication and development into a cost effective commodity has been slow. A breeding and selection program for agronomic traits that will provide multiple landscape and ecosystem services that could enhance cost benefits of the agronomy of S. bigelovii was initiated during a two year period while producing seed for a pilot system at the Masdar Institute in Abu Dhabi, U.A.E. A concept for a saline landscape designed to consume and concentrate saline waste streams was developed and demonstrates the feasibility and potential to support agronomy of halophytes within a built landscape ecology akin to coastal marsh systems. Exploration and development of potential services halophytes could provide and field testing of selected halophytes for their potential to produce food, fuel, fiber and habitat under designed and managed domestication in our salinized soils with saline waste irrigation needs our continued investigation.

The phenomenon of plume persistence was observed for five federal Superfund sites by analysis of historical groundwater-withdrawal and contaminant-concentration data collected from long-term pump-and-treat operations. The potential factors contributing to plume persistence are generally recognized to include incomplete isolation of the source zone, permeability heterogeneity, well-field hydraulics, and non-ideal (rate-limited, nonlinear) desorption. However, the significance of each factor, especially the site-specific contribution is undetermined, which is very important for site development and management. One objective of this study is to quantify the impacts of different factors on mass-removal efficiency. Three-dimensional (3D) numerical models were used to simulate the impact of different well-field configurations on pump-and-treat mass removal. The relationship between reduction in contaminant mass discharge (CMDR) and mass removal (MR) was used as the metric to examine remediation efficiency. Results indicate that (1) even with effort to control the source, residual impact of source can still be a factor causing plume persistence, (2) the well-field configuration has a measurable impact on mass-removal efficiency, which can be muted by the influence of permeability heterogeneity, (3) in terms of permeability heterogeneity, both variance and correlation scale influence the overall mass-removal behavior, (4) the CMDR-MR relationship can be used to quantify the impacts of different factors on mass-removal efficiency at the plume scale. It has been recognized that the use of pump and treat for groundwater remediation will require many decades to attain site closure at most complex sites. Thus, monitored natural attenuation (MNA) and enhanced attenuation (EA) have been widely accepted as alternatives because of their lower cost and sustainable management for large, complex plumes. However, the planning and evaluation of MNA/EA applications require greater levels of characterization data than typically collected. Advanced, innovative methods are required to characterize specific attenuation processes and associated rates to evaluate the feasibility of MNA/EA. Contaminant elution and tracer (CET) tests have been proposed as one such advanced method. Another objective of this study is to investigate the use of modified well-field configurations to enhance the performance of CET tests to collect critical site-specific data that can be used to better delineate attenuation processes and quantify the associated rate coefficients. Three-dimensional numerical models were used to simulate the CET test with specific well-field configurations under different conditions. The results show that the CET test with a nested (two-couplet) well-field configuration can be used to characterize transport and attenuation processes by eliminating the impact of the surrounding plume. The results also show that applying select analytical mass-removal functions can be an efficient method for parameter estimation, as it does not require the use of mathematical transport modeling and does not require the attendant input data that are costly and time-consuming to obtain.

To protect public health, detection and treatment technologies have been improved to monitor and inactivate pathogens in drinking water. The goal of this dissertation is to evaluate and utilize multiple online sensors and advanced oxidation processes to document both the detection as well as destruction of microbial contaminants in real-time. Reviews of rapid detection technologies for real-time monitoring of pathogens in drinking water and advanced technologies to inactivate pathogens in water are shown in Appendices A and B. The study in Appendix C evaluated the efficacy of real-time sensors for the detection of microbial contaminants. Bacillus thuringiensis was used in this research as a surrogate for Bacillus anthracis to determine each sensor response and detection capability. The minimum threshold responses of sensors were determined by injecting B.thuringiensis into deionized (DI), raw (unfiltered) tap water, or filtered tap water over a concentration range of 10² - 10⁵ spores/ml. The BioSentry sensor responded to increases in concentration over the range of 10² - 10⁵ spores/ml. Below this range, sensors provided signals undistinguishable from background noise. The select sensors can detect microbial water quality changes, and these advanced technologies can be integrated to monitor intrusion events in water distribution systems. The study in Appendix D evaluated the efficiency of the UV reactor for inactivation of MS2 coliphage. The virus MS2 coliphage (ATCC 15597-B1) has been proposed by the U.S. Environmental Protection Agency as a standard for UV reactor validation in the United States. In addition, MS2 is used as a surrogate for enteric viruses due to its similar size and morphology. Following UV radiation at a flow rate of 2gpm, infective MS2 showed a reduction of 5.3- log₁₀ when quantified with cultural plaque counts, whereas corresponding quantitative polymerase chain reaction (qPCR) data showed only a 1.7- log₁₀ reduction in viral RNA copy number. In contrast, plaque assay revealed a 5.8- log₁₀ inactivation; a slight increase in infective MS2 coliphage reduction at 1 gal per min but qPCR results indicate a 2.8- log₁₀ reduction in viral RNA copy number; a one log more inactivation compared to 2 gpm. When H₂O₂ was added at either 2.5 or 5 mg/l with UV at either flow rate, enhanced MS2 inactivation occurred with a greater than 7 log₁₀ reduction observed via plaque counts, indicating that all added MS2 had been inactivated, since no plaques were formed after incubation at 37°C for 24 hours. Correspondingly, qPCR data only showed a 3-4 log₁₀ reduction in viral RNA copy number. The study in Appendix E utilized online sensor to document the destruction of E.coli and Bacillus thuringiensis spores by UV/H₂O₂ treatment. In this study, Escherichia coli was tested for potential UV/H2O2 treatment in DI water and online sensors were also integrated to monitor the destruction in real-time. Pilot-scale experiments were performed using a Trojan UVSwift SC reactor (Trojan Technologies, London, ON, Canada) at a flow rate of 1 gal./min (gpm). UV radiation and UV/H₂O₂ combination in E.coli cell suspensions resulted in a >6 log₁₀ reduction of the viable counts. Similar exposure to B.thuringiensis spores resulted in a 3 log₁₀ reduction in viable counts. Scanning electron microscopy of the treated samples revealed severe damage on the surface of most E.coli cells, yet there was no significant change observed in the morphology of the B. thuringiensis spores. Following UV/H₂O₂ exposure, the BioSentry sensor showed an increase in the unknown, rod and spores counts, and did not correspond well when compared to viable counts assays. Data from this study show that advanced oxidation processes effectively inactivate E. coli vegetative cells, but not B.thuringiensis spores which were more resistant to UV/H₂O₂.