Understanding the extent of microbial transport, distribution and activity in the subsurface is paramount for effective in-situ bioremediation. In one study, we investigated the impact a substrate pulse has on the movement of inoculated or indigenous bacteria through saturated porous media. In another study, we developed a method to visualize the distribution of bacteria on soil surfaces. The elution of either inoculated or indigenous bacteria was monitored from model (homogenous) sand or natural (heterogenous) soil column systems. Sand columns receiving salicylate resulted in enhanced elution of inoculated P. putida. However, the salicylate pulse did not result in enhanced elution of P. putida from a natural system. For natural heterogenous systems, the salicylate pulse significantly affected the elution of certain indigenous bacteria. Specifically, more heterotrophs were eluted from soil columns receiving salicylate than from those that did not for both loamy sand soils tested. On the other hand, there were consistently fewer salicylate-degrading cells eluted in the presence of salicylate from one of the two soils tested. These data suggest that bacterial transport is a function of both the porous medium and the microbial population(s) under investigation. In the second study, an agar lift-DNA/DNA hybridization technique was developed to visualize the distribution of eubacteria on soil surfaces. Briefly, a single layer of soil was lifted from the surface of soil microcosms onto agar slabs and allowed to incubate. Bacterial colonies were lifted from the agar slabs onto membranes. The location of individual colonies was detected on the membranes by hybridization with a probe complementary to a conserved region of the eubacterial genome. This method was able to detect active microorganisms on different soil surfaces. The probe signal correlated well with the number of metabolically active microorganisms found in soils amended with a carbon source. This technique also allowed for visualization of localized microbial activity. A combined approach utilizing both soil column studies and the agar-lift technique should allow researchers to better elucidate microbial transport, distribution and activity in subsurface environments.

The primary objective of this study was to evaluate the applicability of polymerase chain reaction (PCR) for the detection of enteroviruses in groundwater impacted by reclaimed wastewater. Samples were analyzed by conventional cell culture assay and the reverse transcriptase polymerase chain reaction (RT-PCR), semi-nested PCR, sequencing and dot blot probe hybridization. Viruses were detected in 4/20 samples by cell culture compared to 9/20 by RT-PCR. Semi-nested PCR and probe hybridization increased detection sensitivity to 11/20 and 12/20, respectively. Sequencing of seminested PCR products confirmed enteroviral origin of the amplified sequences, suggesting no cross-reactivity of the primers. Chlorine inactivated viruses were not concentrated as efficiently as cell culture detectable virus (90 percent less efficient). Their ability to be detected by PCR decreased by 90% after five days in secondary effluent and nine days in tap water. These results suggest that PCR is a more sensitive approach for the detection of enteroviruses in the environment. Also, chlorine inactivated viruses are less likely to be detected by PCR than cell culture infectious viruses.

The Atacama Desert of northern Chile is one of the most arid regions on Earth. The central plateau, between the coastal escarpment and the Andes, is devoid of vegetation and receives only millimeters of rain every few years. Though plants are absent in the soils of this desert, perhaps bacteria can survive, and even thrive, in these hyperarid conditions. This dissertation represents the first comprehensive study of bacterial diversity in the driest central latitudes (approximately 24°S) of the Atacama Desert. Study 1 covers the development of a soil DNA extraction method for the study of soil bacterial populations. This method was field tested in an ecology study in the Santa Catalina Mountains of southern Arizona. In Study 2, Atacama soils were sampled in two transects at approximately 24°S and 25°S. The first transect runs across the absolute (plantless) desert and through several narrow bands of sparse vegetation at high altitudes in the Andes. The second transect is within the well-developed fog zone near Paposo on the Pacific coastal escarpment, where an endemic plant community called lomas is established. Analysis of DGGE profiles of bacterial !6S rRNA genes extracted from these soils with Kruskal's Isotonic Multidimensional Scaling indicates that the bacterial populations cluster into several groups, including the low diversity populations of the core absolute desert, and the higher diversity high elevation Andean populations influenced by the vegetation of Andean biomes. Only one group clustered in the lomas; the rest of the profiles were unique, demonstrating the high diversity of bacterial populations within this diverse vegetation community. Soil 3107, which is within the absolute desert, clustered with the Andean bacterial populations. This soil lies within the transition zone between the low precipitation of the absolute desert (approximately 2.4 mm per year) and the higher precipitation of the high elevation Andes (approximately 47.1 mm per year). This Andean bacterial population may extend further into the absolute desert than the Andean vascular plants due to superior aridity tolerance. Alternatively, this bacterial population may be a relic from when the Andean vegetation advanced through this elevation in a wet period 3000 years ago.

A High N fertilizers citrus rates may contribute to a rise in the appearance of groundwater NO₃ around groves in central Arizona. Nitrogen fertilizer recommendations need to be reevaluated for citrus due to recent changes in fertilizers, irrigation technology, and increasing groundwater NO₃. Studies were initiated to optimize fertilizer N management for microsprinkler-irrigated citrus. Navel oranges were planted in Jan. 1997 with varying N rates and frequency of liquid urea NH₄-NO₃ or granular controlled-release fertilizers (CRFs) in order to determine tree response, N partitioning, N balance, and residual soil N. Trees grew slowly in 1997 with no more than 6% of the fertilizer N taken up by trees, while < 94% of fertilizer N remained in the top 0.9 m of soil. Leaf N was higher in fertilized plots than in controls as trees grew rapidly in 1998 with < 25% of the fertilizer N taken up by the trees. The soil contained low NO₃ concentrations, suggesting most of the fertilizer N was leached. Nitrogen is not needed during the first season after planting and rates of 68 to 136 g N tree⁻¹ applied in monthly intervals during the second season maintain adequate tree growth and N reserves. Application of CRFs resulted in little tree response during the two year study. Soil inorganic N was highest in the surface 0.6 m in 1997. In 1998, ammonium sulfate treatments resulted in higher NO₃ leaching than plots that received CRFs. Eight-year old 'Redblush' grapefruit trees were treated with two N rates and three fertigation frequencies in a factorial arrangement. There no differences in trunk diameter, or fruit quality on trees between 1996 and 1998. Leaf N content was > 18 mg kg⁻¹ in all plots in 1996. Leaf N declined in Aug. 1997 and control plots had lower leaf N than the other treatments. Yields tended to be the greatest at high N rates with monthly fertigation. Soil N levels were proportional to fertilizer N inputs. In 1998, the high N treatment at weekly and monthly frequencies increased leaf N compared to the other treatments. Results suggest that N rates of 272 to 408 g tree⁻¹ year⁻¹ at weekly or monthly frequencies may be optimal for desert-grown mature grapefruit.

A study was conducted in Maricopa, AZ over three field cropping seasons from December 2001 through April 2003 in order to determine the effects of fish effluent irrigations on field crops and to determine the sustainability of nutrient recycling through an integrative aquaculture-agriculture system. Treatments were designed to compare current fertilization and irrigation methods to possible integrative strategies in order to conserve natural resources. The discharged outflow from two sources of irrigation water, (well water and effluent from a fish pond/reservoir), were tested throughout the duration of the study. Maricopa's NO3-rich well water, was consistently found to contain slightly higher total N concentrations than the fish effluent, which contained higher NH4, organic N, and PO4 concentrations. Unfavorable spatial distribution of pond sludges (containing significantly higher amounts of N and P than well water) resulted in the remainder of large stores of nutrients along the pond bottom. Because a nutrient sink was created within these pond reservoirs, fish effluent irrigations were found to have no significant effect on cotton or barley yields. Vegetative plant growth, however, was significantly affected in several instances, probably by the slow, yet advantageous process of organic matter degradation near soil surfaces. Any significant increases in vegetative growth were found only in effluent-irrigated plots and occurred later in crop seasons. Analysis of the pond sludge confirmed that if pond sediments could be more efficiently removed and applied to land, the benefits from such an integrative system could have great ecological and financial benefits (i.e. decreasing chemical fertilizer use, using water to a greater potential, producing an extra crop of fish, and having lower fertilization costs).

The occurrence and disinfectant effectiveness for pathogens which are known or thought to be important in waterborne disease was evaluated. In the first study, the occurrence of human pathogenic microsporidia, Giardia cysts and Cryptosporidium oocysts in surface waters used for the irrigation of vegetable crops was determined. Twenty-eight percent of the irrigation water samples tested positive for microsporidia, 60% positive for Giardia cysts and 36% positive for Cryptosporidium oocysts. Concentrations of Giardia cysts and Cryptosporidium oocysts detected in water samples collected in Central America compared to the United States were 559 cysts and 227 oocysts, and 25 cysts and < 19 oocysts per 100 L, respectively. The presence of human pathogenic parasites in irrigation waters used for production of crops traditionally consumed raw suggests that there may be a risk of infection to consumers who come in contact with or consume these products. In the other investigations, the effectiveness of UV light and free chlorine on the inactivation of feline calicivirus (FCV) and enteric adenovirus type 40 (AD40) was assessed and compared to model viruses, poliovirus type 1 (PV-1) and coliphage MS-2. FCV was used as a model for members of the "Norwalk like virus" (NLV) group. The UV doses required to achieve 99% inactivation of AD40, coliphage MS-2 and FCV in buffered demand free (BDF) water were 108.6, 58.5 and 16.8 mWs/cm², respectively. For chlorine reactions, higher Ct values for high pH and low temperature conditions was observed for FCV and AD40. Both viruses were more resistant to chlorine than the well-studied PV-1. FCV and AD40 were inactivated rapidly by ∼0.5 mg/L free chlorine by ≥4.00- and ≥2.54-logs at pH 6 and 5°C whereas, PV-1 was not inactivated by 4.04-logs until 10 min contact time. Experiments conducted with aggregated FCV and PV-1 and experiments conducted in treated groundwater had slower inactivation kinetics than dispersed viral suspensions in BDF water. The high disinfectant decay rate of some experiments was most likely due to the decrease in chlorine concentration throughout the experiment. However, low disinfectant decay rates of the AD40 experiments suggest that aggregation or clumping of the viruses may have occurred. The results of these studies provide information on the effectiveness of two common water treatment disinfectants in waters with different physical and chemical qualities. The results of this study may provide a basis for the establishment of guidelines for proficient application in drinking water treatment.

A finite-element model was developed to simulate the water flow underneath a surface point source using the Galerkin method of weighted residuals and the mixed formulation of the Richards' equation. The saturated radius usually formed during a point source test was estimated by the numerical model. Comparisons with published experimental and analytical results indicated that the model is accurate and reliable. The numerical model aids in understanding the water regime under different point source scenarios. The finite element model was coded in C++ by using an object oriented approach. This allows flexibility for future updating. Finite and infinite elements were combined to obtain a numerical solution for unbounded 1-D flow domains. The results showed that the use of infinite elements may reduce the computational time when solving the flow equations for deep profiles. Although the transient point-source problem can be solved numerically, generalized solutions were developed and their coefficients calculated by best fitting numerical results of dimensionless saturated radius and time. The solutions allow calculation of the transient saturated radius given values of the van Genuchten hydraulic function parameter "m" and dimensionless point-source application rate. The resulting generalized solutions have the advantage of reducing large volumes of data. The estimation of soil hydraulic parameters from field data by using existing flow theory is analyzed. The results obtained from these studies verified that soil type and conditions can limit field estimation of steady state data for some soils. As a consequence, estimation of steady data is highly recommended by fitting field data to empirical equations. An empirical equation for transient saturated radius as a function of time was proposed. This equation is robust to predict steady-state saturated radius. To test the applicability of point source tests, hydraulic properties were estimated from field disc and point source tests. The parameters obtained from the disc and point-source methods matched closely. An overall methodology is also given for conducting point-source tests.

Solid waste is a global issue. As developing countries strive to improve their economic situations and standings in the world community, they face extreme underfunding in vital areas of local infrastructure, especially solid waste management. As populations continue to grow, solid waste and its management will become a very serious issue. This dissertation addressed the problems of insufficient available data and inadequate funding in an urban center in a small developing country with respect to future solid waste management. The aim was to develop a quick, simple and cost-effective check-list that could be used by decision-makers in developing countries of similar characteristics, in dealing with current and future planning for improved solid waste management. Residential municipal solid waste (RMSW) was analysed from three main locations, which where Georgetown, Guyana and Tucson and Sells, Arizona in the United States. Due to the lack of data available in Guyana, several other locations were used for lesser comparisons. These were Miami, Florida, and the Kaibab-Paiute Indian Reservation and Patagonia, Arizona. The waste streams of each were compared, as were the physical, social and economic situations of the main three locations. Past and current solid waste management practises were also compared. Results indicated that RMSW in all places contained little hazardous component. The waste in Georgetown comprised mostly of organic food waste, as has been found in other developing nations. Based on reports of foreign consultants, many solutions and improvements suggested for solid waste management in Georgetown have not been feasible and technologies brought from developed countries have been too high-tech. Solutions in developing countries need to be low-tech and those who try to solve problems must take into consideration local limiting factors and work within their constraints. Since data are seldom available, it is important to communicate with those who work in solid waste management as they are an invaluable source of information.

We introduce a simple nonlinear transformation. The new approach was compared to Kirkland's φ-based method and Ross' p-based method as well as Celia's h-based method. All algorithms use the modified Picard iteration with a linear solver of the Cholesky preconditioned conjugate gradient method (2-D) and with Thomas' method (1-D). An adaptively optimum relaxation procedure was also proposed to improve the efficiency and the robustness for 2-D cases. To test the effects of the transformation and the optimal relaxation. a total of 14 different 1-D and 2-D infiltration cases were considered. The results show that the newly introduced P(t)-based method is the most effective of the four methods and the simplest of the three transformation methods. It is several orders of magnitude faster than the h-based method and also reduces the truncation error using the same grid. The proposed adaptively optimum relaxation procedure, enhances the efficiency and robustness of all four methods to different degrees. Combination of the P(t)-based method with the adaptively optimum relaxation procedure results in a very efficient and robust algorithm. Modeling water flow in variably saturated, porous media is important in many branches of science and engineering. Highly nonlinear relationships between water content and hydraulic conductivity and soil-water pressure result in very steep wetting fronts causing numerical problems. These include poor efficiency when modeling water infiltration into very dry porous media, and numerical oscillation near a steep wetting front when a traditional mass-distributed finite element method is used.

The research objectives of this study were formulated to produce the soil spectral maps using spectral mixture analysis on the AVMS data of the Walnut Gulch Experimental Watershed, Tombstone, Arizona. To accomplish this objective the spectral characteristics of eight soils of this Watershed were determined considering the effect of the source of illumination/sensor viewing geometry, degree of wetness (dry vs wet), surface roughness, and the source of the spectra (field, sieved samples and lab) on the selection of image and reference endmembers. The scale effect of the source of spectra was also studied in connection with AVIRIS spectral response. The soils presented anisotropic behavior which varied inversely with the wavelength, and it was reduced under wet conditions. Loss of information occurred when moving from large scale data set (lab, sieved sample, and field spectra) to small scale data (AVIRIS). Cluster analysis and factor analysis were used to extract information about how soil reference endmembers are grouped in relation to viewing angles, degree of wetness and the source of the spectra. Factor analysis was applied to identify the key set of bands that carried most of the information. Soil spectral classes varied as a result of scale effects, soil conditions (wet or dry), and viewing angles. Factor analysis showed that with four unique bands (located at 0.410, 1.310, 0.650, and 2.400 p.m) it was possible to reconstruct the four basic soil spectral curves (Epitaph, Graham, McAllister, and Baboquivari) from the lab dataset. AVERT S image was modeled using mixture analysis on the basis of image endmembers and reference endmembers. Based on the four dimensions of the AVIRIS data image endmembers were defined by three soil spectra (McAllister, Stronghold-3, and Graham) and by one spectra of green vegetation. The shade fractions were separated from dark soils (Graham and Epitaph)on the basis of the spatial context The target test identified at least seven reference endmembers in the AVIRIS scene of the Watershed however; mixture analysis failed in obtaining fraction images from these reference endmembers. Mixture analysis was able to produce fraction images with a relatively high error for a small set (3) of reference endmembers (McAllister and Graham soils, and walnut leaf). However when applied to a subset of pixel extracted from the AVIRIS image mixture analysis identified the reference endmembers and quantified their proportions.