It has been demonstrated the technical feasibility of using seawater and other saline water for irrigation. Through the use of saline water for irrigation, highly salt-tolerant crops could greatly increase global agriculture. Brackish water and seawater from different sources are available in areas suitable for production of salt-tolerant crops. Dwarf glasswort Salicornia bigelovii Torr. (Chenopodiaceae), is a leafless, succulent, small-seeded, annual saltmarsh plant, with potential as a saline water crop. It is also a potential oilseed, forage, biomass crop, and a promising carbon sequestration plant. In the first chapter of this document we describe a study where we grew Salicornia bigelovii from seedlings, in saline, drying soils in a greenhouse experiment. The effects of drought and salinity stress were additive. Optimal growth and water use efficiency coincided at 0.35-0.53 M NaCl. The plants were tolerant of high salinity but exhibited little drought tolerance. Salicornia bigelovii plants varied little in their uptake of Na+ for osmotic adjustment, with final Na+ contents of 18% on a dry mass basis. Both growth and water use efficiency of Salicornia bigelovii were affected by salinity. Also, Na+, the primary cation involved in osmotic adjustment of this species, apparently stimulates growth by mechanisms apart from its role as an osmoticum. In the second chapter of this dissertation we developed a research study where we evaluated the production and osmotic adjustment of two S. bigelovii lines (Texas and Florida), plants were grown in pot in a green house and irrigated with water treated with three different levels of NaCl (5 ppt, 15 ppt and 30 ppt) combined with inorganic fertilizer. At the end of the experiment sixty plants from each line were measured for height, biomass, seed yield, seed size, dry matter yield, and tissue osmolarity. There was no significant difference among groups in plant height, or final biomass either in salinity irrigation treatments, or S. bigelovii lines. Tissue osmolarity differed among salinity treatments but not among S. bigelovii lines. The highest tissue osmolarity value was 1192 mM kg-1 found at the treatment 30ppt in the Florida line. Total biomass production was 12 000 kg/Ha.

ASSESSMENT OF THE MICROBIAL AND CHEMICAL WATER QUALITY OF INDIVIDUAL AND SMALL SYSTEM GROUNDWATER SUPPLIES IN ARIZONA Roberto Marrero-Ortiz, Ph.D. ABSTRACT Arizona has more non-disinfected drinking water supply systems than any other state in the U.S. All of these systems depend on groundwater that is subject to contamination by waterborne and waterbased pathogens. The goal of this project was to assess the microbial quality of non-disinfected individual and small groundwater drinking water systems in Arizona. In addition, data was collected on the occurrence of heavy metals. The microbiological parameters tested included total and fecal coliforms, enterococci, heterotrophic bacteria, Helicobacter pylori, Aeromonas hydrophila, enteric viruses, and somatic and male specific coliphages. Physical parameters tested included pH, turbidity, total dissolved solids (TDS) and temperature. Chemical parameters tested included nitrate/nitrogen, total organic carbon (TOC) and metals. Forty-nine groundwater sources were tested in seven Arizona counties. A total of 70 samples were collected over 14 months. Forty-three percent of the systems were positive for total coliforms, 16% for fecal coliforms and 4% for E. coli. Twenty-nine percent of the wells were positive for enterococci, and 57% were positive for Aeromonas hydrophila. H. pylori, norovirus and enterovirus were not detected by direct PCR in any samples. At least one primary and/or secondary Drinking Water Standard (DWS) was exceeded for heavy metals in all samples. Metals which exceeded standards included arsenic, aluminum, iron, lead, manganese, molybdenum, selenium, and uranium. Seventy-four percent of the sites sampled exceeded at least one of the primary DWS, 80% exceeded at least one secondary DWS, and 95% exceeded one primary and/or one secondary DWS.

Mining activities and their resulting wastes, mine tailings, have created a sizable problem globally. Semiarid lands have been particularly impacted due to intense mining activities in these areas. Growing concerns regarding human health risks and environmental consequences associated with these tailings has created a need for efficient and effective remediation strategies. Phytostabilization, the establishment of a vegetative cover on mine tailings to reduce erosion and dispersion of material, is emerging as a cost-effective remediation technology. However, due to elevated levels of metal contaminants, acidic pH values and poor substrate quality many tailings sites are inhospitable to plant growth. The addition of compost amendments can mitigate the toxic effects of tailings material and facilitate plant growth; however, in many instances the necessary compost amendments may be cost prohibitive. The use of specialized bacterial isolates, known as plant growth-promoting bacteria (PGPB), to enhance plant growth is a developing technology that has a broad range of applications. The use of PGPB to enhance one or more aspect of plant establishment and growth has been demonstrated to be effective in hundreds of previous studies conducted primarily under agricultural settings. To date, very few studies have utilized PGPB in attempts to enhance plant growth in mine tailings. The current study is an investigation into the potential for utilizing PGPB to enhance plant growth during the phytostabilization of semiarid mine tailings. During this investigation a large collection of bacterial isolates was screened for common plant growth-promoting mechanisms such as siderophore and indole-3-acetic acid production, phosphate solubilization and ACC-deaminase activity. Isolates possessing beneficial qualities were utilized in a series of greenhouse screening studies to evaluate their abilities to enhance the growth of native desert plants in various tailings materials. A number of isolates tested have demonstrated the ability to enhance plant growth in composted and non-composted tailings material. Optimization of this technology has now indicated that alginate-encapsulated inoculation of target plants is a beneficial and practical technology.

This dissertation examines the bacterial diversity of hyperarid and arid regions of the Atacama Desert, Chile, as a first step towards understanding the global biogeochemical significance of arid-land microbial communities. The specific objectives were to characterize bacterial diversity and infer the possible metabolic potential of these bacterial communities, and to evaluate the influence of moisture exposure on community structure. In addition, the strengths and limitations of available tools for probing microbial diversity and activity in terrestrial ecosystems were characterized for their application to extreme oligotrophic communities. Preliminary PCR-DGGE analysis of a west-east elevational transect from the Pacific Ocean near Antofagasta to the western slopes of the central Andes indicated that bacterial communities along this transect belonged to two distinct community types: 1) hyperarid (700 - 2000 m) and 2) arid (2500 - 4500 m) communities that included both vegetated and unvegetated regions. Subsequent diversity analysis of these two regions revealed novel but distinct communities in both regions. A greater diversity was observed in the unvegetated arid regions than in the unvegetated hyperarid areas. The unvegetated arid sites were characterized by a bacterial community harboring a combination of radiotolerant and halotolerant heterotrophs as wells as diverse phylotypes closely related to chemolithoautotrophs. These rare phylotypes may be uniquely adapted to arid ecosystems. Molecular tools evaluated for community diversity analysis included PCR-DGGE, Sanger-clone and 454-pyrosequencing analysis of 16S rRNA gene libraries, and the use of reverse transcriptase quantitative PCR (RT-qPCR) for quantifying the impact of environmental variables on the metabolic activity of a specific organism. These techniques were evaluated using the ecosystems of the Atacama Desert as well as model ecosystems designed to address specific questions. Molecular tools are invaluable to the study of microbial ecology because they facilitate the study of fastidious organisms that are difficult or impossible to culture, but the analysis presented in this dissertation demonstrates that each of these methods has limitations and biases which must be acknowledged to avoid inaccurate conclusions from skewed results. The most complete picture of the taxonomic and functional profile of a microbial community is obtained by employing a combination of molecular techniques.

This research sought to elucidate the molecular mechanism by which a recently described family of ion transport proteins, the cation diffusion facilitators (CDFs), transfer ions across biomembranes. Using the Escherichia coli homologs ZitB, and FieF, as well as CzcD from Cupriavidus metallidurans CH34 as models, the amino acids essential to CDF function were identified, and the transport behavior of ZitB and its homolog FieF, were described.Site-directed ZitB mutants were used to determine the necessity of individual amino acids. The mutation of several well-conserved acidic residues resulted in the loss of a ZitB-mediated zinc-resistant phenotype in the zinc-sensitive E. coli strain GG48. ZitB also complemented the potassium uptake deficient strain TK2420, suggesting that ZitB works as an antiporter, possibly allowing potassium into the cell while effluxing zinc.This result was further investigated in experiments using everted membrane vesicles(EMVs). Vesicles bearing ZitB accumulated 65Zn(II) in a NADH-dependent manner, with an apparent KM of 1 micromolar. This accumulation was inhibitable by the protonophore FCCP, suggesting CDF dependence upon the proton motive force. Similar results were obtained using both EMVs and proteoliposomes containing the CDF homologs CzcD, from C. metallidurans CH34, and FieF from E. coli. Despite facilitating 65Zn(II) uptakeinto EMVs, fieF transcription was zinc and iron-dependent, but independent of the ironuptake regulator Fur. FieF expression in trans complemented the iron-sensitive phenotypeof a strain lacking fur, causing it to accumulate less 55Fe than wild type. Reconstituted proteoliposomes containing FieF also accumulated less 55Fe than those without.This research confirms that CDF proteins likely depend on the cell's proton gradient, effluxing substrate in a metal:proton antiport arrangement. Substrate acquisition and throughput is facilitated by a set of acidic amino acids and histidines. The relatively lowapparent KM of ZitB suggests a homeostatic role for the protein; however, the iron-inducibilityof fieF hints at a role in iron detoxification, so the cellular functions of the CDF family may be quite diverse, even within the bacteria.

The purpose of this research was to identify and characterize novel molecular mechanisms in copper homeostasis. Pseudomonas putida KT2440 is a soil bacterium studied for its potential use in bioremediation of soils contaminated with aromatic organic contaminants. The cinAQ operon was analyzed. cinAQ is transcribed in presence of copper. The product of cinA is a periplasmic azurin-like protein with a methionine and histidine rich region, characterized by a high redox potential (456 ±4 mV). CinQ was shown to be a pyridine nucleotide-dependent nitrile oxidoreductase that catalyzes the reduction of preQ₀ to preQ₁, the first committed step in the biosynthetic pathway leading to the production of the unusual nucleotide queuosine. Gene disruption of cinQ in Pseudomonas putida KT2440 and in Pseudomonas aeruginosa PAO1 did not result in a significant increase in copper sensitivity on disk assays. Furthermore, a P. putida KT2440 cinA mutant also did not present a greater sensitivity to copper on disk assays while cinA mutants in Pseudomonas aeruginosa PAO1 presented increased toxicity to copper compared to the wild-type. CinA is by sequence similarity proposed to be an electron shuttle, and was shown to be upregulated in the presence of copper. Increasing CinA levels in the periplasm after copper stress may represent a mechanism used to regenerate the multicopper oxidase CopA (involved in Cu(I) to Cu(II) oxidation). Alternatively, CinA could act as an electron shuttle that takes part in an alternative electron transport chain once redox active copper is available, or it could represent a periplasmic copper chaperon. CinQ is involved in the biosynthesis of the rare hyper-modified nucleotide queuosine, found in the wobble position of several tRNAs, and required to avoid the readthrough of the stop codon UAG. Transcription of cinAQ was shown to be under the control of the two component system CinR-CinS. CinS is a histidine kinase, with a sensor domain located in the periplasm. CinR is the cognate response regulator that activates transcription of genes upon phosphorylation from CinS. The CinR-CinS two component system was shown to be responsive to 0.5 LM copper. CinS displayed very high metal specificity and elicited a response only in the presence of copper and silver, but not other metals. Modeling of the CinS protein structure, performed using Swiss Model and using the periplasmic sensor DcuS from Escherichia coli as a template, identified a potential copper binding site, containing H37 and H147. Sequence alignment of copper sensing histidine kinases further identified other conserved residues in the periplasmic domain. Site-Directed Mutagenesis was used to generate CinS mutants that were tested for their ability to activate the cinAQ promoter in presence of Cu. When challenged with copper CinS mutant H37R and H147R had an almost 10 fold reduction in copper sensitivity compared to the wild-type, indicating a possible role in Cu coordination. Other CinS mutants responded similarly to the wild-type in the presence of 10 μM of Cu.

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.

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.

Weed control is typically achieved by broadcast spraying postemergence herbicides on the entire orchard floor which wastes chemical by spraying bare ground. Growers can account for spatial variation in weed density and only spray weedy areas instead of applying herbicide to entire fields by using the automatic spot-sprayer, WeedSeeker sprayer. We conducted field experiments in flood- and microsprinikler-irrigated lemon orchards, and flood- and sprinkler-irrigated pecan orchards to measure the amount of herbicide applied, weed control, tree yield, and the economic value of adopting the WeedSeeker sprayer compared to conventional boom spray technology. The WeedSeeker sprayer reduced cumulative herbicide use by at least 36% compared to the conventional boom sprayer at all sites. Weed control obtained using the WeedSeeker sprayer was usually similar to the conventional boom sprayer. There were no effects of the treatments on yield at any location. The partial budget analysis, used to determine the economic value of adopting the technology, showed that as the area of the orchard and the cost of the herbicide increased, the time to recover the initial investment in the WeedSeeker sprayer decreased. The investment in the technology can typically be recovered in less than five years in Arizona lemon and pecan orchards.We also conducted greenhouse experiments to determine the effect of various sensitivity settings and leaf area on the operational efficiency of the WeedSeeker sprayer. The WeedSeeker sprayer did not detect and spray all broadleaf and monocot plants unless a sensitive setting was used. The WeedSeeker sprayer was more efficient when detecting broadleaf plants compared to monocot plants. Our results indicate that operating the WeedSeeker sprayer using a sensitive setting (sensitivity level 2) will result in the most efficient detection of weeds.Finally, field studies were conducted in a non-bearing pecan orchard to evaluate weed management systems using various postemergence and preemergence herbicides. Most postemergence herbicides controlled the weed species present in the orchard. Tank mixing the herbicides generally resulted in greater control compared to applying them alone. All preemergence herbicides reduced the weed emergence compared to not using a preemergence herbicide. No pecan tree damage was observed in any treatment.

Improved knowledge of landscape seasonal variations and phenology at the regional scale is needed for carbon and water flux studies, and biogeochemical, hydrological, and climate models. Amazon vegetation mechanisms and dynamics controlling biosphere-atmosphere interactions are not entirely understood. To better understand these processes, vegetation photosynthetic activity and canopy water and temperature dynamics were analyzed over various types of vegetation in Amazon using satellite data from the Terra-Moderate Resolution Imaging Spectroradiometer (MODIS). The objectives of this dissertation were to 1) assess the spatial and temporal variations of satellite data over the Amazon as a function of vegetation physiognomies for monitoring and discrimination, 2) investigate seasonal vegetation photosynthetic activity and phenology across the forest-cerrado ecotone and conversion areas, and 3) investigate seasonal variations of satellite-based canopy water and land surface temperature in relation to photosynthetic activity over the Amazon basin.The results of this study showed the highly diverse and complex cerrado biome and associated cerrado conversions could be monitored and analyzed with MODIS vegetation index (VI) time series data. The MODIS enhanced vegetation index (EVI) seasonal profiles were found useful in characterizing the spatial and temporal variability in landscape phenology across a climatic gradient of rainfall and sunlight conditions through the rainforest-cerrado ecotone. Significant trends in landscape phenology were observed across the different biomes with strong seasonal shifts resulting from differences in vegetation physiognomic responses to rainfall and sunlight. We also found unique seasonal and temporal patterns of the land surface water index (LSWI) and land surface temperature (LST), which in combination with the EVI provided improved information for monitoring the seasonal ecosystem dynamics of the Amazon rainforest, cerrado, ecotone, and conversion areas. In conclusion, satellite-based, regional scale studies were found to aid in understanding land surface processes and mechanisms at the ecosystem level, providing a "big picture" of landscape dynamics. Coupling this with ground, in-situ measurements, such as from flux towers, can greatly improve the estimation of carbon and water fluxes, and our understanding of the biogeochemistry and climate in very dynamic and changing landscapes.