Egypt witnesses an increasing population growth concomitant with limited water and agricultural land resources. The objectives of this study were to utilize remotely sensed data for the inventory of agricultural lands in the Nile Delta, monitoring spatial and temporal variations in agricultural lands and quantifying agricultural land losses due to urbanization. Inventory of agricultural lands was designed using two approaches: thresholding and linear mixture analysis. We utilized 12 images from the Landsat satellite: 4 from Multi-Spectral Scanner (1972), 4 from Thematic Mapper (1984) and 4 from Thematic Mapper (2003) covering the entire Nile Delta. In addition, a set of 480 NDVI images were obtained from the Advanced Very High Resolution Radiometer (AVHRR) sensor that cover the period 1984-2003. Landsat images were subjected to atmospheric, radiometric and geometric corrections as well as image mosaicking. Normalized Difference Vegetation Index (NDVI) was applied and thresholding for agricultural land cover revealed that the areal extent of agricultural lands was 3.68, 4.32 and 4.95 million acres (one acre = 0.96 Egyptian Feddan) in 1972, 1984 and 2003, respectively. Linear mixture analysis of the AVHRR-NDVI with the TM-NDVI images showed that agricultural lands approached 4.11 and 5.24 million acres in 1984 and 2003, respectively. Using multitemporal Principal Component Analysis (PCA) for the TM and AVHRR images proved that reclamation activities were mostly along the western margins of the Nile Delta. Spatio-temporal analysis showed that middle delta has the highest agricultural vigor compared with the margins. Agricultural land loss was estimated in some cities within the delta as well as in Greater Cairo area. We studied the land cover classification and change in Greater Cairo area based on 5 Landsat images acquired in 1972, 1984, 1990, 1998 and 2003. Agricultural lands lost 28.43% (32,236 acres) between 1972 and 2003 with an annual loss of 1040 acres. Agricultural lands on the peripheries of Cairo and its satellite towns were the most vulnerable areas. Soil salinization was another limiting factor for land reclamation. The main conclusion confirms that remote sensing is an accurate, efficient and less expensive tool for the inventory and monitoring agricultural land change in Egypt.

In this thesis, column experiments were conducted in order to determine the effect of irrigation with local groundwater on mobilization of lead and zinc in 50 years old sulfate-acid mine tailings. In addition, the influence of soluble oxalic acid, a common rhizosphere organic acid, was assessed by varying its concentration across an environmentally relevant range. In general, metal contaminant dissolution was not affected by the presence of oxalic acid. In both tailings, Zn mobilization was higher than Pb suggesting the presence of more kinetically labile Zn phases, regardless of the treatment used. Lead mobilization was also low because effluent solutions were near to equilibrium conditions with respect to gypsum, preventing Pb dissolution from Pb-sulfate minerals. Geochemical modeling also indicated that lead release was controlled by anglesite and plumbojarosite dissolution. Zinc release appears to be controlled by Zn-talc and goslarite.

The acquisition of remote sensing data having an investigated quality level constitutes an important step to advance our understanding of the vegetation response to environmental factors. Spaceborne sensors introduce additional challenges that should be addressed to assure that derived findings are based on real phenomena, and not biased or misguided by instrument features or processing artifacts. As a consequence, updates to incorporate new advances and user requirements are regularly found on most cutting edge systems such as the MODIS system. In this dissertation, the objective was to design, characterize and assess any possible departure from current values, a MODIS VI algorithm for restoring the continuity 16-day 1-km product, based on the new 8-day 500-m MODIS SR product scheduled for MODIS C6. Additionally, the impact of increasing the time resolution from 16 to 8 days for the future basic MODIS C6 VI product was also assessed. The performance of the proposed algorithm was evaluated using high quality reference data and known biophysical relationships at several spatial and temporal scales. Firstly, it was evaluated using data from the ASRVN, FLUXNET-derived ecosystem GPP and an analysis of the seasonality parameters derived from current C5 and proxy C6 VI collections. The performance of the 8-day VI version was evaluated and contrasted with current 16-day using the reported correlation of the EVI with the GPP derived from CO2 flux measurements. Secondly, we performed an analysis at spatial level using entire images (or "tiles") to assess the BRDF effects on the VI product, as these can cause biases on the SR and VIs from scanning radiometers. Lastly, we evaluated the performance of the proposed algorithm for detecting inter-annual VI anomalies from long-term time series, as compared with current MODIS VI C5. For this, we analyzed the EVI anomalies from a densely vegetated evergreen region, for the period July-September (2000-2010). Results showed a high general similarity between results from both algorithms, but also systematic differences, suggesting that proposed algorithm towards C6 may represent an advance in the reduction of uncertainties for the MODIS VI product.

The objectives of dissertation were to examine vegetation and water indices from AVIRIS and MODIS data for monitoring semiarid and upland vegetation communities related with moisture condition and their spatial and temporal dependencies in estimating evapotranspiration (ET). The performance of various water indices, including the normalized difference water index (NDWI) and land surface water index (LSWI), with the chlorophyll-based vegetation indices (VIs), the normalized difference vegetation index (NDVI) and enhanced vegetation index (EVI) was evaluated in 1) investigating sensitivity of vegetation and land surface moisture condition 2) finding optimal indices in detecting seasonal variations in vegetation water status at the landscape level, and 3) their spatial and temporal scale dependency on estimating ET. The analyses were accomplished through field radiometric measurement, airborne-based and satellite data processing accompanied with water flux data.The results of these studies showed vegetation and landscape moisture condition could be identified in VI - WI scatter-plot. LSWI (2100) showed the biggest sensitivity to variation of vegetation and background soil moisture condition as well. Multi-temporal MODIS data analysis was able to show water use characteristic of riparian vegetation and upland vegetation. Results showed water use characteristics of riparian vegetation are relatively insensitive to summer monsoon pulse, while upland vegetation is highly tied to summer monsoon rain. The relationship between water flux measurement from eddy covariance tower and satellite data has shown that MODIS derived EVI and LSWI (2100) have similar merit to estimate ET rate, but better correlation was observed from the relationship between MODIS EVI and ET.Pixel aggregation results using fine resolution AVIRIS data showed moderate resolution spatial scale 250m or 500m, best predicted ET rates over all study areas. Surface fluxes temporally aggregated to weekly or biweekly intervals showed the strongest ET versus EVI relationships. ET measured at flux towers can be scaled over heterogeneous vegetation associations by simple statistical methods that use meteorological data and flux tower data as ground input, and using the MODIS Enhanced Vegetation Index (EVI) as the only source of remote sensing data.

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.

The amoebae Naegleria fowleri, Acanthamoeba spp., and Balamuthia mandrillaris are free-living amoebae found in both water and soil. They are opportunistic pathogens in humans. Acanthamoeba is the most common cause of illness, usually infecting the eyes and sometimes causing a sight-threatening keratitis. Acanthamoeba spp. and B. mandrillaris can cause granulomatous amoebic encephalitis, in addition to infections of the lungs and skin. N. fowleri causes primary amoebic meningoencephalitis . There is little known regarding the ecology and occurrence of these organisms. A total of 36 high-use recreational surface waters in Arizona were surveyed over a period of two years to assess the occurrence of N. fowleri and seasonal and environmental factors. Overall, 9.3% of the warm weather samples collected were positive for N. fowleri, whereas 16.3% of the samples were positive during cold weather. Although the presence of N. fowleri could not be significantly correlated with physical and chemical parameters such as temperature, pH, turbidity, conductivity, and the presence of heterotrophic bacteria, total coliforms, and Escherichia coli, a weak correlation (0.52) with live amoebic activity was observed. Five lakes to the north and northeast of Phoenix tested positive for the N. fowleri on more than one occasion over multiple seasons. Finished drinking water samples (n= 785) from a municipal potable distribution system were evaluated for the presence of N. fowleri, B. mandrillaris and Acanthamoeba spp. from 18 different regions during three different sampling periods. Physical and chemical parameters were also evaluated but provided no significant correlations with the occurrence of amoebae or indicator organisms. A total of 138 samples (17.9%) were positive for viable amoebae in distribution water with more than an adequate chlorine residual (average of 0.86 mg/L). Microorganisms that are typically used to monitor microbial water quality such as coliforms and E. coli would likely not be found under these circumstances. Clusters with three or more samples testing positive for viable amoebae per region were observed during all three periods. Viable amoebae may not only provide a better assessment of the microbial quality of water, but such clustering could reveal areas with potential water quality issues within the distribution system.

The objective of this study was to characterize the pore-scale morphology of organic immiscible liquid residing within natural porous media. Synchrotron X-ray microtomography was used to obtain high-resolution, three-dimensional images of solid and liquid phases in packed columns. The image data were processed to generate quantitative measurements of organic-liquid blob morphology and organic liquid-water interfacial area. Five porous media comprising a range of median grain-sizes and grain-size distributions were used to evaluate the impact of porous-medium texture on organic-liquid blob morphology. The sizes and shapes of the organic-liquid blobs varied greatly, ranging from small spherical singlets to large, amorphous ganglia. The majority of the total organic-liquid surface area and volume was associated with the largest blobs. The distribution of blob sizes was greatest for the porous medium with the broadest particle-size and pore-size distributions. Organic-liquid blob morphology was additionally compared in two-phase (organic liquid-water) and three-phase (organic liquid-air-water) systems. In the three-phase systems, lenses and films of organic-liquid were observed in contact with air. Lenses were not observed in the two-phase systems. The presence of organic-liquid lenses and films resulted in larger surface area-to-volume ratios. The impact of dissolution on organic-liquid configuration and interfacial areas in two-phase systems was assessed. Organic-liquid blobs decreased in size and number as the columns were flushed. Separation of large multi-pore ganglia into distinct units was observed. Decrease in interfacial area correlated well with the decrease in organic-liquid volume. A one-dimensional first-order mass transfer expression was able to match effluent concentrations reasonably well with a single value of the mass transfer coefficient. In the final component of the study, immiscible-fluid configuration and interfacial areas were compared among organic liquid-water, air-water and air-organic liquid systems for two porous media. For both porous media, the nonwetting-phase configuration and interfacial areas were similar for the three two-fluid pair systems. This indicates that nonwetting phase configuration and wetting-nonwetting phase interfacial area are similar irrespective of the specific fluid pair. Properties of the porous medium appear to have a greater influence on the magnitude of specific total interfacial area for a given saturation than fluid properties or wetting-phase history.

The Lower Colorado River Giant Salvinia Task Force has tried a series of physical and chemical activities in an effort to control and eradicate giant salvinia (Salvinia molesta) since 1999. Because these efforts have not produced satisfactory results, biological control using the weevil Cyrtobagous salviniae (Coleoptera: Curculionidae) was applied on the Lower Colorado River by the Animal and Plant Health Inspection Service, United States Department of Agriculture offices in California and Arizona. They released the weevil at four sites in the summer of 2003, four sites in 2004, and eight sites in 2005.We monitored physico-chemical and biological parameters at release and 10 m and 1 km down stream from release sites. Weevils established their colony in the field, but control has not been determined. Integrated pest management (physical, chemical, and biological methods) will be essential for successful management of salvinia in the Lower Colorado River.The low temperature resistance and survival rates of the weevils were tested under three different diurnal temperature regimes (5 to 15 oC , 10 to 20 oC , and 15 to 25 oC ) and two different salvinia densities. At the low temperature range, the survival rate of the weevil was sharply decreased. The relationship between low temperature resistance of weevils and giant salvinia population was tested at the 5 to 15 oC range. The experiment was conducted at three different giant salvinia populations (0, 1, and 3 salvinia per container). The salvinia density had no significant effect on the survival of the weevil.To examine a more efficient method of biological control, we conducted a nitrogen fertilizer experiment on the river. Our goal was to demonstrate that plants fertilized with nitrogen would support a faster growing population of C. salviniae. In the Lower Colorado River, the weevil successfully survived winter and dispersed down the river.

The goals of this dissertation were to determine the viral contribution of combined sewer overflows (CSO) to receiving waters during wet weather conditions, and to compare the use of the primary liver carcinoma (PLC/PRF/5) cells with the buffalo green monkey (BGM) cells for total culturable virus assay (TCV). To assess the contribution of CSO on the viral quality of the receiving water, samples of discharges and effluent receiving waters of three sewage reclamation plants located in Illinois were collected from June to October during two consecutive years. Samples were tested for TCV, adenovirus and norovirus. Viral concentration in the receiving water increases approximately ten times the concentration during CSO events in comparison with dry weather. An assessment comparing TCV by PLC/PRF/5 and BGM cells was also conducted using sewage samples collected before and after disinfection. PLC/PRF/5 cells detected between 10 to 50 times more viruses (?) than the BGM cells. Adenoviruses were detected in the PLC/PRF/5 cells, but not in the BGM cells. In conclusion, CSO events resulted in a significant increase in the concentration of viruses in the receiving waters and PLC/PRF/5 cells are more sensitive for enteric virus detection than the BGM cell line.

This study aimed to address the current status of the United Arab Emirates date palms. The first chapter focused on the development of the date palm sector in the UAE. A huge increase in the date palm number was achieved in the past few decades. In the same time, there are critical issues facing this development, such as water demand, salinity, and Red Palm Weevil. The second chapter is a greenhouse experiment to test the growth of twelve date palm seeds at four NaCl levels, control, 3000, 6000, and 12000 ppm. Optimal growth found at control and 3000 ppm of NaCl. Relative growth rate (RGR), biomass, and NL decreased significantly by increasing salinity; however, no significant differences were observed in the average SGR for any cultivars. Increased NaCl leads to significant decreases in K+, Mg2+, and Ca2+ contents of plants. Na:K ratios were lower in shoots than in roots. Lulu, Fard, Khnaizi, Nabtat Safi, and Razez cultivars showed higher RGR and biomasses whereas Khnaizi, Mesally, and Safri had higher Na:K ratios than other cultivars in the control indicating higher Na+ discriminations from plant parts. The third chapter studied the vegetation change in the eastern region of the UAE. Due to shortage of fresh water resources, the vegetation of the eastern region of the UAE has experienced a series of declines resulting from salinization of groundwater. To assess these changes, field measurements combined with Thematic Mapper (TM) and Enhanced Thematic Mapper Plus (ETM+) based Soil Adjusted Vegetation Index (SAVI) were analyzed. Images from two dates, 1987 and 2000 were acquired to enable the computation of the greenness anomalies for three sites in the eastern region, Fujairah, Kalba, and Hatta. The results show an overall increase in the agricultural area, associated with a severe decrease in vegetation greenness and health conditions, particularly in the Kalba study area. The SAVI values decreased with increased soil salinity, permitting the identification of salt-affected areas. Potential areas of further research range from studying the effects of tree spacing and understory crops as immediate and potential solutions to maintain productivity and mitigate the salinity problem.