The Monument Valley UMTRA Site is a former uranium mining site that is located in Cane Valley, Arizona. The mining that occurred there from 1943 to 1968 created a groundwater contaminant plume that consists of nitrate, sulfate, and uranium. There are only a few viable methods for remediation of these types of contaminants occurring in large, deep plumes. Monitored natural attenuation is a popular approach because it is a green and low-cost alternative. However, it is often ineffective without some form of supplemental enhancement. In-situ biosequestration is one method of enhanced attenuation, which involves injecting an electron- donating substrate that will promote microbial activity and sequester contaminants by bioprecipitation, biomineralization, and enhanced adsorption. Prior tests conducted at the Monument Valley site in the center of the plume using ethanol as the electron donor proved effective in the treatment of nitrate, sulfate, and uranium. Subsequent pilot scale tests are being conducted in the source zone of the Monument Valley Site to further investigate the feasibility and effectiveness of using in-situ biosequestration for treatment of uranium contaminated groundwater. The preliminary results of these tests are discussed.

The feed production cost in tilapia diets is driven by the prices of its ingredients such as fishmeal (FM) and soybean meal (SBM). Fishmeal and soymeal combined with other ingredients provides fish with the nutrients required for growth and sustaining life. Soybean meal is used as an alternative to fishmeal, but prices for this traditional ingredient have increased significantly in recent years as a result of high market demand from other industries. Consequently, there has been an increase interest by tilapia nutritionists and feed manufacturers to find less expensive, alternative feedstuffs for use in tilapia diets. Camelina (Camelina sativa) is an oil seed crop grown in higher latitudes especially along the US - Canada border, northern China and northern Europe. Camelina after removal of most of the edible oil has been proposed as a fish feed ingredient. A sixty-day feeding trial was conducted and diets were formulated to contain various levels of camelina inclusion (0, 5, 10, 15, 20 and 25%) for the "camelina meal" while the "camelina oil" was formulated to contain one level (4.7%) of oil and was divided as "raw" and 4.7 "wash". The results indicated that that fishes fed diets containing camelina ingredients had growth performance and feed utilization results that were similar to fish fed the commercial diet (P>0.05). There were significant differences (P<0.05) for body organ indices and body composition. The 15% camelina meal diet was the lowest cost experimental diet per kilogram gain and therefore, this alternative ingredient might be a potential replacement for soymeal in a more cost effective feed formulation. The fatty acid composition of tilapia fillets was also analyzed at the end of the feeding trial. The inclusion of camelina meal and oil in tilapia diets resulted in significant increases in the Omega-3/Omega-6 ratio in fillets when compared to the control. The 15% camelina meal provided the best results of the experimental diets yielding significantly higher polyunsaturated fatty acid (PUFA) and lower saturated fatty aid (SFA) than the control diet. On a commercial scale, tilapia commercial feeds differ in both formulated nutrient levels and ingredient composition. In intensive system culture, natural food is limited making it important that all nutrients are supplied through a complete pelleted diet. An advantage to feeding a pelleted diet is that the pellet-type feed enables the farmers, feed formulators and manufactures to design a diet that provides an optimal nutritional mix for tilapia. Precise levels in the protein and lipid percentages of tilapia diets can reduce feed costs and also reduce the amount of underutilized protein and lipids stored as fat in tilapia. Feed comprises of over 60% of the variable cost in the intensive aquaculture operation; if feed prices were to increase, it would be a substantial amount for tilapia producers to absorb. Therefore an improved diet formulation designed for tilapia can increase profitability. Results indicated that the experimental diets (28% Crude Protein (CP)-Amino Acid (AA), 28% CP and 40% CP) performed similar to the control diet (32% CP) as it relates to fish growth. The experiment conducted on a commercial scale at an operating farm found that feeding tilapia the lowest protein level diets (28% CP) resulted in higher biomass gain per raceway, biomass gain per fish and significantly higher protein efficiency ratio (PER) when compared to the control diet (32% CP). The 28% CP diet also had the second best FCR value and most importantly higher returns based on its FCR when compared to the control diet (32% CP).

The reduction of pathogenic microorganisms is essential to minimize human health risks associated with the reuse, reclamation, and recycling of wastewater and the land application of biosolids (sewage sludge). The most advanced treatment technologies, as well as, the most representative methods and indicator organisms are necessary to ensure public safety. The goal of this dissertation is to assess advanced Bardenpho wastewater treatment technologies in regards to virus removal, suggest the most appropriate viral indicators of human fecal contamination and/or treatment process controls, and develop an updated method for enumerating Ascaris ova viability in land applied biosolids. Appendix A evaluates the incidence of 11 different virus types in sewage throughout a 12-month time period, and their subsequent reduction via advanced Bardenpho treatment processes. This study showed that wastewater treatment facilities utilizing advanced Bardenpho for secondary treatment are more effective at reducing viruses in wastewater than facilities utilizing conventional aeration basin and trickling filter processes. Appendix B develops a new method for determining the viability of Ascaris ova in land applied biosolids. In this method, early development stages prior to larval-development, are included in the estimation of potential viability. Comparisons between viability enumerations suggests that the conventional microscopy method, in which only ova containing motile larva are considered viable, underestimates the number of eggs that may progress to an infectious stage. Whereas, the method based on early-to-late stage development, considers the potential viability of all eggs, providing a more conservative approach.

NTO (3-nitro-1,2,4-triazol-5-one) is one of the new explosive compounds used in insensitive munitions (IM) and developed to replace traditional explosives, TNT and RDX. Data on NTO fate and transport is needed to determine its environmental behavior and potential for groundwater contamination. In this study, we measured how NTO in solution interacts with different types of soils and related soil properties to transport and fate behavior. We conducted a series of kinetic and equilibrium batch soil sorption experiments and saturated column transport studies under steady-state and transient conditions. NTO adsorbed very weakly to the studied soils. Adsorption coefficients (Kds) measured for NTO in a range of soils in batch experiments were less than 1 cm³ g⁻¹. There was a highly significant negative relationship between measured NTO adsorption coefficients and soil pH (P = 0.00011). In kinetic experiments, first order transformation rate estimates ranged between 0.0004 h⁻¹ and 0.0221 h⁻¹. There was a general agreement between batch and column-determined fate and transport parameters. However, transport studies showed an increase in the NTO transformation rate as a function of time, possibly indicating microbial growth.

Surrogate organisms have been used to study highly pathogenic organisms, or organisms that cannot be cultured in the laboratory. Surrogates are selected based on multiple similarities to the pathogen, such as morphology, genome size and structure, and environmental characteristics. This dissertation utilized MS2 coliphage as a surrogate for norovirus and Ebola virus in three environments. MS2 is an icosahedral, single-stranded RNA bacteriophage. It is a male-specific coliphage that infects the bacteria Escherichia coli. Its properties, such as morphology and survival in the environment, have been likened to those of many enteric viruses. Because of this, it has been used as a surrogate for pathogenic enteric viruses for disinfection testing on surfaces, in water and in food; modeling the movement and survival of pathogens in different environments; and transfer properties from surfaces. This dissertation utilized MS2 as a surrogate in three different studies. In the first, MS2 is used as a surrogate for human enteric viruses in irrigation canals to predict the re-suspension of pathogenic viruses from bed sediment into overlying irrigation water using a flume to re-create field conditions in the laboratory. MS2 re-suspension into the overlying water was characterized at varying flow rates and velocities using two sediment types. Its overall re-suspension was not statistically significantly different (p > 0.05) between flow rates. The additional studies in this dissertation used MS2 as a surrogate for Ebola virus in human waste. Ebola virus is a BSL-4 organism that is spread through direct contact with bodily fluids. It is found in bodily fluids in concentrations between 10^5.5 and 10⁸ genome copies per milliliter. In the first study using MS2 as a surrogate for Ebola virus, efficacies of four disinfectants were tested using 10¹² PFU of MS2 in one liter containing 2.25% (w/v) organic matter at three contact times (1, 15 and 30 minutes). The purpose of this study was to assess the disinfectants on reducing virus in waste before toilet flushing. Peracetic acid and quaternary ammonium formulation were found to reduce the concentration of MS2 in the toilet bowl the fastest (within one minute) with the greatest reduction (2.26 and 1.99 log₁₀), when compared with the other disinfectants. Reductions observed from hydrogen peroxide were significantly less than those from peracetic acid and quaternary ammonium (p < 0.05). The contamination of restroom surfaces by MS2 was also evaluated after toilet flushing with and without disinfectant treatment. All four disinfectants were found to significantly reduce the viral concentrations on fomites after 15 minutes of contact (p < 0.05). Despite disinfectant use, three sites were contaminated in 100% of trials (N = 18). These were the toilet bowl rim, the toilet seat top and underside. The final study evaluated the inactivation of MS2 and several other viruses by thermophilic and mesophilic anaerobic digestion. Little information is available on the influence of the wastewater treatment process, specifically anaerobic digestion, on emerging viruses, such as Ebola virus. It is important to evaluate this process due to the environmental disposal and discharge of wastewater and solids into the environment. All viruses were recoverable after mesophilic digestion (reductions from 1.8-6.6 log₁₀ per mL), except the lipid-containing bacteriophage Φ6. Thermophilic digestion inactivated all viruses significantly (p = 0.0011) more than mesophilic digestion. The reductions by thermophilic digestion ranged from 2.8-7.1 log₁₀ per mL. The inactivation between the initial concentration and both digestion types was statistically significant (p = 0.007).

Water quality, and therefore human health, may be significantly affected by the presence of pathogenic enteric microorganisms derived for improper disposal of wastewater to aquatic environments. Detection of waterborne viruses is complex due to the difficulties in concentrating the sample and then in detecting the virus by cell culture or molecular techniques. Methods used to concentrate enteric viruses from water have remained largely unchanged for nearly 30 years. The U.S. Environmental Protection Agency requires the use of 1MDS electropositive filters for concentrating enteric viruses from water; however, these filters are expensive for routine viral monitoring. The NanoCeram® filter, an electropositive cartridge filter, has been proposed as a new alternative for large volumes of water. The objective of the study was: to evaluate the effectiveness of NanoCeram® filters for the concentration of poliovirus-1 from wastewater samples and compare to 1MDS cartridge filters. This study suggested that NanoCeram® filters are a viable alternative to the use of 1MDS filters for viral monitoring in surface waters and wastewaters. L. monocytogenes outbreaks with Latin-style soft cheese have been well-documented; however, more information to characterize the human health risk associated with the consumption of queso fresco (QF) using unpasteurized milk is needed. The objectives of the study were: i) to evaluate the prevalence of Listeria, Escherichia coli, Salmonella and fecal coliforms in QF obtained from markets in the northwestern state of Sinaloa, Mexico, and ii) to address the human health impact associated with the consumption of QF contaminated with L. monocytogenes using quantitative microbial risk assessment (QMRA). The study suggested that QF produced in Culiacan, Sinaloa, Mexico have microbial loads above the maximum values recommended by the Official Mexican Regulations; and QMRA can be used to interpret microbial contamination data for impacts on public health.

Copper cast alloys de-activate antibiotic-resistant bacteria on contact and could be very effective in decreasing potentially harmful microorganisms in the environment. In this study copper alloys with varying copper contents were utilized to evaluate their antimicrobial effects on Pseudomonas aeruginosa, Escherichia coli, and Enterococcus faecium in changing environmental conditions. The survival rates of P. aeruginosa wild type and its derivative transposon mutants of the cin operon on copper cast alloys were investigated in order to demonstrate the influence of genes involved in copper resistance. The gene disruption of the response regulator of the cin operon resulted in shorter survival rates on copper alloys, which was also influenced by temperature and method of exposure. Bacteria often have acquired copper resistance mechanisms in order to withstand higher copper concentrations in their surroundings, which may be a factor in their survival rates on copper surfaces. Copper- and antibiotic-resistant E. coli and E. faecium strains were obtained from pigs raised on feeds containing copper sulfate and antibiotics. Survival rates of these bacteria were influenced by the percentage of copper in the alloys, varying moisture conditions on copper surfaces, suspension media used, and differences between strains. Survival was also dependent on copper corrosion rates since corrosion inhibition with benzotriazole or a thick surface layer of thermal oxide resulted in prolonged survival on copper surfaces. Corrosion of copper surfaces releases copper ions which directly affect bacterial survival on copper alloys. The results obtained in this study emphasize that copper alloys are effective as antimicrobial materials but changing environmental conditions can significantly influence bacterial survival on copper surfaces. These findings can be applied to a better utilization of copper alloys in water, food, and healthcare environments. Antibiotic- and copper ion-resistant bacteria can be killed on contact with copper alloys which makes the proliferation of these microorganisms less likely and reduces the risk to human health. However, in a very different environment copper ion-resistant microbes can be useful for plant-microbe associations in bioremediation of copper mining wastelands.

In the current study, the antibacterial efficacy of zeolites containing silver or copper ions or a combination of these metals was assessed against several diverse copper resistant (CuR) and copper sensitive (CuS) strains of clinically relevant bacterial species. CuR Pseudomonas putida was significantly reduced in comparison to the unamended zeolite control. Unexpectedly, a CuS P. putida strain with no reported metal resistance appeared to be more resistant to the zeolite containing either Ag or Ag/Cu than the CuR strain. Contrary to expectations, after three and six hours of exposure, the CuS Escherichia coli displayed significantly more resistance to the Ag/Cu and Cu treatments than the reportedly CuR E. coli. All three reportedly CuR strains of Salmonella enterica exhibited resistance to Cu and Ag, as well as to the combination of the two metals after three and six hours of exposure. The reductions observed after 24 hours for all three CuR strains with Cu alone were still statistically significant compared to that of the CuS S. enterica strain. In addition, two of the CuR strains were more resistant to silver after 24 hours of exposure, suggesting a shared resistance mechanism such a copper efflux pump that also removes silver ions from the cell. Both the CuR and CuS strains of E. faecium were highly resistant to all of the treatments. In general, after comparison of all the resistances with all the treatments, E. faecium was the most resistant species, P. putida was the least resistant species, and the Salmonella strains were more resistant than E. coli in most cases.

In this study, the relationship of above-ground net primary productivity (ANPP) with precipitation using the enhanced vegetation index (EVI) from satellite data as surrogate for ANPP was assessed. To use EVI as a proxy for ANPP we extracted the satellite data from areas with uniform vegetation in a 2x2 km area for the multi-site approach.In the multi-site analysis in the United States our results showed a strong exponential relationship between iEVI and annual precipitation across the sites and climate regimes studied. We found convergence of all sites toward common and maximum rain use efficiency under the water-limited conditions represented by the driest year at each site. Measures of inter-annual variability in iEVI with rainfall variation across biomes were similar to that reported by Knapp and Smith (2001) in which the more herbaceous dominant sites were found to be most sensitive to interannual variations in precipitation with no relationships found in woodland sites.The relationship was also evaluated in the southern hemisphere using a multi-site analysis with information from satellite TRMM for precipitation and MOD13Q1 from MODIS for EVI values at calendar and hydrologic year periods. The tested sites were located across the 6 major land cover types inAustralia, obtained from MODIS MCD12Q1 product and used to compare the relationship across different biomes. The results showed significant agreement between the annual iEVI and annual precipitation across the biomes involved in this study showing non-significant differences between the calendar and hydrologic years for the 24 sites across different climatic conditions.At the regional scale we also assessed the ANPP-precipitation relationship across all of Australia. Precipitation data from TRMM was obtained at 0.25x0.25 degrees spatial resolution and monthly temporal resolution and EVI values were obtained from the CGM (Climate Grid Modeling) MOD13C1-16-days and 5.6km temporal and spatial resolutions, respectively. Our results were in fair agreement with those from our first two studies and previous research and provided specific insights regarding the use iEVI as a proxy for productivity over extended regions as well as its combination with data sets from TRMM sensor for precipitation data.

Throughout the arid and semi-arid regions, researchers have been looking at different ways to deal with the salinity problem of the soil and water as well as feed for the livestock. Study 1 focused on a pilot project conducted in an irrigation district in Marana, AZ, USA, looking at using Reverse Osmosis (RO) concentrate on Atriplex lentiformis (quailbush) and then harvesting the plant to be tested for its possible use as a supplement in feed for livestock. Three irrigation treatments were tested based on the potential evapotranspiration rate (ET(o)): (1) plots irrigated at ET(o) adjusted daily via an on-site micrometeorology station; (2) plots irrigated at 1.5 ET(o) adjusted daily; (3) plots irrigated at a constant rate throughout the year based on the mean of annual ET(o). The plants produced 15-24 tons ha⁻¹ year⁻¹ of biomass and could be irrigated at the rate of ET(o), ca. 2 m yr⁻¹ at this location. It was concluded that irrigation of halophyte forage crops provide a viable strategy for extending water supplies and disposing of saline water in arid-zone irrigation districts. Study 2 focused on a field data from Study 1 and two greenhouse experiments. The greenhouse experiments were conducted in 2007 and 2010. The 2010 greenhouse trials, under well-watered conditions, showed that the apparent zero-point-salinity for yield was 47.3 g L⁻¹ TDS. An additional greenhouse experiment was conducted in which plants in sealed pots were grown to the wilting point on a single application of water. The experiment was conducted at different salinities to see if salinity and water stress were additive factors in reducing yield and Water Use Efficiency (WUE). To the contrary, yield and WUE actually increased as a function of salinity, perhaps due to conversion from C3 to C4 photosynthesis over the salinity range (noted in other studies with A. lentiformis). We conclude that xerohalophytes such as A. lentiformis could greatly extend the useful range of salinities under which forage crops can be grown in arid-zone irrigation districts.