O nitrogênio é um elemento essencial à vida na Terra. Em geral, a disponibilização desse elemento para os seres vivos se dá por meio da fixação biológica do nitrogênio (FBN). Os micro-organismos capazes de realizar a FBN são denominados de diazotróficos e contêm o complexo enzimático da nitrogenase. Por ser um processo extremamente dispendioso, a FBN é regulada, principalmente, em nível transcricional, em resposta à quantidade de nitrogênio fixado e aos níveis de oxigênio. Os mecanismos de regulação do processo em bactérias Gram-negativas estão bem caracterizados, porém, em bactérias Gram-positivas, os estudos ainda são escassos. Paenibacillus riograndensis é uma bactéria Gram-positiva diazotrófica aeróbia facultativa e formadora de esporos, cujo sequenciamento completo do genoma a capacita como um interessante modelo para o estudo da regulação da FBN. No genoma de P. riograndensis foram identificados três agrupamentos contendo genes relacionados à FBN. Um deles, com uma organização estrutural menos conservada, foi considerado inativo a partir de análises de PCR em tempo real e de atividade de promotor. Os outros dois tiveram seus transcritos identificados e induzidos sob condições de fixação de nitrogênio, sendo um deles responsável pela codificação de um sistema alternativo da nitrogenase, independente de molibdênio. Esse sistema alternativo foi identificado como sendo aquele composto apenas por ferro e validado tanto pela análise das sequências dos genes estruturais, como pela atividade enzimática em meio sem molibdênio. Sequências localizadas a aproximadamente 250 pares de bases (pb) a montante do início da tradução dos primeiros genes dos dois agrupamentos funcionais também tiveram suas atividades como regiões reguladoras validadas pelo reconhecimento em Escherichia coli, com um provável padrão de iniciação da transcrição constitutivo. Uma menor atividade de transcrição foi observada no fragmento de 500 pb localizado a montante do agrupamento dos genes da nitrogenase alternativa, indicando a presença de regiões contendo motivos de regulação negativa do processo. Investigações mais detalhadas dessas sequências podem revelar padrões inéditos para a regulação da FBN em bactérias Gram-positivas, em geral, e em P. riograndensis, em particular. / Nitrogen is an essential element for life. In general, it becomes available to biosphere mainly through biological nitrogen fixation (BNF). Microorganisms named diazotrophs perform BNF and they have the nitrogenase enzyme. As BNF is a very energetic expensive process, it is tightly regulated mainly at transcriptional level in response to available nitrogen and oxygen levels. Regulatory networks comprising BNF systems in Gramnegative bacteria are well characterized, while studies related to Gram-positive bacteria are scarce. Paenibacillus riograndensis is a Gram-positive endospore-forming facultative anaerobic diazotroph, whose complete genome sequence presents it as an interesting model for the study of BNF regulation. In P. riograndensis genome three cluster comprising BNF related genes were identified. One of them, displaying a less conserved structural organization, was stated as inactive from real time PCR and promoter activity analysis. The other ones had their transcripts identified and responded to nitrogen fixation conditions. One of the active clusters comprises genes coding for an alternative nitrogenase system independent of molybdenum, the iron-only system. This alternative system was validated by enzymatic activity under Mo-depleted conditions. Sequences 250 base pairs (bp) upstream from the first open reading frame (ORF) of each active cluster had their promoter activities validated by recognizing in Escherichia coli, showing a probable constitutive expression pattern. A weaker promoter activity was identified in a fragment 500 bp upstream of the first ORF from the alternative cluster, suggesting the presence of a negative regulation motif. Future investigations may provide us with new patterns of BNF regulation in Gram-positive bacteria, in general, and in P. riograndensis in particular.

M.Sc. (Chemistry) / Please refer to full text to view abstract

This thesis describes a series of experiments both in solution systems and soil systems to study the precipitation of calcium carbonate in soils and the effects of the precipitation on soil pH after urea had been applied. (1) A gas bubbling system has been established which introduces ammonia at a steady rate to the reaction solution and keeps it equilibrated at 0.00484 atm partial pressure of carbon dioxide. (2) In a non-seeded system, the effects of calcium, urea, Mg (magnesium), P (phosphate), and DOC (water-dissolved organic matter) on the precipitation were examined individually and in various combinations. Calcite and vaterite were found in the 10 mM CaC1₂ solutions with and without the addition of urea. When the solutions contained Mg, P, and DOC, vaterite was not found. Aragonite was found in the reaction solution containing 5 mM Mg. In high initial concentration of P (5x10^-4 M) , the formation of calcium phosphate (amorphous by X-ray analysis) catalysed the formation of calcite. The effects of urea and Mg on the precipitation are negligible compared with the effects of P and DOC. (3) In a seeded system, 16 sets of experiments with four sizes of calcite-seeds were carried out to study the precipitation rate of calcium carbonate. This was described by the equation LR=-4.113±0.132 + 0.379±0.029 LWA + LSI where LR=log (precipitation rate, PR, in mole litre^-1 min^-1), LWA= log (newly formed calcium carbonate, g ml^-1), and LSI=log (degree of supersaturation of calcium carbonate, SI). (4) A wide range of concentrations of urea (0.05, 0.1, 0.3, 0.5, 0.7, and 1 M) were added to three soils (Beg., Uni., and VWH) with or without the addition of 5 per cent of calcite (10-15 μm) to establish a rate model for the precipitation of calcium carbonate in soils. The precipitation model (in logarithmic form) in soils is lnPR=-9.47±0.30 + lnK_SOIL + 0.379±0.029 InWA + InSI - 1686±703 P - 6.13±3.02 DOC + 3854±1775 (P DOC) where P and DOC are the concentrations in soil solutions, and lnK_SOIL is the effect of soils on the precipitation, which is - 1.98, 0.43, and -0.10 for Beg., Uni., and VWH soils respectively. The amount of newly formed calcium carbonate is about a third to a half of the amount of ammoniacal-N released by urea hydrolysis. It was able to reduce the increase of soil pH by more than 0.6 pH units in some circumstances.

The top-down effects of consumers and bottom-up effects of resource availability are important in determining community structure and ecological processes. I experimentally examined the roles of consumers — both detritivores and predators — and habitat context in affecting nutrient cycling using the detritus-based insect community in bromeliad leaf wells. I also investigated the role of multiple resources in limiting plant productivity using meta analyses. The insect community in bromeliads only increased nitrogen release from leaf detritus in the presence of a predator trophic level. When only detritivores were present, the flow of stable isotope-labeled nitrogen from detritus to bromeliads was statistically indistinguishable from that in bromeliads lacking insects. I suggest that emergence of adult detritivores constitutes a loss of nitrogen from bromeliad ecosystems, and that predation reduces the rate of this nutrient loss. Hence, insects facilitate nutrient uptake by the plant, but only if both predators and detritivores are present. Moreover, predators can affect nutrient cycling by influencing the spatial scale of prey turnover. This mechanism results in a pattern opposite to that predicted by classic trophic cascade theory. Increasing habitat complexity can have implications for nutrient cycling by decreasing the foraging efficiency of both predators and their prey, and by affecting the vulnerability of predators to intraguild predation. Along a natural gradient in bromeliad size, I found that, depending on the relationship between community composition and habitat size, habitat complexity interacts with the changing biotic community to either complement or counteract the impact of predators on nutrient uptake by bromeliads. In contrast to the existing emphasis on single-resource limitation of primary productivity, meta-analyses of a database of 653 studies revealed widespread limitation by multiple resources, and frequent interaction between these resources in restricting plant growth. A framework for analyzing fertilization studies is outlined, with explicit consideration of the possible role of multiple resources. I also review a range of mechanisms responsible for the various forms of resource limitation that are observed in fertilization experiments. These studies emphasize that a wider range of predator and nutrient impacts should be considered, beyond the paradigm of single resource limitation or classic trophic cascades. / Science, Faculty of / Zoology, Department of / Graduate

Experiments were conducted with lettuce at the field and in the glasshouse at the Hatfield Experimental Farm, University of Pretoria. The objectives of the study were to evaluate the performance of selected crisphead lettuce cultivars in relation to yield and quality performance and to investigate which level of nitrogen can produce high quality transplants. In the lettuce cultivar trial, fifteen crisphead lettuce cultivars were grown, during March to May 2004. The experiment was laid out as a randomised complete block design with four replications. At harvest, the centre 20 plants were cut for yield determination and five uniform plants were then cut longitudinally for head quality characteristics. For each cultivar, compactness and uniformity were also evaluated and the number of days to maturity was recorded. Among the cultivars tested, the best yielding cultivars were Dual Purpose (46.8 t•ha-1), Great Lakes (45.8 t•ha-1), Mohawk (44.3 t•ha-1) and Victory (43.9 t•ha-1). Poor yielding cultivars were Taina (30.5 t•ha-1), Cannon (31.5 t•ha-1), Summer Time (32.1 t•ha-1) and Classic (33.2 t•ha-1). Del Rio was the best disease resistant cultivar, producing 100% marketable heads. All cultivars tested had good compactness and uniformity with the exception of Great Lakes 659. Early-maturing cultivars were ready 60 days after transplanting. Seeds of the lettuce cultivar ‘Aviram’ were sown, in the nitrogen nutrition of lettuce transplant’s trial. Two days after seeding, the seedlings were fertigated every second day by floating the trays in the plastic-lined tubs containing nutrient solution at 0, 30, 60,90 and 120 mg•L-1 N until field capacity was reached. Transplants produced with 0 N grew poorly, regardless of the sampling date. Nitrogen at 120 mg• L-1 improved the response of shoot growth, plant height and leaf area, but adversely affected root growth. In general, relative growth rate was improved while net assimilation rate was reduced as N level increased. Root: shoot ratio decreased with applied N. The largest values of root: shoot ratio were obtained with 0 N. Both specific leaf area and leaf area ratio increased with applied N. Leaf mass ratio improved, while root mass ratio was reduced as N levels increased. At 35 days after sowing, leaf tissue N increased from 0.43 to 4.15 mg•kg-1 with N applied. Only 25% of the plants produced without N could be pulled from the seedling trays, whereas 90% could be pulled when 90 mg•L-1 N was added. This work suggested that at least 90 mg•L-1N, supplied via floatation irrigation was required to produce a transplant with sufficient roots for ease of pulling. Applying 90 mg•L-1 N, resulted in improved root and shoot growth, resulting in high quality transplants. / Dissertation (M Inst Agrar (Horticulture))--University of Pretoria, 2007. / Plant Production and Soil Science / unrestricted

An in-house developed method is presented for the purity analysis of nitrogen (N2) built-in purifier (BIPTM)) gas for the trace contaminant gases carbon dioxide (CO2), oxygen (O2)) and carbon monoxide (CO), using gas chromatography with a pulsed discharge helium ionisation detector (GC-PDHID). Nitrogen BIPTM gas is used as a “matrix” gas or diluent gas for the gravimetric preparation of binary reference materials of CO, CO2), sulphur dioxide (SO2)) and nitric oxide (NO) at the CSIR NML gas metrology laboratory. Purity analysis of nitrogen BIPTM is required to decrease the measurement uncertainty of the calculated gravimetric concentrations of the gaseous reference materials produced. The aim of the research was to find a method where amounts <0.25 x 10-6 mol•mol-1 of CO2), O2) and CO could be simultaneously analysed in high purity nitrogen within a short time, with minimum cost and on a routine basis. Gas mixtures of trace amounts of CO2), O2) and CO in N2) were separated and quantified using a parallel dual capillary column configuration with temperature and pressure programming and a pulsed discharge helium ionisation detector (PDHID). The detection limits were 9 x 10-9 mol•mol-1 for CO2), 7 x 10-9 mol•mol-1 for O2) and 37 x 10-9 mol•mol-1 for CO with repeatability precision of 1% for carbon dioxide, 1% for oxygen and 10% for carbon monoxide for a 0.2 x 10-6 mol•mol-1 standard. The detection limits obtained were lower than those reported previously by other investigators for similar methods and the validation for the method as set out in this investigation seems to be the first for trace amounts of CO2), O2) and CO in nitrogen. The method was validated by comparison of the CO2) and CO results with results obtained using a flame ionisation detector and methanisation. The technique of sequence reversal was used to improve the peak shape of CO but there was no improvement on the results obtained with temperature and pressure programming. Although no helium purging was used to reduce atmospheric contamination, it was shown that the main source of contamination from the air was through the sampling system which was reduced to a level of ± 20 x 10-9 mol•mol-1 oxygen simply by using a higher sample flow rate. It was also found that even when large amounts of CO2) were adsorbed onto the molecular sieve column, this made no difference to the column performance at trace levels. The method has also been validated for the analysis of nitrogen in high purity oxygen and may also be used to analyse carbon dioxide and carbon monoxide in oxygen as well. / Dissertation (MSc (Chemistry))--University of Pretoria, 2008. / Chemistry / unrestricted

In this work, the optical properties of ZnO doped with arsenic and nitrogen were studied. The ZnO samples were grown by Metalorganic Chemical Vapor Deposition (MOCVD). The solubility of nitrogen in the ZnO films, as well as its activation upon annealing, was also investigated. Hydrogen is known as a major source for passivation of the acceptors in ZnO:N. Therefore, it is crucial to dissociate the complex(es) formed by nitrogen and hydrogen and diffuse out the hydrogen in order to prevent the reformation of such complexes. High temperatures (≥ 600 C) are required for these purposes. In order to effectively remove the hydrogen impurities from the sample, it is important to know the optical fingerprints of hydrogen and its thermal stability. Therefore, the effects of annealing and hydrogen plasma treatment on bulk ZnO (hydrothermally grown) were first studied. The use of bulk material for this purpose was motivated by the well-resolved photoluminescence (PL) lines observed for bulk ZnO, which allow the identification of the different lines related to hydrogen after plasma treatment. Annealing at 850 C was effective for the removal of most of the hydrogen related transitions in the near-band-edge emission. Also, additional transitions at ~3.364 eV and ~3.361 eV were observed after hydrogen plasma treatment, which were ascribed to hydrogen-Zn vacancy complexes. In this work, a comparative study of the annealing ambient and temperature on ZnO films grown on GaAs substrate, using diethyl zinc (DEZn) and tertiary butanol (TBOH), showed that arsenic diffuses in the ZnO films and gives a shallow level in the band gap, which is involved in an acceptor-bound exciton line at 3.35 eV. This shallow level is visible when annealing is performed in oxygen, but not when annealing is performed in nitrogen, and indeed only for annealing temperatures around 550 C. However, annealing in either ambient also causes zinc to diffuse from the ZnO films into the GaAs substrate, rendering the electrical properties deduced from Hall measurements ambiguous. For ZnO:N, NO was used as both oxygen and nitrogen sources. Monitoring the concentration of nitrogen, carbon and hydrogen in the ZnO films, the formation of different complexes from these impurities were deduced. Furthermore, an investigation of the effect of annealing on the concentrations of impurities showed that their out- diffusion was strongly dependent on the crystalline quality of the ZnO films. For porous ZnO films, obtained at low growth temperatures (≤310 C), the out-diffusion of impurities was efficient, whereas for films grown at higher temperatures, which have improved crystalline quality, the out-diffusion was practically nonexistent. The out-diffusion of unwanted impurities may activate the nitrogen dopant in the ZnO films, as was confirmed by the PL measurements on the different samples grown at different temperatures. PL transitions at ~3.24 eV and ~3.17 eV were related to substitutional NO. These transitions were more dominant in the spectra of samples grown at low temperatures. An additional transition at ~3.1 eV was assigned to a donor-acceptor pair transition involving VZn, instead of NO, as previously reported.

No description available.

Nitrogen-rich materials are of increasing interests for the development of a wide variety of applications. These compounds are prime candidates for ligands used in the complexation of metals since they possess several lone pairs. Resulting complexes have also exhibited a wide variety of interesting properties, ranging from magnetism to gas absorption to energetic properties. This thesis describes the synthesis and characterisation of new metallic complexes with the known energetic ligands: hydrazine and H3bta, as well as that of a new nitrogen-rich compound: H4ttp. Chapter 2 outlines a series of chains bridged by hydrazine and their potential as initiatory compounds. Mononuclear lanthanide H3bta complexes are presented in Chapter 3. The development of the new nitrogen-rich, tetrazole-based H4ttp ligand is described in Chapter 4. This new ligand was used to synthesise various lanthanide complexes through hydrothermal reactions.

Diel patterns of nitrogen (NO₃⁻, NH₄⁺, urea) uptake were investigated in natural assemblages of phytoplankton from neritic and oceanic environments off the coast of British Columbia. This is the first study to report nitrogen uptake rates and extensive measurements of ambient NH₄⁺ and urea concentrations in these waters. Calculated rates of N uptake, 15 based on ¹⁵N incorporation into particulate matter during time course experiments, were maximal during the day and minimal at night. Besides the obvious effects of irradiance, the amplitude of the periodicity in uptake rate was influenced by phytoplankton community composition, ambient nitrogen concentration, forms of nitrogen available, and depth of sampling. Uptake of nitrogen during the night and in artificial darkness were measurable proportions of daytime and light uptake rates, with the importance of dark uptake generally increasing with increasing N limitation. This is the first study of diel urea uptake by marine phytoplankton in the field. The ratios of dark to light urea uptake over a diel cycle were more similar to those of NO₃⁻than those of the other reduced N form, NH₄⁺. Rates of NO₆⁻ and urea uptake by phytoplankton in the shallow and deep chlorophyll layers of the Strait of Georgia were measured over a gradient of irradiances and results of these experiments could be fitted with a hyperbolic function similar to the Michaelis-Menten equation. Half-saturation constants (KLT) for light-dependent uptake of urea and NO₃⁻ ranged from 0 to 14% of the surface irradiance and dark uptake was a variable, but often substantial (> 50%) portion of the total (light + dark) uptake. The uptake response of nitrate-replete and -starved populations of the picoflagellate, Micromonas pusilla (Butch.) Manton et Parke, to urea, NH₄⁺ and NO₃⁻ perturbations was determined by both ¹⁵N accumulation and nutrient disappearance from the culture medium. Maximum specific uptake rates (Vmax) of NH₄⁺ were 0.13 h⁻¹, more than 2 times the Vmax of NO₃⁻ or urea (ca. 0.05 h⁻¹). The half-saturation constants (Ks) for urea, NH₄⁺ and NO₃⁻ were within ± 0.1 µg-at N•L⁻¹ of each other; the average value of 0.41 µg-at. N•L⁻¹ is within the range reported for small, oceanic diatoms. NO₃⁻ uptake was completely inhibited following NH₄⁺ addition (1-10 µg-at. N•L⁻¹), whereas urea addition resulted in only a 28% reduction in NO3- uptake. Starved cultures of M. pusilla exhibited variable uptake of NH₄⁺ and urea as a function of time, with an initial "surge" uptake response. This is the first laboratory study of N uptake by an eucaroyotic picoplankter and demonstrates that many of the transient uptake responses reported for diatoms, with which it competes in the field, are common to this picoplankter. Diel periodicity of nitrogen uptake and assimilation were measured in N-replete batch cultures of M. pusilla and also in N-limited cyclostat cultures (14L:10D) at three growth rates corresponding to ca. 75, 50 and 25% of it's maximal growth rate. Nitrate uptake was continuous and independent of the L:D cycle in the cyclostat cultures at the lowest dilution rate, but NO₃⁻ uptake rates exhibited pronounced periodicity in the batch and higher dilution rate cultures, a response similar to that seen in previous studies of cyclostat cultures of some diatoms. Diel patterns in cell division, mean cell volume, potential uptake rates and internal pools of NO₃⁻ were also observed and are discussed with respect to the nutritional status of the cells. The effect of irradiance on the uptake of NH₄⁺ and NO₃⁻ by M. pusilla was also described by Michaelis-Menten kinetics; with increasing N limitation the importance of light for nitrogen uptake decreased and dark uptake increased from 5-20% to 21-39% of NO₃⁻ and NH₄⁺ uptake rates, respectively, at saturating irradiance. / Science, Faculty of / Earth, Ocean and Atmospheric Sciences, Department of / Graduate