The potential shortage of phosphorus (P) fertilizer is a threat to food security and closing the nutrient loop through recycling human excreta, especially urine, has been considered, so as to mitigate this crisis. Struvite (magnesium, ammonium phosphate), a material derived from human urine, is a product which is gaining credence with regards to using urine as a P amendment since more than 90% of P in urine can be captured during struvite production. A study to evaluate the potential of struvite as a P amendment in three contrasting soils was conducted. The soils used were an A horizon of Inanda (Ia), A horizon Sepane (Se) and an E horizon of Cartref (Cf). Phosphate adsorption properties of the soils were studied and the Freundlich model used to derive sorption parameters. From these studies, Pmax was related to the Kf parameter of the Freundlich equation. Two sets of incubation studies were then conducted. The first ran for 122 days and the second for 22 days to examine in closer detail the early stages of dissolution of the struvite as the major P release occurred during this time period of the incubation. A pot experiment was conducted in a controlled environment so as to determine the effect of P released from struvite on maize growth. The Ia, with high content of iron and aluminum oxides, displayed high sorption and affinity for P, whereas soil texture was a principal factor in the sorption properties of the Se (clayey) and Cf (sandy). The Kf decreased in the order Ia > Se > Cf and external P requirements decreased in the order Se > Ia > Cf. In the incubation studies solution P content increased with an increase in application rate of struvite. Struvite dissolution and P release varied between the different soils and the dissolution was found to be related to the P adsorption maximum of each individual soil and soil pH. The magnesium content also increased with time. In the glasshouse study, drymatter yield after six weeks growth was improved by the addition of struvite. There were no benefits achieved by using more than the recommended application rates for each soil. Struvite was as effective as conventional single superphosphate in the Ia and Cf, while superphosphate outperformed struvite on the Se. The findings of this study suggest that struvite has the potential to release P in an available form although its effectiveness and capability to release P could depend on soil pH, exchangeable acidity and initial P levels. Further research needs to focus on the effect of pH on struvite dissolution, the effect of struvite on soil pH, as well as comparison of nutrient release patterns between struvite and rock phosphate. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2013.

This study examined the influence of different management practices under sugarcane production on soil chemical, biological and physical properties on a long-term (59yr) field experiment in KwaZulu-Natal. These management practices included conventional post-harvest burning of crop residues, with the tops either left on the soil surface or with tops removed, and green cane harvesting with the retention of crop residues on the soil surface as a trash blanket. Each of these treatments were either fertilized or did not receive fertilizer. The data collected was used to evaluate the effect of crop residue management on soil quality under sugarcane production. Soil organic matter content increased from 39 g C kg¯¹ soil, under conventional burning to 55 g C kg¯¹ soil in the surface 10 cm under green cane harvesting where crop residues are returned to the soil. It also resulted in greater recycling of nutrients and increases in exchangeable K and Ca and extractable P. Fertilizer application resulted in a build-up of soil nutrients in combination with trash retention. Fertilizer application induced increases in exchangeable P and also some accumulation in soil organic P. Exchangeable and non-exchangeable K concentrations were also higher in fertilized than non-fertilized treatments. However, nitrogen fertilizer application and, to a lesser degree, organic matter mineralization, resulted in soil acidification to a depth of 30 cm. Acidification in the fertilized treatments resulted in a concomitant increase in exchangeable acidity and exchangeable Al, due to the increase in H⁺ ions and solubilized Al species on exchange sites. Base cations moved into soil solution and were leaching to lower soil layers. The decrease in soil pH resulted in the surface charge conferred on the variable charge surfaces on soil colloids becoming less negative and as a result there was a decrease in ECEC. Acidification in fertilized treatment not only increased exchangeable Al but also the buffering reserve of non-exchangeable al; both that complexed with soil organic matter (CuCl₂- extractable) and that present as hydroxy - Al associated with mineral colloids (ammonium acetate - extractable). The increased organic matter content under trash retention resulted in an increase in ECEC. This enabled the soil to retain greater amounts of Ca²⁺, Mg²⁺ and K⁺ which were returned to the soil in the trash. Both residue retention and fertilizer application had a positive effect on the microbial biomass C and N and the microbial quotient increased from 0.39% to 0.86% as organic C increased from 39 g C kg¯¹ soil under burnt treatments to 55 g C kg¯¹ soil under trashed, fertilized treatments. This increase was associated with increased concentrations of labile organic material (K₂S0₄₋extractable) present as well as increased amounts of nutrients being cycled through the plant-soil system. The light fraction organic matter also increased with increasing returns of organic residues. However, the large active microbial biomass under the trashed, fertilized treatment resulted in an increased turnover rate of this fraction and consequently resulted in lower LF dry matter, C and N than in the unfertilized treatment. Aggregate stability increased with increasing amounts of organic material returned due to trash retention. Nevertheless, fertilized treatments induced a lower aggregate stability than unfertilized ones, despite the tendancy for the latter to have higher organic C and microbial biomass values. This was attributed to an increase in the proportion of exchangeable cations present in monovalent form (due to application of fertilizer K and leaching of Ca and Mg) favouring dispersion and a decline in aggregate stability. Green cane harvesting resulted in an increase in microbial activity (basal respiration, FDA hydrolytic activity, arginine ammonification rate and dehydrogenase activity) and in the activity of specific soil enzymes involved in turnover of C, N, P and S to a depth of 30 cm. Increased activities of these enzymes reflect a higher rate of turnover of C, N, P and S. The metabolic quotient decreased with increasing residue return, indicating a more metabolically efficient microbial community. Fertilizer application resulted in a variable effect on enzyme activity. Long-term fertilizer application resulted in an increase in invertase and acid phosphatase, a decrease in L-histidase and arylsulphatase and had little effect on protease and alkaline phosphatase. These variable effects were explained in terms of an interaction between fertilizer - induced increases in Corg and soil nutrient status and fertilizer - induced soil acidification. The size and activity of the soil microbial biomass was studied in the plant row and in the inter-row of a sugarcane field under burning or green cane harvesting. Soils were sampled to 30 cm depth in (i) the centre of the plant row, (ii) 30 cm out from the row centre and (iii) 60 cm out from the row centre (i.e. the middle of the inter-row area). Under burning, the only substantial input of organic matter to the soil was from root turnover in the row area where the root biomass was concentrated. As a consequence, the size (microbial biomass C) and activity (basal respiration of the soil microbial community were concentrated in the row. However, under green cane harvesting there was a large input of organic matter in the inter-row area in the form of the trash blanket itself and through turnover of crop roots that were concentrated in the surface 10 cm of the soil below the blanket. As a result, soil microbial activity was considerably higher in the interrow area under green cane harvesting than under burning. Phospholipids are essential membrane components of microorganisms and a good correlation was found between the total PLFA's extracted from soils and the microbial biomass C, indicating that phospholipids are an accurate measurement of living biomass. Mutivariate statistical analysis (PCA) was used to separate different PLFA profiles under burning versus trash retention and under different land uses (sugarcane, maize, annual and perennial pasture and undisturbed veld). Soil organic matter content contributed the greatest variance in the data along the first axis. That is increasing soil organic matter return not only increased the size of the microbial biomass, but also affected the composition of the microbial community. There was a shift in the different sub-fractions under different management practices. MUFA's are general biomarkers of Gram negative bacteria and were found to be a sensitive indicator of higher substrate availability (i.e they increased under green cane harvesting). Fungal biomarkers indicated an increased fungal biomass associated with surface application of residues. Soil physical conditions were considered to be a contributing factor to the shift in microbial community structure. Increased organic matter content improved soil physical conditions and preferentially stimulated the growth of aerobic microorganisms. In addition to this, the proportion of SATFA (gram positive bacteria) was found to increase in response to burning. This increase was attributed to the survival mechanisms of these microorganisms (i.e. endospore formation). It was found that the conversion from burning to trash management changes the composition of the soil microbial community. The effect of management practices on soil functional diversity was also evaluated using two methods (i.e. Biolog plates and substrate induced respiration (SIR)). Biolog plates are a selective technique that stimulate growth of a small proportion of the soil microbial community whereas the SIR technique measures the activity of the metabolically active microbial community in situ. As a result the SIR method separated treatments more effectively than Biolog plates (i.e. annually tilled treatments, permanent grassland sites and fertilized and unfertilized treatments). The quantity and the quality of organic C supply influenced the catabolic diversity. Conversion from burning to green cane harvesting greatly increased catabolic evenness and richness and therefore presumably also tended to increase the resilience of the soil to stress and disturbance particularly in relation to decomposition functions. It was concluded that conversion from preharvest burning to green cane harvesting results in an increase in soil organic matter content, an improvement in soil structure and soil nutrient status, an increase in the size, activity, taxonomic and functional diversity of the soil microbial community. The practice should therefore be promoted to the South African sugar industry. / Thesis (Ph.D.)-University of Natal, Pietermaritzburg, 2003.

Laboratory studies and field trials were carried out to investigate the effect of addition of some organic residues to acid soils on soil pH, exchangeable and soluble AI, nutrient status, microbiological and biochemical indices and maize response. The organic wastes used in the first laboratory study included plant materials (maize. sorghum, kikuyu grass, soybean, red clover residues and acacia prunings), animal manures (kraal, pasture-fed and feedlot cattle manure, layer and broiler poultry manure and pig manure), household compost, sewage sludge, and filter cake. The poultry manure, pig manure and leguminous plant residues had the highest content of basic cations while sewage sludge had the highest N content. Poultry manure had very high values for proton consumption capacity, CaC03 content and ash alkalinity. Proton consumption capacity, ash alkalinity, total basic cation content and CaC03 content were closely correlated with one· another. Soil pH was increased and exchangeable AI and total (AIT) and monomeric (AIMono) AI in solution were decreased by addition of all the organic wastes: the effect was greater at the higher rate of application. Strong correlations were recorded between the rise in soil pH and proton consumption capacity, ash alkalinity, CaC03content and basic cation content of the residues. The major mechanisms responsible for the elevations in pH were suggested to be the substantial CaC03content of poultry and pig manures, and filter cake, the proton consumption capacity of humic material present in household compost and manures and decarboxylation of organic acid anions during the decomposition of plant residues and manures. It was proposed that ash alkalinity is a suitable laboratory test for predicting the potential Iiming effect of organic residues since it is strongly correlated with the rise in pH that occurs, it is relatively simple to measure and the values reflect the initial content of organic acid anions, humic materials and CaC03in the residues. A preliminary field experiment was set up to investigate the effectiveness of kraal manure as a Iiming material in an acid soil (pHwater =4.1) at a site close to a Zulu village. The experiment consisted of two rates of lime (L1 = 2.5 and L2 = 5.0 t ha1) and two rates of kraal manure (K1 = 10 and K2 = 20 t ha-1 ) which were banded and incorporated in a 30 cm wide strip down the plant rows. Treatments were arranged in a randomized block design with three replicates. A commercial maize cultivar PAN 6710 and a traditional variety EMBO, used by the farmers in the locality, were grown. Soils in the plant row were sampled at tasselling and at harvest. The addition of kraal manure significantly raised soil pH and reduced concentrations of exchangeable AI and those of both total and monomeric AI in soil solution. Lime raised pH and the pH continued to increase between tasselling and harvest. Maize yields for control, kraal manure (K1 and K2) and lime (L1 and L2) for PAN 6710 were 2.5, 3.7, 5.1, 5.3 and 6.3 t ha-1 ; respectively and for EMBO they were 3.0, 5.4, 5.8, 5.9and 8.2 t ha-1 , respectively. These results demonstrate the high yield potential of the traditional maize variety under small scale farming conditions, and show that large yield increases can be obtained by applying kraal manure. The long-term effects (24 weeks) of incubation of organic wastes (soybean residues, poultry, pig and kraal manures and sewage sludge) with an acid soil were investigated in a laboratory study. After incubation for six weeks incubation, soil pH was raised and exchangeable AI and Air and AIMono in soil solution were decreased . by addition of the wastes. Soil pH generally declined and exchangeable and soluble AI increased over the remainder of the incubation period. The decline in pH was attributed mainly to nitrification of NH4+ originating from mineralization of wastes-derived organic N. Addition of organic materials generally resulted in a decrease in the proportion of solution Air present as AIMono. That is, the effects of addition of organic materials was two-fold; an increase in pH in the short term and complexation of AI by organic matter. Since these effects occur simultaneously, it would be desirable to separate them. For this reason, short-term equilibration experiments (3 days) were conducted to study the solubility of AI in aqueous solution or in an Oxisol when in equilibrium , with 3 manures (kraal, pig and poultry) at pH values of 4.0, 4.5, 5.0, 5.5, 6.0 and 6.5. Addition of manures tended to reduce the concentrations of total AI in solution (AIT) in the lower pH range (Le. pH 4.0 and 4.5) but increased AIT concentrations compared to the control, at higher pH values (Le. at pH 5.5 and above). This was explained in terms of the complexing ability of both the solid and solution phases. At lower pH, where AI is highly soluble, complexation by added solid phase manure-organic matter results in a reduction of AI solubility. However, at high pH, where AI solubility is limited, the most important mechanism is complexation of AI by soluble organic matter and this increased AI solubility. Additions of manure reduced the proportion of Air present in monomeric form (AIMono). This effect was more pronounced in aqueous solution but was also clearly evident above pH 5.0 in the Oxisol. This reflects the fact that a large concentration of soluble C in solution can maintain relatively high concentrations of complexed AI in solution but at the same time maintain low concentrations of AIMono. It was concluded that formation of AI-organic matter complexes caused by additions of organic manures can alter the solubility of AI and reduce the amount of phytotoxic AIMono present in soil solution. A second field trial was conducted to compare the effects of additions of kraal manure, grass residues, lime and fertilizer (N-P-K) under field conditions, on soil pH, AI solubility and maize response and, at the same time follow concomitant changes in the size and activity of the soil microbial biomass and enzyme activity. The greatest effects of kraal manure in increasing soil pH and decreasing AI toxicity were recorded six weeks after planting whereas those of lime and grass residues were recorded at harvest. Kraal manure and fertilizer increased significantly AMBIC extractable P and exchangeable K and Zn. In addition, Kraal manure, and to a lesser extent lime significantly increased exchangeable Ca and Mg.. Soils in the plant row in the grass residue treatments had the highest microbial biomass C and microbial quotient,followed by kraal manure, lime and controls. Basal respiration rates and arginine ammonification, protease, aryl sulphatase, and acid phosphatase activity rates were significantly increased by addition of all treatments and these increases tended to be accentuated by fertilizer. Low values for metabolic quotient in the grass residue treatments were associated with high values for microbial biomass C in these treatments. The addition of all treatments tended to increase maize yields and, in general, these yields were greater for the high rate of application of each amendment. Yields for unfertilized kraal manure were markedly greater than those for the unfertilized grass residue and lime treatments. This was attributed to the ability of kraal manure to both increase pH and add nutrients to the soil. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2004.

Most natural products and xenobiotic molecules, irrespective of their molecular or structural complexity, are degradable by some microbial species/associations within particular environments. Atrazine- and selected petroleum hydrocarbon (benzene, toluen~ and 0-, m- and p-xylene (BTX))-degrading associations were enriched and isolated"trom atrazine- and petroleum hydrocarbon (PHC)-contaminated KwaZuluNatal loamy and sandy soils, respectively. In total, eight pesticide- and forty BTXcatabolizing associations were isolated. Electron microscopy revealed that, numerically, rods constituted the majority of the populations responsible for both atrazine and PHC catabolism. Cocci and, possibly, spores or fungal reproductive bodies were observed also. For the BTX-catabolizing associations, the population profiles appeared to be dependent on the enrichment pH and the molecule concentration. After combining selected associations, to ensure that all the isolated species were present, batch cultures were made to determine the optimum pH and temperature for growth; With an atrazine concentration of 30 mgr1, the highest specific growth rates, as determined by biomass (OD) changes, were recorded at 30DC and pH 4 although the rate§ at 25DC and pH 5 were comparable. For the BTX (50 mgr1)-catabolizing associations, the highest growth rates were recorded at pH 4 for the four temperatures (15, 20, 25 and 30DC) examined. The sole exception was p-xylene with the highest specific growth rate recorded at pH 5 and 30De. Batch and continuous (retentostat) cultivations in the presence/absence of methanol and under C- and N-limited conditions were used to investigate the impacts of the solvent and the catabolic potentials of a combined atrazine-catabolizing culture (KRA30). In general, different degradation rates were recorded for the culture in response to element limitation. Addition of citrate as the primary carbon source / effected atrazine (100 mg!"l) degradation rates comparable to that of Pseudomonas sp. strain ADP while succinate addition effected herbicide co-metabolism. Carbon supplementation may, therefore, be considered for site amelioration practices. To complement conventional culture-based microbiological procedures, molecular techniques were employed to explore the diversities and analyze the structures of the microbial communities. In parallel, anaerobic microbial associations which targeted atrazine were also characterized. The soil DNA isolation/characterization protocol adopted consisted of a clean-up step followed by the polymerase chain reaction (peR) and 16S rDNA fingerprinting by denaturing-gradient gel electrophoresis (DGGE). The preliminary results suggested that despite different, but chemically similar, petroleum hydrocarbon molecules, the common selection pressures of the primary enrichments effected the isolation of similar and complex aerobic microbial associations. Some similar numerically-dominant bands characterized the aerobic and anaerobic atrazine-catabolizing associations although distinct differences were also recorded on the basis of the enrichment/isolation pH value and the concentration of the herbicide. Cloning and sequencing were then used to identify some of the numerically-dominant and non-dominant association members. Community-level physiological profiling (CLPP) for physiological fingerprinting was made with Biolog EcoPlates and highlighted the differences in the isolated aerobic atrazine-catabolizing associations depending on the enrichment pH and molecule concentration. Logarithmic-phase cultures of the combined atrazine- and BTX-catabolizing associations were used to explore the association profiles following pH and temperaiure optImIzation. Although some common numerically-dominant components were maintained, differences in numerical and, possibly, activity dominance were observed in the 16S rDNA profiles in response to changes in pH and temperature. This indicated that environmental parameter optimization and characterization of catabolic association structure must precede bioaugmentation so that control of key variables will facilitate maintenance of the dominant site-specific species. Following KRA30 cultivation in the presence/absence of methanol and under carbon and nitrogen-limited conditions, the population fingerprints showed that the presence of methanol effected shifts in species numerical dominance and, possibly, changes in atrazine catabolic capacity. Also, Coulter counter results, optical density readings and 16S rDNA characterization by DGGE indicated that degradation rate changes were accompanied by shifts in species numerical/activity dominance within the association. Although N-limitation effected the highest rates of herbicide catabolism, a potential versatility of the combined association for bioaugmented and/or biosupplemented remediation with acceptable rates regardless of any elemental limitation was recorded. To determine if the contaminated and pristine source soils contained comparable catabolic populations and, thus, offered potential for intrinsic bioremediation, PCRDGGE was used to characterize the populations in comparison with the enriched/isolated associations. Some similar dominant bands characterized the contaminated soils and the enriched/isolated associations. The significance of this, in relation to a possible correlation between numerical and activity dominance in the component species, is discussed with respect to the use of PCR-DGGE to identify natural attenuation potential and monitor sustained intrinsic and enhanced (bioaugmented and biosupplemented) bioremediation. / Thesis (Ph.D.)-University of Natal, Pietermaritzburg, 2001.

In many acid, highly leached South African soils, Na levels are very low. Applications of Na to highly leached soils may be advantageous in some situations as Na has been shown to interact with soil acidity, P availability, and K nutrition of plants. It was found that an increased level of Na at constant anion concentration in the soil solution resulted in lower soil solution pH and Al3 + activity, and improved maize root penetration into an acid subsoil (pot trial). In another pot trial, Na did not improve lucerne root growth into the same subsoil. In a field trial on a limed, low-Na soil with severe subsoil acidity, the effects off our rates of Na, three Na carriers, and three rates of gypsum on maize growth were compared. In three out of four seasons grain yield responses to the Na applications were positive, and of a similar magnitude to the response to gypsum (455-925 kg ha). In another field trial with maize, responses to Na (of up to 1027 kg grain ha) were recorded in two out of three years on plots with topsoil acid saturations of greater than 45%. The reason for the responses to Na was probably improved subsoil rooting as a result of modified soil solution composition in the presence of Na. In a field trial with Italian rye grass on an acid, highly weathered soil, the effect of sodium applications were investigated at different levels of lime and K. In the first season, 200 kg ha Na as NaCl increased dry matter yield from 11289 kg ha to 12815 kg ha , Sodium responses were possibly due to enhanced P uptake, or Na substitution for K, or a combination of the two mechanisms. No consistent lime x Na interaction was observed. Potassium and Na applications affected the mineral balance of the herbage produced. Potassium depressed herbage Ca, Mg and Na concentrations, and Na depressed herbage Ca and Mg where herbage K was low, but had no effect on herbage K. Where soil P and K reserves are marginal, rye grass pastures may benefit from Na applications. / Thesis (Ph.D.)-University of Natal, Pietermaritzburg, 2000.

The environmental impact of anthropogenic disturbances such as agriculture, on the soil ecosystem, and particularly on soil microbial structural and functional diversity, is of great importance to soil health, conservation and remediation. Therefore, this study assessed the effects of various land use and management practices on both the structural (genetic) and functional (catabolic) diversity of the soil bacterial and fungal communities, at two long-term sites in KwaZulu-Natal. The first site is situated at Baynesfield Estate, and the second at Mount Edgecombe Sugarcane Research Institute. At site 1, the land uses investigated included soils under pre-harvest burnt sugarcane (Saccharum officinarum, Linn.) (SC); maize (Zea mays, Linn.) under conventional tillage (M); permanent kikuyu (Pennisetum clandestinum, Chiov) pasture (KIK); pine (Pinus patula, Schiede) plantation (PF); and wattle (Acacia mearnsii, De Wild) plantation (W), all fertilized; and undisturbed native grassland (NAT) that had never been cultivated or fertilized. At site 2, a sugarcane (Saccharum officinarum × S. spontaneum var. N27) pre-harvest burning and crop residue retention trial was investigated. The treatments studied included conventional pre-harvest burning of sugarcane with the tops removed (Bto), and green cane harvesting with retention of crop residues on the soil surface as a trash blanket (T). Each of these treatments was either fertilized (F) or unfertilized (Fo). The polymerase chain reaction (PCR), followed by denaturing gradient gel electrophoresis (DGGE) were used to determine the structural diversity, and community level physiological profiling (CLPP) using BIOLOG plates, the catabolic diversity. In addition, the soils were analysed with respect to selected physicochemical variables, and the effects of these on the soil microbial communities were determined. Replicate soil samples (0–5 cm) were randomly collected from three independent locations within each land use and management, at both sites. Soil suspensions for the CLPP analyses were prepared from fresh soil subsamples (within 24 h of collection) for the bacterial community analyses, and from 8-day-old soil subsamples (incubated at 4°C to allow for spore germination) for the fungal community analyses. BIOLOG EcoPlates™ were used for the bacterial CLPP study and SF-N2 MicroPlates™ for the fungal analysis, the protocols being adapted and optimized for local conditions. This data was log [X+1]-transformed and analysed by principal component analysis (PCA) and redundancy analysis (RDA). For PCRDGGE, total genomic DNA was isolated directly from each soil subsample, and purified using the MO BIO UltraClean™ soil DNA Isolation kit. Protocols were developed and optimized, and fragments of 16S rDNA from soil bacterial communities were PCR-amplified, using the universal bacterial primer pair 341fGC/534r. Different size 18S rDNA sequences were amplified from soil fungal communities, using the universal fungus-specific primer pairs NS1/FR1GC and FF390/FR1GC. Amplicons from both the bacterial and fungal communities were fingerprinted by DGGE, and bands in the fungal DGGE gels were excised and sequenced. The DGGE profiles were analysed by Bio-Rad Quantity One™ Image analysis software, with respect to band number, position, and relative intensity. Statistical analyses of this data then followed. Soil properties [organic C; pH (KCl); exchangeable acidity; total cations (ECEC); exchangeable K, Ca and Mg; and extractable P] were determined by PCA and were shown to have affected the structural and catabolic diversity of the resident microbial communities. At Baynesfield, canonical correspondence analysis (CCA) relating the selected soil variables to bacterial community structural diversity, indicated that ECEC, K, P and acidity were correlated with CCA1, accounting for 33.3% of the variance, whereas Mg and organic C were correlated with CCA2 and accounted for 22.9% of the variance. In the fungal structural diversity study, pH was correlated with CCA1, accounting for 43.8% of the variance, whereas P, ECEC and organic C were correlated with CCA2, and accounted for 30.4% of the variance. The RDA of the catabolic diversity data showed that the same soil variables affecting fungal structural diversity (organic C, P, ECEC and pH) had influenced both the bacterial and fungal catabolic diversity. In both the bacterial and fungal RDAs, organic C, P and ECEC were aligned with RDA1, and pH with RDA2. However in the bacterial analysis, RDA1 accounted for 46.0%, and RDA2 for 27.5% of the variance, whereas in the fungal RDA, RDA1 accounted for only 21.7%, and RDA2 for only 15.0% of the variance. The higher extractable P and exchangeable K concentrations under SC and M, were important in differentiating the structural diversity of these soil bacterial and fungal communities from those under the other land uses. High P concentrations under M were also associated with bacterial catabolic diversity and to a lesser extent with that of the soil fungal communities under M. Similarly, the higher organic C and exchangeable Mg concentrations under KIK and NAT, possibly contributed to the differentiation of these soil bacterial and fungal communities from those under the other land uses, whereas under PF, the high exchangeable acidity and low pH were possibly influencing factors. Under W, low concentrations of P and K were noted. Other factors, such as the presence/absence and frequency of tillage and irrigation, and the diversity of organic inputs due to the diversity of the above-ground plant community, (in NAT, for example) were considered potentially important influences on the nature and diversity of the various land use bacterial and fungal communities. At Mount Edgecombe, CCA showed that organic C and Mg had a significant effect on soil bacterial structural diversity. Organic C was closely correlated with CCA1, accounting for 58.7% of the variance, whereas Mg was associated with CCA2, and accounted for 41.3% of the variance. In the fungal structural diversity study, ECEC and pH were strongly correlated with CCA1 and accounted for 49.1% of the variance, while organic C was associated with CCA2, accounting for 29.6% of the variance. In the functional diversity studies, RDA showed that both bacterial and fungal community catabolic diversity was influenced by soil organic C, pH, and ECEC. In the bacterial analysis, RDA1 was associated with organic C and pH, and accounted for 43.1% of the variance, whereas ECEC was correlated with RDA2, accounting for 36.9% of the variance. In the fungal analysis, RDA1 was correlated with ECEC and accounted for 47.1% of the variance, while RDA2 was associated with pH and organic C, accounting for 35.8% of the variance. The retention of sugarcane harvest residues on the soil surface in the trashed treatments caused an accumulation of organic matter in the surface soil, which did not occur in the pre-harvest burnt sugarcane. This difference in organic C content was a factor in differentiating both bacterial and fungal communities between the trashed and the burnt treatments. Soil acidification under long-term N fertilizer applications caused an increase in exchangeable acidity and a loss of exchangeable Mg and Ca. Thus, as shown by CCA, a considerably lower exchangeable Mg concentration under F compared to Fo plots resulted, which was influential in differentiating the bacterial and fungal communities under these two treatments. In the structural diversity study at Baynesfield, differences were found in bacterial community species richness and diversity but not in evenness, whereas in the fungal analysis, differences in community species richness, evenness and diversity were shown. The soil bacterial and fungal communities associated with each land use were clearly differentiated. Trends for bacterial and fungal diversity followed the same order, namely: M < SC < KIK < NAT < PF < W. At Mount Edgecombe, no significant difference (p > 0.05) in bacterial structural diversity was found with oneway analysis of variance (ANOVA), but two-way ANOVA showed a slight significant difference in bacterial community species richness (p = 0.05), as an effect of fertilizer applications. A significant difference in fungal species richness (p = 0.02) as a result of management effects was detected, with the highest values recorded for the burnt/fertilized plots and the lowest for the burnt/unfertilized treatments. No significant difference was shown in species evenness, or diversity (p > 0.05), in either the bacterial or the fungal communities. In the catabolic diversity study at site 1, the non-parametric Kruskal-Wallis ANOVA showed that land use had not affected bacterial catabolic richness, evenness, or diversity. In contrast, while fungal catabolic richness had not been affected by land use, the soil fungal community catabolic evenness and diversity had. At site 2, the land treatments had a significant effect on soil bacterial community catabolic richness (p = 0.046), but not on evenness (p = 0.74) or diversity (p = 0.135). In the fungal study, land management had no significant effect on the catabolic richness (p = 0.706), evenness (p = 0.536) or diversity (p = 0.826). It was concluded, that the microbial communities under the different land use and trash management regimes had been successfully differentiated, using the optimized protocols for the PCR-DGGE of 16S rDNA (bacteria) and 18S rDNA (fungi). Sequencing bands produced in the 18S rDNA DGGE, enabled some of the soil fungal communities to be identified. CLPP of the soil microbial communities using BIOLOG plates showed that, on the basis of C substrate utilization, the soil bacterial and fungal communities’ catabolic profiles differed markedly. Thus, it was shown that the different land use and management practices had indeed influenced the structural and catabolic diversity of both the bacterial and fungal populations in the soil. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2011.

Soil organic matter (SOM) is a dynamic soil property, sensitive and responsive to many factors. The possibility of increasing soil carbon (C) sequestration by changing land use and management practices has been of great interest recently due to concerns with global changes in the atmospheric carbon dioxide (CO2) balance. Nonetheless, as a result of the complex dynamics of SOM, there is still the need for SOM characterization procedures capable of monitoring SOM stabilization, taking into account all the factors involved. This study characterized SOM stabilization as affected by management practices in three long-term field experiments, considering physical, chemical and biological components. The field experiments are located near Lexington, Kentucky, on a Maury silt loam (fine, mixed, mesic Typic Paleudalfs). The first experiment evaluates tillage and nitrogen (N) rate effects. The second experiment studies manure and N rate effects. The third experiment evaluates the five corn components of three crop rotations [continuous (monoculture) corn, corn-wheat/double crop soybean, and hay-hay-corn-corn-corn]. Soil organic matter content, stability, and composition, for physically separated fractions, were assessed using δ13C natural abundance and diffuse reflectance Fourier transformed infrared (DRIFT) spectroscopy. In addition, management effects on microbial biomass and microbial function as indicated by phenol oxidase enzyme activity were evaluated. The results indicate that management practices affect SOM content, stability, and composition, and these effects differ by the soil aggregate fraction. No-tillage (NT), N fertilization, manure application and increased corn in crop rotations enhanced SOM levels. However, the effect of NT was observed mainly at the soil surface. Soil organic matter storage was determined by the aggregate size distribution. The proportion of recently deposited C was generally positively related to aggregate size, especially for the first and third experiments. Most of the recently deposited C was stabilized in microaggregates within macroaggregates, across the management treatments and field experiments. In addition, this fraction consistently exhibited low to medium SOM reactivity. These results suggest that SOM stabilization, as influenced by management practices, required achieving a specific composition and location within the soil matrix. This implies that soil C forms and aggregate size and stability are closely interrelated.

Spatial variability of soil properties complicates the understanding of water and solute transport at the field scale. This study evaluated the impact of land use, soil surface roughness, and rainfall characteristics on water transport and Br- leaching under field conditions by means of a new experimental design employing scale-dependent treatment distribution. On a transect with two land use systems, i.e., cropland and grassland, rainfall intensity and the time delay between Br- application and subsequent rainfall were arranged in a periodically repetitive pattern at two different scales. Both scales were distinct from the scale of surface roughness as described by elevation variance. Nests of tensiometers and suction probes were installed at 1-m intervals along the transect to monitor matric potentials and Br- concentrations at different depths, respectively. After rainfall simulation, soil samples were collected at every 0.5 m horizontal distance in 10 cm vertical increments down to 1 m depth for Br- analysis. Soil Br- concentration was more evenly distributed with soil depth and leached deeper in grassland than cropland, owing to vertically continuous macropores that supported preferential flow. Frequency-domain analysis and autoregressive state-space approach revealed that the dominant factors controlling Br- leaching varied with depth. In shallow layers, land use was the main driving force for Br- distribution. Beyond that, the spatial pattern of Br- was mostly affected by rainfall characteristics. Below 40 cm, the horizontal distribution of Br- was dominated by soil texture and to a smaller extent by rainfall intensity. Bromide concentrations obtained from soil solution samples that were collected through suction probes showed similar results with respect to the influence of rainfall intensity. The spatial variation scale of temporal matric potential change varied with both time and depth, corresponding to different boundary condition scales. Matric potential change in some cases, reflected the impact of soil properties other than the boundary conditions investigated, such as hydraulic conductivity, contributing to the scale-variant behavior of Br- leaching. These findings suggest the applicability of scale-dependent treatment distribution in designing field experiments and also hold important implications for agricultural management and hydrological modelling.

Wine sensory attributes are associated with quality of wines. Cabernet Franc did not possess good coloration of its wine. Therefore, in the 2009 and 2010 growing seasons, studies including the sampling of four red wine grape cultivars from the end of flowering throughout the rest of the season and applying treatments to Cabernet Franc grapevines at veraison were commenced to address suitability and color enhancement, respectively. The study examining Cabernet Franc, Cabernet Sauvignon, Chambourcin, and Norton looked at sampling their grapes at two-week intervals from times post-flowering to understand the demands of each cultivar during key stages of berry development, in particular berry maturation post-veraison. The French-American hybrids Chambourcin and Norton were found to accumulate high levels of anthocyanins, also termed high cultivar performance, while the Vitis vinifera L. cultivars of Cabernet Franc and Cabernet Sauvignon remained stable in their anthocyanin content post-veraison. The results of the treatments applied to Cabernet Franc as a possible exogenous amelioration for anthocyanin pigment deficit in this cultivar support use of treatments for improving coloration in Cabernet Franc in Kentucky.

Several types of antibiotics (roxarsone, virginiamycin, and bacitracin) are widely included in poultry feed to improve animal growth yields. Most of the antibiotics are excreted in manure which is subsequently applied to soils. One concern with this practice is that antibiotics may affect several microbially-mediated nutrient cycling reactions in soils that influence crop productivity and water quality. The main objectives of this study were to determine the effects of livestock antibiotics on nitrification, denitrification, and microbial community composition in soils along a topographic gradient. These objectives were addressed in a series of lab experiments by monitoring changes in inorganic N species and ester-linked fatty acid methyl ester profiles after exposing soil microorganisms collected from different topographic positions to increasing levels of antibiotics. It was discovered that roxarsone and virginiamycin inhibited nitrification and soil microbial growth and also influenced microbial community composition, but only at levels that were much higher than expected in poultry litter-applied soils. Bacitracin did not affect nitrification, microbial growth, or microbial community composition at any concentration tested. None of the antibiotics had a strong affect on denitrification. Thus, it is unlikely that soil, water, or air quality would be significantly impacted by the antibiotics contained in poultry litter.