Headwater streams are extremely vulnerable to the consequences of land-use change as they are tightly coupled with the surrounding landscape. Understanding the natural processes that influence the structure and function of these ecosystems will improve our understanding of how land-use change affects them. Benthic substratum habitat was investigated in a sub-tropical headwater stream by quantifying temporal change to sediment texture of surface sediments (less than 10cm), over four years. Hydrological characteristics were also surveyed in detail, as hydrological regime is a primary determinant of sediment transportation. Additionally, measures of hydro-geological features - hydraulic conductivity and groundwater depth were made in order to explore features of sediment habitat that extend beyond the sediment-water interface. Whilst the typical discharge pattern was one of intermittent base flows and infrequent, yet extreme flood events associated with monsoonal rain patterns, the study period also encompassed a drought and a one in hundred year flood. Rainfall and discharge did not necessarily reflect the actual conditions in the stream. Surface waters were persistent long after discharge ceased. On several occasions the stream bed was completely dry. Shallow groundwater was present at variable depths throughout the study period, being absent only at the height of the drought. The sediments were mainly gravels, sand and clay. Changes in sediment composition were observed for fine particulates (size categories less than 2mm). The grain size change in the finer sediment fractions was marked over time, although bedload movement was limited to a single high discharge event. In response to a low discharge regimen (drought), sediments characteristically showed non-normal distributions and were dominated by finer materials. High-energy discharge regimes (flood) were characterised by coarsening of sands and a diminished clay fraction. Particulate organic matter from sediments showed trends of build-up and decline with the high and low discharge regimes, respectively. Benthic habitats were described according to prevailing hydro-geological parameters. Faunas from sediment substratum samples were associated with identified habitat categories. The fauna reflected the habitat variability in terms of hydrological disturbance of the substratum structure and intermittency of discharge. An applied multivariate procedure was used to correlate temporally changing environmental parameters and faunal abundance data. Faunas were correlated with a group of variables dominated by either discharge variables or sediment textural parameters. Sediment characteristics that affect substratum quality and substratum preference at the micro-scale were investigated via hypotheses testing. A model of carbon loss was used to determine how long particulate organic matter could potentially sustain microbial activity under experimental conditions. An estimate of up to 200 days was determined from this laboratory experiment. Secondly, enriched carbon isotopes were used in a field-based experiment to establish a link between sediments and macrofauna. Enrichment via organic sediments was found for various detritivorous and carnivorous taxa. In the 'third' experiment, artificial treatments were applied to elucidate substratum preference. Fauna was offered the choice of variable quantities of clay and/or quality of organic matter. There were no significant preferences found for the different substratum treatments, although further investigation is needed and a different outcome from this method may be achieved under more benign field conditions than those encountered during this experiment. Finally, the study was set within a context of the primary features of scale. Climate and hydrological features, including linkages with the alluvial aquifer and terrestrial ecosystem, and their potential to change within 'ecological time' are perceived as critical to understanding the role of benthic sediment substratum.

The scarcity of feed resources often imposes a major challenge to the development of animal production in the tropics and subtropics. However, by-products have long been recognised in providing cheaper alternative feed ingredients relative to conventional feed ingredients, thus alleviating the challenge. The aim of the present study was to investigate the potential of three waste products from the subtropical fruit processing industry in animal feeding. The products include avocado meal (AM), macadamia oil cake (MOC) and macadamia chips (MCH). The samples were obtained from the processing plants in Nelspruit of Mpumalanga Province, Makhado (Louis Trichardt) and Tzaneen of Limpompo Province. Eight samples of each waste product were collected, prepared and their chemical composition, in vitro dry matter digestibility and, in situ ruminal dry matter and crude protein (CP) degradability were determined. A broiler growth trial was conducted as well to determine the effect of replacing maize with AM on performance of broilers under commercial production thus establishing the replacement value of avocado meal in broiler feeds. As the products under study were from the oil extraction process of the two fruits, there were high remnants of oil in all three waste products. As a result the ether extract (EE) content of the three waste products was higher compared to any of the commonly used oilseed meals. The MCH had the highest EE concentration, followed by the MOC and the AM had the lowest. However, after defatting the AM had the highest (P<0.05) EE concentration compared to either the MOC or MCH. The CP concentration of the MOC was significantly higher than that of the AM and MCH. There was no significant difference observed between the AM and MCH in CP concentration. A better amino acid profile was observed with the MOC compared to the AM and MCH. None of the products can be regarded as a protein source. The fibre fractions of the MCH were significantly higher than that of AM and MOC, with the exception of the acid detergent lignin (ADL) concentration. The ADL concentration of the AM and MCH did not differ significantly although the MCH concentration was higher. The MOC had the lowest (P<0.05) ADL concentration compared among these waste products. Generally, the fibre concentration in the MOC was lower compared to other waste products but higher compared to the SBM and POCM. The acid detergent insoluble nitrogen (ADIN) concentration of the AM was significantly higher than that of MOC and MCH. There was no significant difference observed between MOC and MCH. The condensed tannin (CT) concentration of the waste products differed significantly with the AM being the highest and the MOC the lowest. The ADIN concentration of the MOC could be compared to that of the SBM and lower than that of the POCM. There were some significant differences observed in the mineral composition between the waste products under study. The mineral concentrations were below the maximum tolerable levels of animals except for iron (Fe) in AM which can be toxic to sheep as it was above the maximum tolerable level of 500mg/kg. The in vitro dry matter digestibility of the three waste products differed significantly, with the MOC being the highest and the MCH the lowest. Huge variation within waste products was observed and it could be due to the contamination levels of the products with the indigestible portions of the parent fruits. The in situ degradability of dry matter and CP of the AM and MOC differed significantly, with the MOC surpassing the AM in most of the degradability characteristics. The potential degradable fraction (“b”) and the degradation rate of the b fraction (“c”) fractions of the AM and MOC did not differ significantly. The MCH had more indigestible particles of the kernel and as a result it could not be analysed statistically and was therefore omitted. The effect of replacing maize with AM at different inclusion rates led to decreased feed intake and the final mass of the broilers during the trial period. The feed intake of the broilers on commercial diet was significantly higher than that of the broilers on commercial diets with avocado meal, except for the inclusion rate of 10% AM. The final mass, the ADG and the FCE of the broilers on commercial diet were significantly higher compared to the broilers on diet with AM irrespective of the inclusion rate. No mortalities observed during the experimental period. Copyright / Dissertation (MSc(Agric))--University of Pretoria, 2012. / Animal and Wildlife Sciences / unrestricted

Citrus is grown in almost all countries with a sub-tropical or tropical climate. Africa produces about 7% of global citrus production representing 67 362 564 tonnes in the 2003-04 season. Of these countries, South Africa is the most important citrus producer with the bulk of its fruit being exported to mainly European countries. Although South Africa is the world’s fourteenth biggest producer, it is currently ranked third in terms of global export volumes. An increase in the number of foodborne disease outbreaks over the past few decades has been related to the shift towards consumption of fresh produce and growing world trade. Other factors include changing demographic profiles, changing farm practises, extensive distribution and handling networks, increased consumption of unprocessed products, emergence of new pathogens and more effective detection methods. Shigella spp., Listeria monocytogenes, Hepatitis virus, Caliciviridae virus, Salmonella spp., Escherichia coli and Vibrio cholera are some of the microorganisms implicated in disease outbreaks caused by the consumption of fresh produce. This dissertation focuses on citrus fruit safety and a selected foodborne pathogen, Salmonella enterica serovar Typhimurium. Salmonella has been implicated in several outbreaks associated with the consumption of unpasteurized orange juice, mangoes, cantaloupes, sprouts and tomatoes. S. enterica sv. Typhimurium is also a water-borne pathogen, and its importance in agricultural irrigation and packhouse wash water was also studied. The presence of S. enterica sv. Typhimurium in biofilms in packhouse water and on fruit was finally investigated since biofilms are known to harbour a number of these pathogens. Biofilm formation was monitored in the warm water dip tank using a photo acoustic monitoring device and confirmed by scanning electron microscopy and enumeration. Water sources, i.e. bathroom, handwash stations, irrigation water and warm water baths had high total viable bacterial counts and faecalassociated contamination. Biofilms also formed within the packhouse dip tank at an increased rate. The Polymerase Chain Reaction (PCR) was used to investigate the presence of Salmonella in the citrus export chain. No Salmonella spp. could be detected. S. enterica sv. Typhimurium survived for up to four weeks on the surface of citrus fruit under simulated export conditions. However, Salmonella is not able to survive uninterrupted cold storage conditions for a period longer than two or three weeks. Scanning Electron Micrographs showed that Salmonella is capable of attaching to and colonizing the citrus fruit surface and is able to be incorporated into existing biofilms in warm water tanks of packhouses. This study showed that Salmonella can thrive in packhouse water and potentially be a continuous source of contamination for fruit moving through the infected warm water dip tank. Everyone participating in fruit production, storage and post-harvest handling of fresh fruit should be involved in ensuring quality and safety, since events in the orchard can affect storage life, and incorrect handling during marketing may nullify all previous efforts of quality maintenance. To minimize the occurrence of these pathogens in the fruit chain from production to consumption, several basic good agricultural practices and food safety systems needs to be incorporated and managed correctly. / Dissertation (MSc)--University of Pretoria, 2009. / Microbiology and Plant Pathology / unrestricted

Effective daylighting can substantially reduce the energy use and greenhouse gas emissions of commercial buildings. Daylight is also healthy for building occupants, and contributes to occupant satisfaction. When productivity improvements are considered, effective daylighting is also highly attractive financially. However, successful daylighting of sub-tropical buildings is a very difficult task, due to high direct irradiances and excessive solar shading. A device was created that combined effective solar shading and efficient daylight redirection. The micro-light guiding shade panel achieves all objectives of an optimal daylighting device placed on the façade of a sub-tropical, high rise office building. Its design is based on the principles of non-imaging optics. This provides highly efficient designs offering control over delivered illumination, within the constraints of the second law of thermodynamics. Micro-light guiding shade panels were constructed and installed on a test building. The tested devices delivered daylight deep into the building under all conditions. Some glare was experienced with a poorly chosen translucent material. Glare was eliminated by replacing this material. Construction of the panels could be improved by application of mass-manufacturing techniques including metal pressing. For the micro-light guiding shade panel to be utilised to its full potential, building designers must understand its impact on building performance early in the design process. Thus, the device must be modelled with lighting simulation software currently in use by building design firms. The device was successfully modelled by the RADIANCE lighting simulator. RADIANCE predictions compared well with measurements, providing bias generally less than 10%. Simulations greatly aided further development of the micro-light guiding shade panel. Several new RADIANCE algorithms were developed to improve daylight simulation in general.

Gram-positive bacteria are part of the normal flora of fish from different aquatic environments. They are mesophilic bacteria and demonstrate optimum growth at ambient temperature. In the sub-tropics, marine fish are caught from seas at temperatures of 16 to 34C, they are usually not iced and are handled at ambient temperature. It was hypothesized that under these conditions Gram-positive bacteria will be abundant in sub-tropical marine fish and will have roles in the spoilage of fish. A review of literature showed that there is a gap in understanding the Gram-positive bacterial populations in sub-tropical marine fish. This is partly due to the fact that the selective media used for isolating Gram-positive bacteria have limitations. Ecological and speciation studies have revealed that the ecology and speciation of many Gram-positive bacteria have not been clearly elucidated. The effect of ambient storage on the individual genera and species of Gram-positive bacteria in fish has been rarely studied. The spoilage potential of Gram-positive bacteria of marine fish origin has not been clearly determined. Therefore, the main aims of this study were to isolate Gram-positive bacteria from fresh and ambient-temperature-stored sub-tropical marine fish, speciate the isolates and study the spoilage potential of the isolates. The practical components of this study were conducted in four parts. The first part dealt with validation of tryptone soya agar with 0.25% phenylethyl alcohol (PEA-TSA) to enumerate Gram-positive bacteria. The second part enumerated Gram-positive bacteria from the muscles, gills and gut of Pseudocaranx dentex (Silver Trevally), Pagrus auratus (Snapper) and Mugil cephalus (Sea Mullet) stored at 25C for 15 hours using PEA-TSA. The third part dealt with the speciation of the isolates using appropriate methods such as polymerase chain reaction, 16S rRNA gene sequence, the VITEK JR system and conventional biochemical methods. In the fourth part, the isolates were assayed qualitatively for their ability to produce volatile sulphur compounds (VSC), reduce trimethylamine oxide and decarboxylate histidine, lysine and ornithine at mesophilic temperature, 32C. Initial studies indicated that PEA-TSA significantly (P< 0.05) reduced the total aerobic bacterial count of fish whereas control Gram-positive bacteria were not affected (P> 0.05). Gram-positive aerobic bacterial counts (GABC) significantly (P< 0.05) increased in the muscles and gills during ambient storage for 15 hours. Within each species, no significant (P> 0.05) differences were found in GABC between muscles and gills. Moreover, there were no significant differences (P> 0.05) in GABC between fish species during storage. In total, 390 bacteria were isolated from the fresh and stored fish; 339 isolates (87%) were found to be Gram-positive. Two hundred and sixty-six isolates (78%) of Gram-positive bacteria were identified to fall into 13 genera, namely Staphylococcus, Micrococcus, Bacillus, Virgibacillus, Brevibacillus, Corynebacterium, Streptococcus, Enterococcus, Aerococcus, Exiguobacterium, Carnobacterium, Vagococcus and Sporosarcina and 30 species. In fresh fish, Staphylococcus epidermidis and Micrococcus luteus were the most frequent isolates. The effect of storage at 25C for 15 hours resulted in a change of Gram-positive bacterial populations; while S. epidermidis, S. xylosus and Bacillus megaterium were no longer present, S. warneri, B. sphaericus, Brevibacillus borstelensis, Enterococcus faecium and Streptococcus uberis increased. Three species, E. faecium, Str. uberis and B. sphaericus, were the most prevalent at the end of storage. Micrococcus luteus and S. warneri were the most prevalent isolates from Pseudocaranx dentex, but E. faecium and Str. uberis were the most frequently isolated from Pagrus auratus and Mugil cephalus. With respect to different parts of the fish body, E. faecium, Str. uberis and B. sphaericus were the most frequent isolates from the muscles, E. faecium, Str. uberis from the gills and M. luteus from the gut. Among the 228 isolates examined, Br. borstelensis 73, Br. borstelensis 291, Str. uberis 339, Vagococcus fluvialis 31 and Vag. fluvialis 132 produced VSC from sodium thiosulphate, cysteine and methionine. However, strains varied in sulphur source utilization. Exiguobacterium acetylicum 5, Exiguobacterium spp. 191, Carnobacterium spp. 338, Br. borstelensis 73, Br. borstelensis 291, Str. uberis 30, Str. uberis 339, Vag. fluvialis 31 and Vag. fluvialis 132 reduced TMAO. No histidine decarboxylase activity was found in the Gram-positive bacterial species tested. Lysine and ornithine were decarboxylated mainly by different strains of S. warneri, S. epidermidis and M. luteus. During ambient storage of fish, the frequency of lysine-decarboxylating bacteria increased and became more diverse after 5 hours of storage. Among fish species examined, the frequencies of lysine- and ornithine-decarboxylating bacteria were higher and more diverse in Pseudocaranx dentex than in Pagrus auratus and Mugil cephalus. This study found that Gram-positive bacteria were abundant and diverse in sub-tropical marine fish; however, their frequencies were affected by fish habitat and fish body part. Ambient temperature storage determined which Gram-positive bacterial species were dominant. With the exception of one isolate of S. aureus, Gram-positive bacteria isolated from sub-tropical marine fish caught from unpolluted water were not potential pathogens. The study also showed that Gram-positive bacteria had greater ability to decarboxylate lysine and ornithine than to produce VSC or reduce TMAO, and the spoilage potential of a bacterial species was a strain-dependent behaviour. This is a significant study as it is the first study on this aspect sub-tropical marine fish. It validated a selective medium that can be used to enumerate most Gram-positive bacteria from a marine environment. Most of the Gram-positive bacterial species from sub-tropical marine fish identified in this study were documented for the first time. The effects of ambient storage and the spoilage potential of Gram-positive bacteria from sub-tropical marine were clearly elucidated.

Fuels management in eucalyptus plantations is essential to minimise the impact of wildfire. Prescribed burning has the potential to reduce the fuel hazard in plantations, but is not routinely conducted due to concerns relating to tree damage. Through a series of experimental burns, the issues of tree damage are addressed and minimum tree sizes are recommended that are capable of withstanding the effects of low to moderate intensity fires. Data was collected between 2005 and 2007 over six sites, two species, and three age classes. Tree response results came from multiple measurements of over 1700 individual trees. The fuel characteristics commonly found in sub-tropical eucalypt plantations from age four to eleven are described and quantified. These fuel characteristics are related to fire behaviour and new fire behaviour models, specific to young eucalypt plantations, are presented. The fuel characteristics that most influence fire behaviour in young eucalypt plantations are fuel load, fuel height, and fuel moisture content. These characteristics can be used to predict the rate of spread of a plantation fire under benign wind conditions. A novel technique for assessing the extent of stem damage in eucalypts is developed and described. This technique enables immediate assessment of stem damage following fire; previous assessment techniques recommend waiting a considerable period of time (up to 2 years) until dead bark dropped off and fire scars were evident. This new assessment technique is likely to be suitable for post-fire assessment of any eucalypt species and will provide forest managers with the capability of deciding whether to leave a stand to ???grow-on??? or commence recovery operations. Minimum stem sizes recommended to ensure no long-term damage are between 5 ??? 8 cm DBH (diameter at breast height, i.e. 1.3m above ground level) for Eucalyptus dunnii (Dunn???s white gum) and 5 ??? 13 cm DBH for Corymbia spp. (spotted gum) depending on the quantity of fuel around the stem. Stem sizes vary between species because of the variation in bark thickness between species. This thesis provides all the necessary information to conduct prescribed burning operations in young eucalypt plantations.