Interfacial partitioning tracer tests (IPTT) are one method available for measuring air-water interfacial area (A(ia)).This study used the standard approach comprising tracer injection under steady unsaturated-flow conditions with a uniform water-saturation distribution within the column. Sodium dodecylbezene sulfonate (SDBS) and pentafluorobenzoic acid (PFBA) were used as the partitioning and nonreactive tracers, respectively. Three types of porous media were used for the study: a sandy soil, a well-sorted sand, and glass beads. Initial water saturations, S(w), were approximately 80%, 80%, and 26 % for the soil, sand, and glass beads, respectively. Water saturation was monitored gravimetrically during the experiments. The maximum interfacial areas (A(ia)/(1-S(w))) calculated from the results of the experiments are compared among the three porous media used in this work, and compared to previous air-water interfacial area studies.

Antibiotic resistance (AR) is reducing options for effective treatment of bacterial infections for clinically ill patients throughout the world. Our investigation examined the impact solids retention time (SRT) may have on the degradation of antibiotic compounds, proliferation of AR bacteria, and the persistence of antibiotic resistance genes (ARGs) during the wastewater treatment process. Results indicate the presence of ARGs related to clinically relevant antibiotics. Data analysis showed that antibiotic classes exhibit different removal efficiencies in the biological treatment processes (i.e. SRT); therefore, operating conditions at each WWTP can be optimized for highest efficiency removal. SRT of 19 days and higher indicated a high removal efficiency for all six ARGs of concern. Ultimately, identifying a critical value to optimize SRTs, where antibiotic degradation is maximized and AR is minimized, will provide information to WWTP operators, allowing treatment optimization to decrease harmful loading of Trace Organic Contaminants (TOrCs) in the environment.

Recent advancements in molecular biology such as next generation sequencing and more sensitive and rapid molecular detection methods like qPCR, have historically been developed for clinical applications in human genetics and for health care diagnostic purposes. The high demand for faster and more accurate molecular assays in the health care field has driven rapid development of inexpensive molecular techniques that when applied to the science of environmental microbiology, provides an unprecedented level of understanding of the microbial world around us. The goal of this dissertation is to begin to apply more advanced molecular technologies to problems in applied environmental microbiology. Appendix A is a brief literature review of next generation sequencing technologies for applications in environmental microbiology. Appendix B focuses on the development of a more robust virus nucleic extraction kit for the detection of viral genomes from environmental samples found to contain high concentrations of qPCR inhibitors, such as humic acids or heavy metals. Appendix C summarizes one of the largest virus surveys done in the US, using state of the art qPCR technologies in both wastewater influent and effluent from two wastewater treatment plants in the Southwest. Data suggests that traditional virus indicators may not be a viable tool to evaluate fecally impacted source water or virus removal during water treatment. The third study summarized in Appendix D, provides one of the first insights into the microbial ecology of biofilms utilized as biological treatment media using Roche 454 amplicon sequencing of the 16S rRNA gene.

Extensive research conducted over the last decade has demonstrated the great potential of phytostabilization for the reclamation of abandoned mine tailing piles. The right combination of plant species and soil amendments can facilitate the growth of a permanent vegetative cover on the tailings that will help minimize the mobilization of metal-bearing particles by means of wind dispersion and water erosion. Despite previous research efforts, the diversity and potential role of microbial populations inhabiting the root zone of the plants on the stabilization of the metal(loid) contaminants remains mostly unresolved. The study presented in this dissertation represents one of the first comprehensive efforts aimed to understand the ecology and dynamics of microbial communities colonizing both bulk and rhizosphere tailings during phytostabilization as an initial step towards elucidating the role of microbes in the stabilization of metal(loid) contaminants during the remediation treatment. This study was divided into two main projects: (1) the first aimed to monitor the temporal variations in functional and taxonomic diversity of prokaryotic populations in acid-generating metalliferous mine tailings during phytostabilization to determine how they respond to and/or influence changes in environmental parameters and to identify key patterns in their composition that may serve as bioindicators of soil health and the success of the remediation treatment; and (2) the second aimed to expand our understanding of the dynamics of root-associated bacterial, fungal and archaeal communities during mine tailing phytostabilization and how the dynamic behavior of the communities correspond to the growth of plants, the addition of soil amendments, and fluctuations in environmental conditions. The results presented here demonstrate that different microbial groups respond differently to changes in environmental conditions during phytostabilization, suggesting that by monitoring the behavior of specific microbial groups in the systems (as bioindicators) we may be able to assess the effectiveness of the remediation treatment. Furthermore, the results from the taxonomic and functional analysis of the microbial communities served as the basis for the development of a model that explains the ecology and distribution of dominant microbial groups in the tailings that may significantly contribute to the oxidation of iron-sulfides, the production of acid mine drainage, and to facilitate plant establishment and survival during phytostabilization.

The increasing food demand as well as the need to predict the impact of warming climate on vegetation makes it critical to find the best tools to assess crop production and carbon dioxide (CO₂) exchange between the land and atmosphere. Photosynthesis is a good indicator of crop production and CO₂ exchange. Chlorophyll fluorescence (ChF) is directly related to photosynthesis. ChF can be measured at leaf-scale using active techniques and at field-scales using passive techniques. The measurement principles of both techniques are different. In this study, three overarching questions about ChF were addressed: Q1) How water, nutrient and ambient light conditions determine the relationships between photosynthesis and ChF? Which is the optimum irradiance level for detecting water and nutrient deficit conditions with ChF?; Q2) which are the limits within which active and passive techniques are comparable?; and Q3) What is the seasonal relationship between photosynthesis and ChF when nitrogen is the limiting factor? To address these questions, two main experiments were conducted: Exp1) Concurrent photosynthesis and ChF light-response curves were measured in camelina and wheat plants growing under (i) intermediate-light and (ii) high-light conditions respectively. Plant stress was induced by (i) withdrawing water, and (ii) applying different nitrogen levels; and Exp2) coincident active and passive ChF measurements were made in a wheat field under different nitrogen treatments. The results indicated ChF has a direct relationship with photosynthesis when water or nitrogen drives the relationship. This study demonstrates that the light level at which plants were grown was optimum for detecting water and nutrient deficit with ChF. Also, the results showed that for leaf-average-values, active measurements can be used to better understand the daily and seasonal behavior of passive ChF. Further, the seasonal relation between photosynthesis and ChF with nitrogen stress was not a simple linear function. Our study showed that at times in the season when nitrogen was sufficient and photosynthesis was highest, ChF decreased because these two processes compete for available energy. These results demonstrated that ChF is a reliable indicator of crop stress and has great potential for better understand the CO₂ exchange between the land and atmosphere.

A series of studies were conducted on an emerging disease in farmed penaeid shrimp. This disease was first named as Early Mortality Syndrome (EMS) or more descriptively as Acute Hepatopancreatic Necrosis Syndrome (AHPNS). As part of the outcome of this research, the etiology of EMS/AHPNS was demonstrated. EMS was first classified as an idiopathic disease because no causative agent had been identified. Preliminary studies conducted in Vietnam in 2012 by the University of Arizona Aquaculture Pathology Laboratory (UAZ-APL) indicated that EMS is infectious (Tran et al., 2013). The agent was identified as a unique strain of Vibrio parahaemolyticus. Hence, EMS has a bacterial etiology confirmed by satisfying Koch's Postulates. Further studies focusing on the bacterial isolate causing EMS revealed that the agent could produce toxin(s), which is responsible for the primary pathology in affected shrimp. Since the causative agent has been identified, we propose a new name for EMS as Acute Hepatopancreatic Necrosis Disease (AHPND). Characterizations of the AHPND-causing Vibrio parahaemolyticus: Biochemical methods and molecular methods were used. Based on these results, various diagnostic methods were developed including polymerase chain reaction (PCR) test and biochemical tests. Other aspects of the AHPND causing V. parahaemolyticus were also run to determine such as antibiogram and the development of resistance mechanism of the bacteria exposed to farm conditions with antibiotic medications, pathogenicity, and infection dose of the bacteria, mode of infection, mechanisms governing the toxin production, and effects of environmental parameters on the invasion of the agent. Some proposed control measures for AHPND: Several antibiotic-free approaches were tested to determine viable control methods for AHPND. The principle proposed control method is to increase biosecurity. With the PCR method that has been developed, potential sources of the pathogen such as post-larvae and broodstock can be tested. As more and more insights of the pathogen were explored, the behavior of the pathogen was further elucidated. Based on this, control methods such as using polyculture with tilapia, probiotics, and bioflocs system were also tested. Several improvements in shrimp farming practices that may reduce the outbreak of the disease were also proposed.

Microbes survive for an extended period of time on fomites. With new strains of pathogens constantly emerging, it is important to understand their survival and spread and to evaluate the efficiency of new disinfection methods. The purpose of this study was to determine the occurrence of pathogens on fomites, and evaluate different disinfection methods (household bleach and steam vapor). Fomites were sampled in a variety of environments for the presence of pathogens including methicillin intermediate- and resistant- Staphylococcus aureus, Clostridium difficile, Penecillium brevi-compactum, Alternaria alternata and novel H1N1 influenza A. Samples were assayed using both cultural and genetic techniques to determine the microbial occurrence. In disinfection studies, samples were collected before and after disinfectant application. Steam vapor was effective at reducing microbial occurrence by>90% with a minimal contact time of 10-20 seconds on hospital fomites. The material and shape of the surface had an effect on the reduction rate, due to access of the disinfecting agent. In addition, low levels of initial contamination limited the reduction rate. Many surfaces had a starting contamination level of less than 3 log10 and after disinfection the contamination levels, in 69% of the samples, were at or near the limit of detection. This suggests a higher reduction is feasible. Household bleach reduced the presence of mold spores and mycelium by >99% on gypsum-wall board. Reduction rates were influenced by the growth stage of mold, with the mycelium requiring additional disinfectant application to achieve the 99% reduction rate. Novel H1N1 influenza A was not recovered on any surfaces in day care facilities and elementary schools. This is consistent with previous studies looking at H1N1 influenza occurrence in similar environments, though it is different from H3N2 influenza A studies. Survival differences among varying influenza strains are expected to have an impact on pathogen spread and human health risks. Differences can be quantitatively evaluated and used to develop more advanced risk assessment models. Steam vapor and household bleach are effective at reducing risks of pathogens in the environment and are critical interventions in an overall strategy to minimize exposure and prevent disease.

As of 2010, there are approximately twenty one surface water locations classified as impaired for Escherichia coli (E. coli) contamination in the State of Arizona. Of note is the San Francisco River (SFR) which is currently listed on the US EPA 303d list of impaired waters due to E. coli bacteria present at higher concentrations than the US EPA standards for partial- and full-body contact. In 2010-2011 surface water samples were collected at sites within the impaired region to monitor E. coli and areas known for heavy recreational uses. Of 70 samples collected over 1 year, 81% were positive for universal Bacteroides marker (Allbac). Of the 57 Allbac-positive samples, 68% show contributions of the human-specific marker and 60% were positive for bovine-specific marker. While 28% of the total samples assayed showed elevated levels of E. coli (>235 MPN/100mL), there were minimal significant correlations between Bacteroides and generic E. coli across all samples. While this information is significant, past research has suggested that successfully distinguishing the sources of fecal contamination will not alone reduce or eliminate disease associated with contaminated water unless these investigations are coupled with public outreach and education. With this in mind a survey was developed to gather information about water quality perceptions, water use, peoples' attitudes, knowledge, and behaviors related to the water resources in Clifton, AZ. Survey questions consisted of multiple choice and Likert scales questions and were provided in both English and Spanish and were conducted during the summer of 2012 and winter of 2013. A total of 150 surveys were deployed with 38 surveys completed for a response rate of 25%. Our study findings indicate mixed attitudes on water quality with 80% reporting the SFR has poor water quality for drinking and 39% agree the SFR has poor water quality for swimming. Yet, 84% consider the river safe enough for picnics and activities near the water. Also, it was interesting to note participants' opinions regarding consequences of poor water quality with 66% of respondents indicating that they are concerned with poor water quality and their health. Clifton is a very tight knit community so it was not unexpected that the majority of the respondents (61%) get water quality information by having conversations with other people and 68% from newspapers, factsheets and brochures. Based on the survey responses, our team worked to develop two peer reviewed Extension publications entitled; Microbial Source Tracking: Watershed Characterization and Source Identification (Arizona Cooperative Extension, #AZ1547) and Water Quality, E. coli, and Your Health (#AZ1624). Publications have been developed in both English and Spanish and will be part of future outreach to this and other Arizona communities. It is our goal that these survey findings can be used to better tailor outputs appropriate for the targeted audience, namely the local Hispanic population. These results are important because they add to understanding perceptions of water quality and health risks in this rural community; and can lend towards enhanced outreach practices in other similar communities.

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.