Utilization of areas adjacent to rivers for agricultural and industrial purposes can have detrimental effects on water quality and can potentially impact human and ecosystem health downstream. In this study we tested water quality along a stretch of the effluent-dependent Santa Cruz River near Nogales, AZ. This stretch of river has historically been impaired, but prior to upgrades to the Nogales International Wastewater Treatment Plant (NIWTP) in 2009. Our work endeavored to assess water quality according to the Arizona Department of Environmental Quality (ADEQ) standards, and identify sources of pollution entering the river system. Heavy metals were analyzed via ICP. Three IDEXX quantification systems were used to detect E. coli, Enterococcus, and P. aeruginosa as fecal indicators or potential threats to public health. Potential fecal sources were analyzed using quantitative PCR targeting Bacteroides DNA markers for total, human, and bovine feces (Allbac, HF183, and CowM2, respectively). The NIWTP effectively removed chemical and biological contaminants. The lowest E. coli counts occurred at the site located at the NIWTP outfall (mean = 5 MPN/100ml) while the highest counts (mean = 348 MPN/100 ml) came from Nogales Wash, a tributary receiving untreated flow from Nogales, Mexico. The Allbac marker was detected in all samples, while approximately 97% of samples tested positive for HF183 and 33% tested positive for the CowM2 marker. Continued monitoring of effluent effects on river quality and evaluation of water quality degradation will lead to improvements in the management of Arizona's riparian areas and will ultimately contribute to healthy water bodies.

The dryland ecosystems of the US Desert Southwest (SW) are dependent on soil moisture for aboveground productivity; the generation of soil moisture in the SW is dependent on both soil physical properties and climate forcing. This study is one of the first regional point-scale analyses that explores the role of soil physical properties in modulating aboveground vegetation dynamics in response to climate forcing in the SW. Soil texture accounted for significant differences in average aboveground primary productivity across the SW. However, soil texture could not account for differences in inter-annual aboveground productivity variation across the SW. Subsurface soil texture was tightly coupled with precipitation seasonality in accounting for differences in long-term average seasonal aboveground productivity in the Mojave and Sonoran Deserts. The results of this study indicate that the subsurface is a significant factor in modulating aboveground primary productivity, and needs to be included in future modeling exercises of dryland ecosystem response to climate forcing and change.

I estimated patterns of shorebird abundance and species diversity in the Colorado River Delta and Upper Gulf of California wetlands in order to determine the relative contribution of intertidal wetlands and non-tidal anthropogenic wetlands to support shorebird habitat use. Species richness varied from 15 to 26 species among sites and 29 species were detected across sites. Density during the peak migration month was higher at the anthropogenic wetland Cienega de Santa Clara (mean = 168 ind/ha, 95% C.I. 29-367), and the intertidal Golfo de Santa Clara (mean = 153 ind/ha, 95% C.I. 17-323). Anthropogenic wetlands (playa and lagoons) supported high abundance of shorebirds along with intertidal wetlands in the Colorado River Delta (mudflats). In contrast, intertidal wetlands farther south on the Sonoran Coast presented lower abundance but higher diversity of shorebird, likely as a result of the higher diversity of habitats (rocky shore, sandy beach, estuary). I modeled water management scenarios for the Cienega in order to determine the response of the dominant vegetation (southern cattail, Typha domingensis Pers.) and the area of the outflow pool below the marsh to different scenarios of water management. The model indicates that if the inflow rate is reduced below the current 4-5 m³s⁻¹ the vegetated area of the Cienega that supports habitat for marsh birds would decrease in proportion, as would the area of the outflow pool in the Santa Clara Slough identified previously as shorebird habitat. Increases in salinity will also reduce the vegetated area due to the low salt tolerance of T. domingensis. In winter about 90% of inflow water exits the Cienega into the Santa Clara Slough due to low evapotranspiration contributing to inundate areas that are used by wintering and migrating shorebirds. Lastly, I explored the feasibility of using Vegetation Indices (NDVI and EVI) to model Yuma Clapper Rail detections in the Cienega de Santa Clara as well as the effects of adding other habitat variables and the presence of fire events in the performance of linear models based on NDVI. Both NDVI and EVI were positively related to the Yuma Clapper Rail detections. The relationship was weak to moderate, but significant (P<0.001), which suggests other factors besides the vegetation condition play an important role in the bird distribution pattern. A model including all the variability among years was a better predictor of the rails detected per transect, than models for fire and non-fire years. We did not find a significant effect from adding habitat features (water % or vegetation %), and we recommend to include variables at both microhabitat level and landscape level, relevant before and during the breeding season in order to increase the explanatory power of models.

The air-water interface in variably saturated porous media is recognized to influence interfacial retention of organic and inorganic contaminants, and mediate various mass-transfer processes. The formation and presence of water films commonly solvating the surfaces of soil/sediment grains in unsaturated systems, as well as their impact on flow and retention processes have been of sustained interest. X-ray microtomography was used to measure air-water interfacial area at multiple wetting-phase saturations for natural porous media. First, a study was conducted to evaluate image-processing procedures suitable for characterizing fluids and associated interfaces in natural porous media. A simple method was developed for the analysis of all phases in the system, using global threshold for phase identification and combination of binary files (M1). This method was then compared to a simultaneous multiphase segmentation approach using locally adaptive threshold selection (M2). Both methods were used to process data sets comprised of multiple drainage steps for water-saturated packed columns imaged via synchrotron x-ray microtomography. The results of both methods were evaluated based on comparison of values determined for porosity and specific solid surface area to independently measured porosity and specific solid surface areas. The results show both methods are suitable for determination of total air-water interfacial area, which requires characterization of only the non-wetting phase. Conversely, determination of capillary interfacial area requires characterization of all phases present and thus, is more sensitive to the challenges associated with image processing. The simultaneous multiple-phase segmentation (M2) method provides an integrated and consistent analysis of the phases, and anticipated to improve water-phase detection. Using the advanced segmentation approach, the air-water interfacial area is presented as a result of direct measurement of contact areas between the two fluids. This is in contrast to previously reported data, which were derived indirectly from calculations based on individually measured phase surface areas and conceptualizations of fluid distributions. The effects of these assumptions on the capillary interfacial behavior are evaluated. Results from this study confirmed the initial hypothesis that the behavior of fluid surface areas will affect the theoretical shape of the capillary curve. The results support the understanding of the capillary interfacial area behavior in response to changes in the configuration of fluid surface areas during a drainage cycle. Furthermore, results for the measured air-water interface allows for further identification of fluid domains, such as the relationship between film interfacial area, capillary domains (menisci), and the total-measurable interfacial area. Experiments were also conducted using aqueous-phase interfacial partitioning tracer tests for comparison. Results support the hypothesis that different methods provide characterization of different interfacial domains. Overall, this study provides an imaging-based approach for evaluation of water configuration, and presents a measurement-based framework for further understanding of the role of fluid-fluid interfaces in natural porous media.

The critical zone is the interface between abiotic and biotic constituents that spans from the vegetation canopy through the groundwater and represents an open system shaped by the climate, topography, and vegetation communities of a given environment. Four studies were completed to examine soil development, specifically mineral weathering and soil carbon storage, across semiarid sites spanning the Santa Catalina Mountain Critical Zone Observatory (SCM-CZO). The Santa Catalina Mountain Critical Zone Observatory is located along an environmental gradient in southern Arizona where co-varying climate and vegetation community properties have generated distinct changes in soil development across a relatively short distance (<20 miles). Soil, saprock, and parent rock were sampled on north-facing slopes from five climate-vegetation zones spanning desert scrub to mixed conifer forest. Within each climate-vegetation zone, samples were collected from two divergent summit and two convergent footslope landscape positions to account for topographic controls on mineral transformation. In the first study, the soil morphologic, physical, and chemical properties collected for all samples were combined with profile development indices to quantify soil variation with landscape position across the SCM-CZO. The results of this research demonstrated that climate and landscape position exert significant control on soil development in semiarid ecosystems, and that the profile development index is an effective tool for detecting these regional to hillslope scale variations in soil properties. The second study consisted of a cross-scale analysis of feldspar mineral transformation across the selected research sites to connect measures of pedon-scale soil development, depletions of feldspar and sodium in bulk soil, and elemental losses across feldspar grains at the microscale. Results indicated that greater soil development in the mixed conifer pedons corresponded to increased total feldspar and sodium losses. Desert scrub soils presented less evidence for feldspar transformation including lower profile development indices, gains in total feldspar percentages attributed to dust deposition, and less Na chemical depletion at the microscale. Greater soil development in convergent positions relative to adjacent divergent sites was consistent across all sites, with the highest degree of total feldspar depletion occurring in the conifer convergent locations. The third study focused on the physical distribution and mean residence time of soil organic carbon (SOC) in the SCM-CZO soils described for the first two studies. Surface (0-10 cm) and subsurface (30-40 cm) samples were collected from the aforementioned granitic regolith profiles. The soils were characterized using total C and N, δ¹³C, Δ¹⁴C, and radiocarbon derived mean residence time (MRT) estimates of bulk soil and physically separated C fractions to quantify SOC change with climate, vegetation, and landscape position. The results document a shift in SOC stabilization mechanisms across bioclimatically distinct ecosystems from mineral-associated SOC in the desert scrub soils to a mixture of mineral and occluded SOC in the conifer soils. Soils in the convergent landscapes concentrated the most SOC and typically exhibited the longest residence times across all locations. The fourth study examined the geochemical and mineralogical properties of the SCM-CZO soils across regional and hillslope scales of study to quantify soil development in semiarid environments. X-ray fluorescence and x-ray diffraction were used to characterize the elemental and mineralogical properties of the soils and parent material. Desert scrub dust samples were analyzed using x-ray fluorescence. The results indicate that mineral and base cation depletion were greatest in the convergent landscape positions at both sites and increased from the hot, moisture-limited desert scrub sites to the wetter, more productive conifer ecosystems. Enrichments in mica and select elements (i.e., Fe, Mg) suggested that dust deposition was a significant contributor to soil development across all sites. Geochemical estimates of dust fraction inputs confirmed this finding with dust composing up to 35% of the regolith material in the mixed conifer convergent soils. Clay mineral assemblage was dominated by halloysite and smectite minerals in the desert scrub site, reflecting complex climatic and mineral microtextural interactions in the dry, silica-rich desert environment. Clay minerals at the mixed conifer site exhibited the greatest degree of mineral transformation in the SCM, consisting of vermiculite, illite, kaolinite, and minor amounts of smectite and gibbsite. These findings confirm the interactive role of climate, vegetation, and landscape position in shaping the critical zone, where greater moisture availability and biological production are likely driving increased soil organic carbon storage and mineral weathering across various scales of study.

Heavy metals have been known to possess antimicrobial properties against bacterial, fungal, and viral pathogens. Silver and copper in particular have been used for millennia to control bacterial and fungal contamination. Metal nanoparticles (aggregations of metal atoms 1-200 nm in size) have recently become the subject of intensive study for their increased antimicrobial properties due to their increased surface area and localized release of metal ions when attached to pathogens. In the current studies, metal and metalhalide nanoparticles including silver (Ag), silver bromide (AgBr), silver iodide (AgI), and copper iodide (CuI) nanoparticles were evaluated for their antibacterial efficacy against two common bacterial pathogens. All of the nanoparticles significantly reduced bacterial numbers within 24 hours of exposure and were more effective against the Gram-negative Pseudomonas aeruginosa than the Gram-positive Staphylococcus aureus. CuI nanoparticles were found to be highly effective, reducing both organisms by >4.43 log₁₀ within 15 minutes at 60 ppm Cu. CuI nanoparticles were selected for further evaluation against a range of microorganisms to determine their broad spectrum efficacy. CuI nanoparticles formulated with different stabilizers (sodium dodecyl sulfate, SDS; PVP) were tested against representative Gram-positive and Gram-negative bacteria, Mycobacteria, a fungus (Candida albicans), and a non-enveloped virus (poliovirus). Both nanoparticles caused significant reductions in most of the Gram-negative bacteria within five minutes of exposure (>5.09-log₁₀). The Gram-positive bacterial species were more sensitive to the CuI-SDS than the CuI-PVP nanoparticles. Likewise, C. albicans was also more sensitive to the CuI-SDS than the CuI-PVP nanoparticles. In contrast, the acid-fast Mycobacterium smegmatis was more resistant to the CuI-SDS than the CuI-PVP nanoparticle solutions (2.54-log₁₀ vs. 3.80-log₁₀ after 30 minutes). Poliovirus was more resistant than the other organisms tested except for Mycobacterium fortuitum. M. fortuitum was more resistant to both CuI nanoparticle solutions than any of the other organisms tested, requiring longer exposure times to achieve comparable reductions (~4.15 log₁₀ after 24 hours). As an example of a real world antimicrobial application, polymer surface coatings with embedded CuI nanoparticles were investigated to determine their potential use as self-disinfecting surfaces. Brushed polyurethane, spincoated acrylic, and powder coated polyester-epoxy coatings containing various concentrations of CuI nanoparticles were tested for antibacterial efficacy against P. aeruginosa and S. aureus. Polyester-epoxy powder coatings were superior to the other coatings in terms of uniformity and stability under moist conditions and displayed antimicrobial properties against both organisms (>4.92 log₁₀) after six hours at 0.25% Cu. Polyester-epoxy coatings were selected for more rigorous testing under adverse conditions. These surfaces were negatively impacted when tested under dry conditions with high organic content, with organic content appearing to have a greater impact on antimicrobial efficacy. At 0.25% Cu, the antibacterial activity of the powder coatings was not impacted by washing with several commercial cleaners; however, at concentrations of 0.05% Cu, antibacterial activity was reduced by multiple washings with water, Windex®, and Pine Sol®. Additionally, ultrasonic cleaning of the coatings appeared to decrease their antimicrobial efficacy. Despite this, CuI nanoparticles were found in all studies to have great potential as a new class of fast-acting, broad-spectrum antimicrobial.

The Dolores River in Utah and the Virgin River in Nevada are ecosystems under pressure from increased groundwater withdrawal due to growing human populations, climate change and introduced species such as Tamarix spp. (tamarisk). Tamarisk is reputed to take excessive water from its environment. Controlling tamarisk is of concern in the western United States where plants grow quickly in already fragile and diminishing riparian areas. For this reason, biologic control beetles Chrysomelidae: Diorhabda carinulata were released to weaken the tamarisk population, thus reducing its water use. The studies for this dissertation were conducted between 2010 and 2011. We quantified tamarisk water use over multiple cycles of annual defoliation using sap flow measurements, leaf area index (LAI), well data, allometry and satellite imagery from EOS-1 Moderate Resolution Imaging Spectrometer (MODIS) sensor. Study objectives for the Virgin River were to measure evapotranspiration (ET) before beetles ever arrived and to examine the effects on tamarisk ET in the year after beetle arrival. This site showed plant ET from sap flow averaged about 4.3 mm m⁻² leaf day⁻¹ in 2010. In 2011, ET from sap flow averaged 6.4 mm m⁻² leaf area day⁻¹ pre beetle arrival, but dropped to 3-4 mm m⁻² leaf area day⁻¹ after beetle arrival. Stand level ET measured by MODIS was 2.2 mm d⁻¹ in 2010 and approximately 1.5 mm day⁻¹ when beetle arrival was measured in 2011. Significant visual change was apparent as the trees senesced. Results showed the first year of beetle arrival resulted in reduced ET but did not result in significant water savings. We also compared the reaction of the newly defoliated (in 2011) Virgin River site to the long-term defoliated (since 2007) Dolores River site to explore if all beetle invasions were created equal. This paper views the two sites as fairly extreme examples of tamarisk stand reaction to the beetle. While no mortality was reported at the Dolores River site, the site is much older, less photosynthetically active and covers far less ground when compared to the younger tamarisk monoculture on the Virgin River. Pre-beetle arrival Normalized Difference Vegetation Index (NDVI) values were higher on the Virgin River than on the Dolores River. Beetle arrival at each site was captured with Landsat NDVI and a reduced NDVI signal (13% drop in NDVI at Dolores River, 5% drop at Virgin River) was seen after beetle arrival.

This study involves tracing inputs, partitioning, and outputs of phosphorus (P) through an aquaponics system. A mathematical model was developed to describe the dynamics of phosphorus in an aquaponics nutrient solution, and to maximize P use efficiency and minimize P waste. We assessed the influence of pH on the availability and speciation of phosphorus in an aquaponics nutrient solution. By using Visual MINTEQ, a freeware chemical equilibrium model for the calculation of element speciation, solubility equilibria, and sorption for natural waters, it was discovered that high pH values favor the formation of calcium phosphate complexes, decreasing the concentration of free phosphorus in aquaponics nutrient solutions. In addition, the mineralization of organic phosphorus in aquaponics systems was evaluated using treatments with phytase supplementation to fish diets, and incorporation of a microbial inoculant in the aquaponics nutrient solution. Overall, dietary phytase and microorganisms promoted phosphorus mineralization and enhanced phosphorus utilization in aquaponics systems. In the end, we conclude that aquaponics systems can keep the same growth performance and quality of vegetable crops grown in conventional systems when the availability and dynamics of phosphorus are well managed.

Landscape position and depth in the soil column influence the movement of microbial substrate throughout a catchment, from upslope areas to downslope areas, thereby impacting nutrient cycling rates and capabilities of the microbial communities in those areas. Wildfire also shapes the biogeochemistry of the landscape, creating a mosaic with variations in substrate type and concentration that also influence microbial communities and biogeochemical cycling. Nitrogen (N) in particular is altered by wildfire, as it is easily volatilized and the removal of organic matter (OM) reduces N inputs. We aimed to understand how landscape position and soil depth, first and foremost, influence microbial communities and their N-cycling, but also how this may differ from wildfires and their relative impacts on the soil microbial communities. Landscape position proved to influence few soil and microbial characteristics, while movement from soil surface to deep in the column and the incidence of wildfire caused many variations in soil physical and biogeochemical cycling properties. The interaction of landscape position and soil depth also showed little variation in any measurements, while wildfire and soil depth interactions showed drastic changes that indicate high order controls over the soil microbial community. It can be surmised that while landscape position is important for many soil properties, it is soil depth and wildfire that truly control the soil microbial communities and their N-cycling capabilities.

Challenges at hazardous waste and contaminated sites are persistent, complex, and multifactorial, and unfortunately the progress in implementing solutions is slow. This delay can be attributed to the lack of collaboration, information transfer to the end-user, and partnership building among academia, government and the affected community. As a solution, Environmental Research Translation (ERT), a framework that is rooted in existing participatory models, and encompasses many of the key principles from informal science education and community-based participatory research is proposed. The ERT framework lead to a community-academic partnership called: Gardenroots: The Dewey-Humboldt, Arizona Garden Project. Vegetable gardening in contaminated soils presents a health hazard. A controlled greenhouse study was conducted in parallel with a co-created citizen science program to characterize the uptake of arsenic by homegrown vegetables near the Iron King Mine and Humboldt Smelter Superfund Site in Arizona. Community members, after training, collected soil, water and vegetable samples from their household garden. The greenhouse and home garden arsenic soil concentrations ranged from 2.35 to 533 mg kg⁻¹. In the greenhouse experiment four vegetables were grown in three different soil treatments and a total of 63 home garden produce samples were obtained from 19 properties neighboring the site. All vegetables accumulated arsenic, ranging from 0.01 - 23.0 mg kg⁻¹ dry weight. Bioconcentration factors were determined and arsenic uptake decreased in the order: Asteraceae > Brassicaceae >> Amaranthaceae > Cucurbitaceae > Liliaceae > Solanaceae > Fabaceae. Concentrations of arsenic measured in potable water, soils and vegetable samples were used in conjunction with reported US intake rates to calculate daily dose, excess cancer risk and Hazard Quotient for arsenic. Relative arsenic intake dose decreased in order: potable water > garden soils > well washed homegrown vegetables, and on average, each accounted for 79, 14 and 7%, of a residential gardener's daily arsenic intake dose. The IELCR ranges for vegetables, garden soils and potable water were 10⁻⁸ to 10⁻⁴, 10⁻⁶ to 10⁻⁴; and 10⁻⁵ to 10⁻², respectively. The ERT framework improved environmental health research, information transfer, and risk communication efforts. Incorporating the community in the scientific process lead to individual learning and community-level outcomes.