Banerjee, Monisha J. (The University of Arizona., 2009)
Three experiments were conducted to examine restoration of disturbed land in Arizona. The first experiment attempted to revegetate abandoned farmland by direct seeding native seeds and using various soil preparation techniques, amendments, and weeding of Salsola iberica. Only irrigation and weeding had a significant effect on seed germination and canopy cover. Irrigation increased plant cover on plots, but weeds dominated the cover. A seedbank study conducted near the end of the second growing season found the soil was dominated by weeds and contained few viable native seeds. The results illustrate the difficulty of establishing native plants on abandoned desert farmland due to the dominance of weedy species, the presence of salts in the soil, and the lack of adequate soil moisture.The second experiment, a lysimeter study, tested the efficacy of different evapotranspiration (ET) soil cover designs for stabilization of acidic copper mine tailing piles. The study evaluated the effectiveness of capillary barriers (CB) to contain the waste found in tailings and different plants to revegetate the piles. The ET covers reduced infiltration of water into tailings. Copper concentrations increased significantly in plant tissue grown on the ET covers compared to plants grown in the greenhouse. Plants did not exhibit signs of phytotoxicity and concentrations were below levels toxic to all domestic animals except sheep. The CB did not reduce water infiltration into the tailings or upward migration of copper into the soil cover. Vegetation is vital to an effective ET cover. A mix of transplanted shrubs and seeded grasses and forbs establish long-term, sustainable vegetation.The third experiment examined the influence of biosolids on the bacterial communities within mine tailings by bacterial counts and bacterial diversity. The diversity of neutral copper mine tailings two weeks after biosolid application was compared with that of desert soil via cloning and sequencing of PCR amplified community 16S rRNA. Culturable heterotrophic plate counts (HPC) increased following biosolid addition. Total direct counts exceeded HPC by approximately two orders of magnitude. Overall, biosolid-amended tailings contained large numbers of bacteria diverse in nature and with many of the traits of normal desert soil bacterial communities.
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.
Hernandez - Barraza, Cesar Arturo (The University of Arizona., 2010)
Improving the efficiency of production, profitability and nutrient utilization are the most important factors for aquaculture companies. Many research efforts have been focused to develop strategies that improve the productive performance of shrimp farms. One recognized strategy is polyculture, which can considerably improve farm production yields by optimizing use of available resources.Tilapia production in shrimp ponds (with and without shrimp) has increased rapidly in many countries including Thailand, the Philippines, Honduras, Mexico, Peru, and the inland desert of Arizona.A current practice in extensive, semi-intensive and intensive culture systems is the integration of tilapia with shrimp to increase total productivity. I tested this hypothesis in the present trials experimentally by co-cultivating tilapia and Pacific white shrimp in closed recirculating systems. The present series of experiments were carried out over a period of three years between 2007 and 2009. All of these studies were developed and conducted at the facilities of the Environmental Research Lab (ERL) of the University of Arizona in Tucson, AZ.A preliminary study included three treatments in low salinity water (5 ppt). White shrimp post larvae were stocked into cylindrical plastic pools and Red tilapias were stocked into aquaria. Equal numbers of shrimp were placed in all the treatments whereas fish (Red tilapia) density was variable. We found good growth and 100 % survival of shrimp and tilapia.The first experiment included five treatments with four replicates each with saline water of 10 ppt. Shrimp and Nile tilapia were weighed and distributed in 20 fiberglass tanks with capacity of 200 liters. There were evaluated finding statistically significant differences in growth of tilapia (P< 0.05) but no significant difference in growth of shrimp at different fish densities (P> 0.05)The second and third experiments included four treatments with four replicates each using the same shrimp density in each study but different fish density by treatment. Results of one-way analysis of variance (ANOVA) for the second experiment showed a significant effect of the shrimp- tilapia polyculture on the growth of Pacific white shrimp (P< 0.05) but not for tilapia (P> 0.05) compared with monoculture. In the third experiment, there were significant differences in the growth of shrimp (P< 0.05) but not significant differences in the growth of fish (P> 0.05). These experiments were conducted using slightly different culture systems.
Mexicano Vargas, Maria de Lourdes (The University of Arizona., 2012)
The Cienega de Santa Clara is a 5600 ha, anthropogenic wetland in the delta of the Colorado River in Mexico. It is the inadvertent creation of the disposal of brackish agricultural waste water from the U.S. into the intertidal zone of the river delta in Mexico, but has become an internationally important wetland for resident and migratory water birds. The marsh is dominated by Typha domengensis with Phragmites australis as a sub-dominant species in shallower marsh areas. The most important factor controlling vegetation density was fire. The second significant (P<0.01) factor controlling NDVI was flow rate of agricultural drain water from the U.S. into the marsh. Reduced summer flows in 2001 due to canal repairs, and in 2010 during the YDP test run, produced the two lowest NDVI values of the time series from 2000 to 2011 (P<0.05). Salinity is a further determinant of vegetation dynamics as determined by greenhouse experiments, but was nearly constant over the period 2000 to 2011, so it was not a significant variable in regression analyses. Evapotranspiration (ET) and other water balance components were measured in Cienega de Santa Clara; we used a remote sensing algorithm to estimate ET from meteorological data and Enhanced Vegetation Index values from the Moderate Resolution Imaging Spectrometer (MODIS) sensors on the Terra satellite. We used Landsat NDVI imagery from 1978-2011 to determine the area and intensity of vegetation and to estimate evapotranspiration (ET) to construct a water balance. Remote sensing data was supplemented with hydrological data, site surveys and literature citations. The vegetated area increased from 1978 to 1995 and has been constant at about 4200 ha since then. The dominant vegetation type is Typha domingensis (southern cattail), and peak summer NDVI since 1995 has been stable at 0.379 (SD = 0.016), about half of NDVI(max). About 30% of the inflow water is consumed in ET, with the remainder exiting the Cienega as outflow water, mainly during winter months when T. domingensis is dormant.
Vasquez, Edward (The University of Arizona., 2006)
An invasive variety of the common reed Phragmites australis, the M haplotpye, has been implicated in the spread of this species into North American salt marshes normally dominated by the salt marsh grass Spartina alterniflora (smooth cordgrass). Phragmites australis is spreading into North American coastal marshes that are experiencing reduced salinities, while Spartina spp. are spreading into northern European brackish marshes that are experiencing increased salinities. We compared the salt tolerance and other growth characteristics of the invasive, M haplotype with two native haplotypes (F and AC) in greenhouse experiments. The M haplotype retained 50% of its growth potential up to 0.4 M NaCl, whereas the F and AC haplotypes did not grow above 0.1 M NaCl. The M haplotype produced more shoots per gram of rhizome tissue and had higher relative growth rates than the native haplotypes on both freshwater and saline water treatments. The M haplotype also differed from the native haplotypes in shoot water content and the biometrics of shoots and rhizomes. The results offer an explanation for how the M haplotype is able to spread in coastal salt marshes and support the conclusion of DNA analyses that the M haplotype is a distinct ecotype of P. australis.We then compared the growth, competitive ability, salt tolerance and osmotic adjustment of M haplotype P. australis and S. alterniflora along a salinity gradient in greenhouse experiments. Spartina alterniflora produced new biomass up to 0.60 M NaCl, whereas P. australis did not grow well above 0.2 M NaCl. When the two species were grown in mixed cultures, P. australis was less affected by competition than S. alterniflora at lower salinities but the competitive advantage reversed above 0.2 M NaCl. The greater salt tolerance of S. alterniflora compared to P. australis was due to its ability to use Na+ for osmotic adjustment in the shoots. On the other hand, at low salinities P. australis was more competitive because it produced more shoots per gram of rhizome tissue than S. alterniflora. These studies illustrate how ecophysiological differences shift the competitive advantage from one species to another along a salinity gradient.
Neilson, Julia Worsley (The University of Arizona., 2012)
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.
Gonzalez-Alanis, Pablo (The University of Arizona., 2007)
As aquaculture has become a significant provider of the human diet, the interest to have better quality of sea and fresh products has been increasing. However the potential hazards associated with pathogenic agents resulting in losses to the industry are major concerns that provided the motivation for this study.The use of ultraviolet irradiation is an alternative to disinfect water in inlet and outlet water sources. However the ultraviolet disinfection method has some drawbacks including no disinfectant residuals and high cost of lamp fouling and replacement. The ultraviolet system needs to be calibrated according with the life time of the ultraviolet lamps.The MS-2 coliphage in this study is an approach to determine a good indicator for determining if an ultraviolet system can be effective in an aquaculture recirculation system. The susceptibility of this system can provide an indication if WSSV can be inactivated and possible other pathogenic agents.The WSSV experiment was successful in reducing mortality. Further studies have to be completed and analyzed before recommending for control of other pathogens.
Haney, Christopher J (The University of Arizona., 2007)
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.
Iker, Brandon Charles (The University of Arizona., 2013)
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.
Abd-Elwahed, Mohammed Saifeldeen (The University of Arizona., 2005)
This study is aimed at addressing the capability of using remote sensing data in detecting and tracking soil salinization variability using a series of experimental methodologies. In a controlled experiment, the spectral reflectance changes associated with salt crust formation on soil surfaces were tracked in order to detect the optimum moisture levels for salinity detection and recognize the influence of soil texture on salinity-induced spectral changes. In another experiment, lettuce plants were utilized to assess plant biophysical responses to moderate salinity levels with canopy-level reflectance data. An FR-ASD spectrometer was used to collect reflectance data in the 400-2500 nm spectral region. Finally, MODIS satellite data were employed to analyze the temporal profiles of selected high (8-11 dS/m), moderate (4-6 dS/m) and none (1-3 dS/m), salt affected sites in the Nile Delta, Egypt. The analyses of spectral data revealed that the use of remote sensing data to discriminate salinity levels in soils is highly affected by moisture content and texture. At low moisture contents, salts have high reflectance in the VIS-NIR spectral region but low reflectance in SWIR region. Spectral ambiguity with soil salinity was found across soil texture types.Significant relationships were found between plant chlorophyll content and the REP index (R2 =0.97), and dry biomass with SAVI values (R2 =0.94) under different salinity treatments. The spectral vegetation indices (VI's), SAVI and REP, and water indices (WI's) were found to be effective in discriminating between plants growing under moderate conditions of soil salinity and a non-saline condition. The combination between VI's and WI's was found to be useful in improving the ability to assess salinity stressed plants from non-stressed plants. Finally, MODIS results showed separability between canopy seasonal growth under high saline (HS) and non-saline (NS) conditions based on phenology. Canopies growing under HS conditions had lower VI and WI values in the green-up period. It may be concluded that using plant biophysical response to detect soil salinity could be useful in detecting early stages of salinity. Also using the combination between VI's and WI's using MODIS data is a useful to discern between high saline and none saline areas.
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