Faculty of AgriSciences

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The Faculty of AgriSciences at Stellenbosch University (SU) is held in high esteem at national and international levels for the quality of its training and research and also as consultant in the agricultural and forestry industry.

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The 2009 late blight pandemic in the eastern United States - causes and results
(American Phytopathological Society, 2013) Fry, W. E.; McGrath, M. T.; Seaman, A.; Zitter, T. A.; McLeod, A.; Danies, G.; Small, I. M.; Meyers, K. L.; Everts, K.; Gevens, A. J.
The tomato late blight pandemic of 2009 made late blight into a household term in much of the eastern United States. Many home gardeners and many organic producers lost most if not all of their tomato crop, and their experiences were reported in the mainstream press. Some CSAs (Community Supported Agriculture) could not provide tomatoes to their members. In response, many questions emerged: How did it happen? What was unusual about this event compared to previous late blight epidemics? What is the current situation in 2012 and what can be done? It's easiest to answer these questions, and to understand the recent epidemics of late blight, if one knows a bit of the history of the disease and the biology of the causal agent, Phytophthora infestans.
3-way networks : application of hypergraphs for modelling increased complexity in comparative genomics
(PLoS, 2015-03) Weighill, Deborah A.; Jacobson, Daniel A.
We present and develop the theory of 3-way networks, a type of hypergraph in which each edge models relationships between triplets of objects as opposed to pairs of objects as done by standard network models. We explore approaches of how to prune these 3-way networks, illustrate their utility in comparative genomics and demonstrate how they find relationships which would be missed by standard 2-way network models using a phylogenomic dataset of 211 bacterial genomes.
The 3Ps (Profit, Planet, and People) of sustainability amidst climate change : a South African grape and wine perspective
(MDPI, 2021-03-08) Gbejewoh, Omamuyovwi; Keesstra, Saskia; Blancquaert, Erna
Conventional agriculture has made the search for sustainability urgent, more so with regards to climate change. This has extended to the grape and wine industry, an important industry in South Africa in terms of labor employment and foreign exchange. This paper aims to review the current state of knowledge with regards to the three pillars of sustainability and with regards to climate change. In order to understand sustainability in South Africa, a historical context is needed, because the welfare of farm workers still retains vestiges of past Apartheid. Ecological responsibility and higher profits are the main reasons for sustainable practices. Additionally, water use, chemical use, and soil erosion are important environmental sustainability concerns. With regards to climate change, in terms of economic sustainability, there will be winners and losers and social sustainability issues will intensify as changes occur in farms. Table grape producers are relatively more profitable than wine grape producers. Furthermore, pest, disease, irrigation pressure will worsen as the climate warms. However, there are long- and short-term adaptation strategies such as changes in viticulture practices and grape cultivars, respectively, to stem the effects of climate change, but this may be stymied by cost and farmers’ perceptions of climate change.
The 3Ps (profit, planet, and people) of sustainability: a South African grape and wine perspective
(Stellenbosch : Stellenbosch University, 2021-12) Gbejewoh, Omamuyovwi; Blancquaert, Erna; Keesstra, S.; Hoffman, W. H.; Stellenbosch University. Faculty of AgriSciences. Dept. of Viticulture and Oenology.
ENGLISH ABSTRACT: Ever since the discovery of the environmental impacts of modern production in agriculture, sustainability and sustainable production has been at the forefront of efforts to reduce the external pressures on the system. The initial focus of the sustainability model was only on the environment and was later expanded to include the economic and social dimensions as evidenced in the millennium and sustainable development goals of the United Nations. Industrial agricultural production produces its fair share of greenhouse gas emissions. However, the grape and wine sectors were traditionally not considered environmentally demanding. Regardless of this increased interest in sustainability and sustainable production, the question remains: What does sustainability mean? How to measure and achieve it? It is still hotly debated which is open to various subjective interpretations. This project was aimed at studying the three pillars of sustainability equally and together in the grape and wine sector in South Africa. The objectives of the project were to: (i) evaluate what sustainability and its three pillars mean and how climate change is affecting these three pillars, (ii) determine context-specific indicators for the three pillars of sustainability and (iii) finally assess the feasibility of balancing the three pillars in a farm. The results of the first objective showed that sustainability is still highly subjective as all the respondents defined it differently and the environmental dimension still dominated their perceptions of sustainability in its importance, but they considered the social dimension the most difficult to achieve. In terms of climate change, extremes like drought, temperature and rainfall variations affected profits and the gains seen in other wine-producing countries are not present in South Africa. With regards to the environment, water demand was severely increasing irrigation pressure followed by increased reliance on chemicals for pest control. Spill-over effects of the economic dimension affected the social dimension in terms of limited work opportunities and stagnant wages for workers. The results of the second objective showed that economic indicators selected as relevant speak to the precarious situation of grape and wine farmers. The environmental indicators considered relevant were interesting given that actual practices were different given various regional environmental contexts. While the social dimension showed that respondents believe in improving the welfare of workers but are limited in what they can do to improve this dimension given the economic situation of many farms. The final objective showed that even though combined improved environmental and social practices reduced the profitability of farms, only improved social practices had the least effect. This showed that even significant improvement in the social dimension did not have to impact the bottom line of farms adversely. However, these results should be interpreted with caution as it involves simulating a complex system. Finally, as this study was exploratory, more research is needed in terms of more diverse participants (foreign retailers and consumers), more rounds of indicator selection and simulating the entire farm and not just the production process.
A cost-effective protocol for molecular detection of fungal pathogens in soil
(Academy of Science for South Africa, 2005) Damm, Ulrike; Fourie, Paul
DNA EXTRACTION FROM FUNGI IN SOIL often fails because of humic substances that are co-extracted with the DNA and subsequently inhibit PCR analyses. Moreover, it is difficult to release the fungal DNA because of the diverse fungal structures residing in soil. Since available DNA extraction protocols and commercial kits are expensive or time-consuming, we have devised a superior method by testing different components of these procedures on grapevine nursery soils. The best DNA yield and sensitivity were obtained by a short and easy extraction method with sodium dodecyl sulphate buffer using the FastPrep homogenizer. An easy-to-prepare spin column with polyvinylpoly-pyrrolidone was developed to remove PCR inhibitors. In the presence of bovine serum albumin, PCR reactions were possible without further dilutions of the DNA. Our method was more sensitive for detecting Phaeomoniella chlamydospora, the organism responsible for Petri grapevine decline, and Cylindrocarpon black-foot pathogens in grapevine nursery soils than the FastDNA SPIN Kit for Soil and enabled us to perform 25 extractions for the price of one with the kit. This is the first report of molecular detection of Cylindrocarpon macrodidymum from soil and the first account of Pa. chlamydospora from soils in South Africa.
Die aanwending van die CPM dairy model in formulering van voerrantsoene in 'n melkkudde
(Stellenbosch : Stellenbosch University, 2005-04) Vermaak, Jacobus Vermaak; Cruywagen, C. W.; Stellenbosch University. Faculty of Agrisciences. Dept. of Animal Sciences.
ENGLISH ABSTRACT: CPM Dairy was developed to maintain amino acid balance. because the correct amino acid relationship has an influence on milk production and milk composition (Schwab e/ af. 1992, Rulquin e/ af. 1993). Rulquin e/ af. (1993) found that an increase in lysine and methionine concentration in the diet had no meaningful effect on milk production and milkfat production. However, milk protein production is described as a function of lysine and methionine concentration. In order to balance the amino acid relationships, the CNCPS model has been adopted, using the following guidelines: I. a dairy cow feed characteristic scheme, described by Van Soest e/ af. (1991) and Sniffen e/ aI. (1992), II. a model for rumen fermentation and bacterial growth in the dairy cow, described by Russel e/ af. (1992), Ill. feed val ues for dairy cow feeds, described by Sniffen e/ af. (1992). IV. a set of formulas describing the feeding needs of dairy cows under different circumstances, assembled by Fox e/ af. (1992). Bateman e/ af. (2001) studied the accuracy of formulation models according to crude protein (CP) and amino acid (AA)-flow to the duodenum in lactating dairy cow diets. CPM Dairy does not calculate direct flow of CP to the duodenum, but the following adjustment was made: the change-over of metabolizable protein (MP) to CP is done by increasing bacterial protein from 60% to 100% of bacterial-CP. Intestinal digestion of fraction B3-protein is increased from 80% to 100%, whereas fraction C-protein is increased from 0 to 100% to change feed-MP to feed-CP. CP from feed and microbes are summed to indicate total CP-flow to the duodenum. AA-flow, as calculated by CPM Dairy, is used without adjustments. A rise in MUN-Ievels are typical to spring and summer months. which can be ascribed to high soluble protein and low soluble carbohydrates in grasses and legumes. This gives rise to an excess N-uptake in the bloodstream. Grass silage, when fed as primary feeding source. has the same reaction. Blood-urea-nitrogen (BUN) is the amount of urea-N found in the blood of the cow. MUN is the fraction ofN in the milk in the form of urea. MUN is normally 85% the concentration of BUN. Studies show that an increase in BUN/MUN levels leads to a negative effect on the reproductive ability of the cow. An increase in BUN-levels leads to an increase in urea in the reproductive tract of the animal. Urea passes between the blood plasma and the reproductive tract. It is therefore obvious that a high BUN-concentration leads to high levels of urea in the reproductive tract. In order to eradicate this problem. the use of deodorise in the supplemental feed of the lactating dairy cow \vas recommended. Deodorise is a natural product manufactured by Alltech. The product is derived from the Yuccha Schidigera plant. Two glycocomponents (CI and C II) of this plant binds gasses such as N1-I3. (Alltech information sheet) During .June to August 2002 data were collected regarding the effect of deodorise on lactating dairy cows. No meaningful difference between the two groups in this experiment was found.
Die aanwending van distillasieprodukte by die gisting van mos
(Stellenbosch : Stellenbosch University, 1958-12) Zeeman, A. S. (Adriaan Siebrits); Theron, C. J.; De Waal, C. T.; Stellenbosch University. Faculty of AgriSciences. Dept. of Viticulture and Oenology and Institute for Wine Biotechnology.
ENGLISH ABSTRACT: no abstract available
Abiotic and biotic drivers of African aquatic insect distribution
(Stellenbosch : Stellenbosch University, 2020-03) Deacon, Charl; Samways, Michael J.; Pryke, James S.; Stellenbosch University. Faculty of AgriSciences. Department of Conservation Ecology and Entomology.
ENGLISH ABSTRACT: Freshwater habitats are disproportionately rich in biodiversity, and are among the most threatened, yet poorly protected ecosystems. Aquatic insects make up much of the total freshwater fauna and contribute greatly to ecosystem functioning. At the broad-scale, aquatic insect distribution is driven by combinations of traits, as well as regional climate gradients and historical landscape context. Locally, both aquatic insect species richness and diversity are driven by various aspects related to vegetation and to physiochemical environments. Effective conservation requires thorough understanding of species distribution patterns at various spatial scales. My overall aim here is to combine broad-scale, theoretical biogeography, and local-scale empirical ecology to investigate drivers of aquatic insect distribution across Africa. Species are often binarily classified as ‘widespread generalists’ or ‘narrow-range specialists’ based on their ecological traits. Results in Chapter 2 show that ecological and biological traits are highly interactive among dragonflies, and inferring geographical range size based on ecological preference and/or biotope specialization alone should be approached with caution. Biological traits related to phenology and mobility were also strong drivers of dragonfly range size, indicating that conservation efforts should include multiple species across all habitat types. Regional climates show considerable variation across latitudinal and longitudinal gradients, and determine areas of high species richness and diversity. In Chapter 3, I show strong latitudinal and longitudinal gradients for South-African dragonfly species richness and endemism. Dragonfly assemblage-turnover boundaries coincided with significant geographical features and/or areas where contemporary climate changed from one condition to another. However, these dragonfly assemblage turnover-boundaries were gradual rather than discrete throughout South Africa. At the local scale, natural and artificial ponds contribute greatly to overall biodiversity, especially when they are of high quality and occur in networks across the landscape. I show that ponds characterized by high heterogeneity support diverse aquatic insect assemblages (Chapters 4 and 5). Chapter 4 showed artificial reservoirs, occurring alongside natural ponds in ecological networks, to expand the area of occupancy for most widespread dragonflies, aquatic beetles and true bugs. Some species with specific habitat requirements were confined to natural ponds, suggesting the significance of natural ponds for conserving the full range of insects. Dragonflies, aquatic beetles and true bugs occupy low-quality artificial reservoirs at low abundance to survive the adverse effects of drought (Chapter 5). However, many insects exclusively occupied natural ponds, emphasizing the overall importance of naturalness, and suggests that there is merit in improving artificial reservoirs. This would most likely be by having macrophytes and vegetated banks similar to those of natural ponds.Investigating aquatic insect distribution patterns is important for conservation, and here, I demonstrate the value of dragonflies as model organisms for investigating the drivers of broad-scale distribution patterns. Studying other taxa is also appropriate, as I have demonstrated at the local scale, but not always possible due to limited distribution knowledge. I recommend broad-scale investigations of other complementary taxa to determine their added value for elucidating the drivers of overall insect distribution patterns, and so address our current shortfalls to improve insect conservation.
Abiotic stress-induced accumulation of raffinose in Arabidopsis leaves is mediated by a single raffinose synthase (RS5, At5g40390)
(BioMed Central, 2013) Egert, Aurelie; Keller, Felix; Peters, Shaun
Background: The sucrosylgalactoside oligosaccharide raffinose (Raf, Suc-Gal1) accumulates in Arabidopsis leaves in response to a myriad of abiotic stresses. Whilst galactinol synthases (GolS), the first committed enzyme in Raf biosynthesis are well characterised in Arabidopsis, little is known of the second biosynthetic gene/enzyme raffinose synthase (RS). Conflicting reports suggest the existence of either one or six abiotic stress-inducible RSs (RS-1 to -6) occurring in Arabidopsis. Indirect evidence points to At5g40390 being responsible for low temperature-induced Raf accumulation in Arabidopsis leaves. Results By heterologously expressing At5g40390 in E.coli, we demonstrate that crude extracts synthesise Raf in vitro, contrary to empty vector controls. Using two independent loss-of-function mutants for At5g40390 (rs 5–1 and 5–2), we confirm that this RS is indeed responsible for Raf accumulation during low temperature-acclimation (4°C), as previously reported. Surprisingly, leaves of mutant plants also fail to accumulate any Raf under diverse abiotic stresses including water-deficit, high salinity, heat shock, and methyl viologen-induced oxidative stress. Correlated to the lack of Raf under these abiotic stress conditions, both mutant plants lack the typical stress-induced RafS activity increase observed in the leaves of wild-type plants. Conclusions Collectively our findings point to a single abiotic stress-induced RS isoform (RS5, At5g40390) being responsible for Raf biosynthesis in Arabidopsis leaves. However, they do not support a single RS hypothesis since the seeds of both mutant plants still contained Raf, albeit at 0.5-fold lower concentration than seeds from wild-type plants, suggesting the existence of at least one other seed-specific RS. These results also unambiguously discount the existence of six stress-inducible RS isoforms suggested by recent reports.
Aboveground biomass and carbon in a South African mistbelt forest and the relationships with tree species diversity and forest structures
(MDPI, 2016) Mensah, Sylvanus; Veldtman, Ruan; Du Toit, Ben; Kakai, Romain Glele; Seifert, Thomas
ENGLISH ABSTRACT: Biomass and carbon stocks are key information criteria to understand the role of forests in regulating global climate. However, for a bio-rich continent like Africa, ground-based measurements for accurate estimation of carbon are scarce, and the variables affecting the forest carbon are not well understood. Here, we present the first biomass study conducted in South Africa Mistbelt forests. Using data from a non-destructive sampling of 59 trees of four species, we (1) evaluated the accuracy of multispecies aboveground biomass (AGB) models, using predictors such as diameter at breast height (DBH), total height (H) and wood density; (2) estimated the amount of biomass and carbon stored in the aboveground compartment of Mistbelt forests and (3) explored the variation of aboveground carbon (AGC) in relation to tree species diversity and structural variables. We found significant effects of species on wood density and AGB. Among the candidate models, the model that incorporated DBH and H as a compound variable (DBH2 × H) was the best fitting. AGB and AGC values were highly variable across all plots, with average values of 358.1 Mg·ha−1 and 179.0 Mg·C·ha−1, respectively. Few species contributed 80% of AGC stock, probably as a result of selection effect. Stand basal area, basal area of the ten most important species and basal area of the largest trees were the most influencing variables. Tree species richness was also positively correlated with AGC, but the basal area of smaller trees was not. These results enable insights into the role of biodiversity in maintaining carbon storage and the possibilities for sustainable strategies for timber harvesting without risk of significant biomass decline.
Accelerated microbial degradation of nematicides in vineyard and orchard soils
(South African Society for Enology and Viticulture, 2014-03) Hugo, H. J.; Mouton, C.; Malan, Antoinette P.
Accelerated microbial degradation (AMD) of organophosphate and carbamate nematicides is a phenomenon whereby biodegradation in the soil is increased, leading to a dramatically shortened persistence of nematicides. More intensified agriculture practices in South Africa in response to the future demand for food may lead to increased pest and disease pressure, which in turn will lead to more frequent pesticide application. The same principle applies to plant-parasitic nematode control practices, and the overuse and misuse will have a pronounced effect on the enhancement of AMD. With limited management options available, the responsible use of nematicides becomes more pertinent. Producers should be aware of the problems associated with multiple soil applications of organophosphates and carbamates against plant-parasitic nematodes. This article reviews factors contributing to the AMD of carbamate and organophosphate nematicides in soil and makes practical recommendations to avoid the occurrence of AMD in vineyard and orchards.
Acclimation of apple peel to light and temperature and the effect thereof on red colour development and tolerance to sunburn
(Stellenbosch : Stellenbosch University, 2017-12) Barasu, Prince Dogbeda; Midgley, S. J. E.; Schmeisser, M.; Steyn, Willem Jakobus; Stellenbosch University. Faculty of AgriSciences. Dept. of Horticulture.
ENGLISH SUMMARY: Sunburn is the biggest abiotic quality defect affecting apple orchards in South Africa. In blushed cultivars, inadequate red colour development at harvest is of similar importance as sunburn as quality defect. The presence of these two quality defects negatively affects profitability of South African apple orchards. This study was undertaken to assess the response of apple peels from trees on different rootstocks of differing vigour to photothermal stress. Rootstocks are purported to produce different microclimatic conditions to developing fruit depending on their vigour. The objective was to identify whether previous acclimation to light and temperature affected the sensitivity of ‘Rosy Glow’ (RG) and ‘Golden Delicious’ (GD) apple peel from a range of rootstocks, to damage (photosystem and visible peel damage) under induced natural photothermal stress and whether such acclimation affected the ability of ‘Rosy Glow’ apples to colour under different temperature conditions. We found that damage to peel photosystems occurred at all exposure periods in both cultivars, with peels under one hour exposure showing general indications of progressive recovery over the five-day period. Duration of exposure to the stress condition, the recovery period, and canopy position were identified as the dominant influences on damage and recovery of RG photosystems with duration of exposure and recovery period being the dominant influences on GD photosystems. Likewise, duration of exposure, the length of the evaluation period together with canopy position were the dominant influences on visible peel damage observed on both RG and GD apples. However, rootstock plays a role in the visible peel damage observed on RG apples in 2016. Fruit from the different canopy positions acclimated differently which showed in their response to the photothermal stress. Slightly lower peel sensitivity occurred in fruit from trees on the rootstock G3007 and a higher sensitivity in M793. To ascertain the effect of rootstock on the colouring potential of RG apples, fruit peel discs were subjected to six temperature treatments. The effect on red colour development of RG apples under lab conditions is rootstock related and not related to vigour. Although fruit colour development varied between different rootstocks under different temperatures, results indicate different optimum temperature ranges for different rootstocks in the red colour development of RG apples. Geneva rootstocks G222 and G3007 rootstocks showed the highest potential for good colour development following a cold front under warm late-season conditions on par with the current industry standard M793. In our final experiment, the effect of fruit cooling (as a means of modifying fruit microclimate) on the red colour response of ‘Cripps’ Pink’ (CP) apples at harvest was evaluated. The cooling treatments applied showed different responses on change in hue of CP apples at harvest, but all cooling treatments were beneficial to red colour development. Late cooling treatment from mid-February to mid-March was more effective in decreasing hue of CP apples at the end of the trial.
Accomplishments in wheat rust research in South Africa
(ASSAf, 2020-11-26) Pretorius, Zacharias A.; Prins, Renee; Wessels, Elsabet; Bender, Cornel M.; Visser, Botma; Boshoff, Willem H. P.
Rust diseases, although seasonal, have been severe constraints in wheat production in South Africa for almost 300 years. Rust research gained momentum with the institution of annual surveys in the 1980s, followed by race identification, an understanding of rust epidemiology, and eventually a focused collaboration amongst pathologists, breeders and geneticists. Diversity in South African populations of Puccinia triticina, P. graminis f. sp. tritici and P. striiformis f. sp. tritici has been described and isolates are available to accurately phenotype wheat germplasm and study pathogen populations at national, regional and global levels. Sources of resistance have been, and still are, methodically analysed and molecular marker systems were developed to incorporate, stack and verify complex resistance gene combinations in breeding lines and cultivars. Vigilance, capacity, new technologies, collaboration and sustained funding are critical for maintaining and improving the current research impetus for future management of these important diseases.
Acidification of sands in citrus orchards fertilized by drip irrigation
(Stellenbosch : Stellenbosch University, 2002-12) Kotze, Theunis Gerhardus; Fey, M. V.; Hoffman, J. E.; Stellenbosch University. Faculty of AgriScience. Dept. of Soil Science.
ENGLISH ABSTRACT: The use of drip irrigation in citrus orchards is becoming increasingly important in the Citrusdal region of the Western Cape. Drip irrigation provides an opportunity to optimize water and fertilizer use by inducing a smaller root zone that can be managed more effectively. Ammoniacal fertilizers are an integral part of any drip fertilization (fertigation) programme. However, a disadvantage is that they generate soil acidity upon nitrification. If insufficient plant uptake of nitrate occurs during the fertigation season, soil acidification may become an important yield-limiting factor. This study investigated the effect of drip fertigation on four sandy soils with different buffer capacities, near Citrusdal. Spatial variation in soil chemical properties below irrigation emitters was investigated to determine the nature and extent of soil acidification from drip fertigation. The response ofthe four sands to acid and base addition (and laboratory incubation) was also studied in order to assess the magnitude and origin of pH buffering. The soil types in the four orchards included two poorly buffered and two moderately buffered soils. Both the poorly buffered soils, at Brakfontein and Swartvlei, were classified in the Kroonstad form and contain less than 5% clay. The two moderately buffered soils, at BoHexrivier and OnderHexrivier, were classified in the Vilafontes and Constantia forms, respectively, and contained more than 10% clay in the subsoil. X-ray diffractometry revealed that kaolinite and quartz dominate the clay fraction of all four soils. Organic carbon content in the topsoils ranged from 0.2-0.98 percent. Drip fertigation for a period of between 4 and 10 years at all four sites has resulted in large decreases in soil pH to depths of up to 1 m below the emitter with a sharp increase in acid saturation at pHKc1 values below 4.5. The Brakfontein and Swartvlei orchard soils were the least acid saturated with levels of about 50-60 percent. At the BoHexrivier site acid saturation values of 70 percent were recorded for the topsoil immediately below the emitter, while the whole soil profile of the OnderHexrivier site had extreme acid saturation levels, exceeding 90 percent in the deeper parts of the profile. It was also revealed that a large proportion of the 1M KCI-extractable acidity \ consisted of A~ although Al saturation showed a poorer relationship to pHKCIthan did acid saturation. The Al component of exchangeable acidity in the OnderHexrivier subsoil was significantly larger [Al = 0.84(acidity)] than in the other soils [AI = 0.69(acidity)]. It was found that most of the wetted soil volume was deficient in exchangeable Ca, Mg, K and enriched with Al. No accumulation of NH/ or N03- was found in any of the soils directly below the emitter, indicating either a sufficient degree of nitrification or the leaching of both NH/ and N03- to greater depths. The mobile anions cr and sol- also appeared at the periphery of the wetting front. Phosphate generally accumulated in the soil just below the emitter, except in two of the soils where P showed some degree of leaching. Spatial variation in soil chemical properties indicated that nitrification and over-irrigation had resulted in a significant volume (between 0.1 and 1.1 rn') of severely acidified soil (pHKcl <4.5) below the emitter at all four study sites. Buffering in these naturally acidic sandy soils from the Citrusdal area is weak as a result of the low clay and organic matter contents. The low content of clay, dominated by kaolinite and quartz, implied that organic carbon plays an important role in pH buffering, especially in the topsoils. Laboratory incubation with acid or base confirmed the fact that CEC becomes increasingly saturated by acidic cations (Ir and Ae+) once soil pHKCIvalues decrease below 4.5. Again Al was found to be the major acidic cation [AI = 0.69(acidity)], especially in the subsoils. This confirmed that, even in these poorly buffered, quartz-rich sandy soils, toxic amounts of Al could enter the soil solution quite rapidly following acidification. Lime requirement calculated from the slope of titration curves following incubation provided a useful way of assessing the magnitude of the acidification problem, even though liming the acidified subsoil may present practical difficulties under field conditions in drip-fertilized irrigation systems. These lime requirement values, ranging from 0.9-10.3 tonnes of CaC03/ha, can be applied to field conditions with some calibration refinements.
Acoustic monitoring and response of katydids (Orthoptera: Tettigoniidae) to the landscape mosaic in a Biosphere Reserve
(Stellenbosch : Stellenbosch University, 2017-03) Thompson, Aileen Celeste; Samways, Michael J.; Bazelet, Corinna S.; Stellenbosch University. Faculty of AgriSciences. Dept. of Conservation Ecology and Entomology.
ENGLISH SUMMARY: A charismatic group within the Orthoptera, katydids can be found in a variety of habitat types world-wide due to their excellent bark and leaf mimicry skills. Most male katydids produce species-specific calls to attract female mates. If katydids, like their close relatives the grasshoppers, can function as effective biological indicators, then acoustic monitoring of katydid songs may result in a novel and non-invasive method to rapidly assess local biodiversity. Furthermore, information regarding threat statuses, distributions and life history traits can be inferred for all South African katydid species, leading to the development of a Katydid Biotic Index (KBI) based on the highly effective Dragonfly Biotic Index. If proven effective, the KBI would allow for biodiversity assessments to account for detailed aspects of katydid species composition in addition to the diversity measures normally utilized for biodiversity assessment (e.g. species richness and abundance). In this thesis, I provide the first steps towards determining whether the KBI could be an effective assessment technique. First I assess the utility of the KBI at a coarse-scale by determining its ability to identify regions of high conservation priority. Secondly, I conduct a fine scale study to determine the response of the katydid assemblage to habitat quality. And lastly, the first two aims are combined to determine whether the KBI is an appropriate method to assess habitat quality at a fine-scale. In Chapter 2, by using a subset of museum records, I investigate the distribution of the katydids within the Cape Floristic Region (CFR), a global biodiversity hotspot. The katydids found within the CFR follow the same trends with regards to threat status, endemism and life history traits to the overall South African katydid assemblage. The KBI assessment method was able to select, at this coarse-scale, the ecosystems of conservation priority. For Chapters 3 and 4, the Kogelberg Biosphere Reserve (KBR) was selected as a study area as it allowed for the acoustic monitoring and direct comparison of katydid assemblages and responses across the core, buffer and transition zones through the use of passive recordings. In Chapter 3 I found that the katydids of the KBR are not complementary across the zones. However, they respond positively in terms of abundance to measured habitat quality when the entire assemblage is considered. In Chapter 4 I found that katydids responded towards coarse-scale habitat quality and they were not as sensitive towards habitat change as was expected. By including abundances of the katydid species in to the KBI calculations, the sensitivity of the KBI as an assessment method was improved. For this reason, katydids in the fynbos biome are likely to not be effective indicators of habitat change on a small scale, likely due to the surprisingly low diversity of katydid species in the KBR. However, if the KBI were to be tested out in forest patches or areas with higher diversity, the KBI may prove more promising. For these reasons, a rapid assessment technique based on the KBI is likely to be more appropriate for some habitat types over others.
Acoustic profiling of the landscape
(Stellenbosch : Stellenbosch University, 2014-04) Grant, Paul Brian Charles; Samways, Michael J.; Stellenbosch University. Faculty of AgriSciences. Dept. of Conservation Ecology and Entomology.
ENGLISH ABSTRACT: Soft, serene insect songs add an intrinsic aesthetic value to the landscape. Yet these songs also have an important biological relevance. Acoustic signals across the landscape carry a multitude of localized information allowing organisms to communicate invisibly within their environment. Ensifera are cryptic participants of nocturnal soundscapes, contributing to ambient acoustics through their diverse range of proclamation songs. Although not without inherent risks and constraints, the single most important function of signalling is sexual advertising and pair formation. In order for acoustic communication to be effective, signals must maintain their encoded information so as to lead to positive phonotaxis in the receiver towards the emitter. In any given environment, communication is constrained by various local abiotic and biotic factors, resulting in Ensifera utilizing acoustic niches, shifting species songs spectrally, spatially and temporally for their optimal propagation in the environment. Besides the importance of Ensifera songs from an ethological point of view, the multitude of species-specific signals provide an acoustic tapestry representing species diversity across ecological gradients and over time. Acoustic inventorying and monitoring of the landscape can reflect the environmental status of ecological systems, from natural to disturbed by human influence. In contrast to traditional survey techniques, sound recording and interpretation is a non-invasive method that allows for the detection and classification of highly cryptic, yet insightful indicators of ecosystem change. Here, acoustic monitoring was used across diverse ecological gradients to improve understanding of species diversity patterns, and how they change in response to both natural gradients and in response to the human dominated landscape mosaic. This study was undertaken in three geographic locations from tropical rain forest of Brunei, Borneo, to the landscapemosaic of plantation forestry in KwaZulu-Natal, South Africa, and to the botanically rich, mountain fynbos region of the Cape Floristic Region, also in South Africa. Each region provided a diverse and particular landscape to test the value of acoustic surveys for determining local diversity patterns across natural gradients and to assess the value of the technique for assessing the impact human influence across landscapes. In tropical rainforests, an entire acoustic guild was investigated to determine how acoustic species partition their acoustic communication channels spectrally, temporally and spatially, to avoid acoustic interference. The overall assemblage showed considerable spectral partitioning. Diurnally active species showed low temporal niche overlap, whereas nocturnal species did not utilize temporal partitioning. Lack of nocturnal temporal partitioning suggests other mechanisms of acoustic avoidance are sufficient to avoid acoustic overlap, or that there are insufficient cues to partition nocturnal acoustic environments. Acoustic species also utilized spatial partitioning, with distinct acoustic assemblages at vertical heights and with elevation. Utilization of a range of different strategies allow many species to communicate with conspecifics with little or no interference from other species in a signal rich environment. Acoustic profiling was also undertaken in KwaZulu-Natal, South Africa, across a plantation forestry landscape mosaic with diverse ecological gradients containing both alien and indigenous vegetation, as well as boarding large natural protected areas. Areas covered in alien timber or non-endemic grass were devoid of acoustic signals. Managed areas that were mowed and heavily grazed were not effective in maintaining the natural complement of nocturnal acoustic species. Within natural vegetation patches inside plantations, acoustic species richness increased with plant heterogeneity and patch size. Patches of indigenous vegetation within the plantation matrix effectively reduced the contrast of transformed landscapes with surrounding natural areas, with indigenous forest patches containing a highly characteristic acoustic species assemblage. Within the botanically rich, mountain fynbos region of the Cape Floristic Region, acoustic profiling was conducted across gradients of elevation, season and vegetation. Across these gradients, katydid acoustic signals were identified and characterized for the first time. This resulted in the discovery of two new katydid species and a novel sound producing structure in a carabid beetle, a species previously unknown to produce sound. Acoustic diversity across seasonal and elevational gradients increased with increasing temperatures. Climatic variability along the elevational gradient produced variation in seasonal phenology. Katydids also utilized high frequency acoustic signals, which is probably an adaptation to overcome background noise from wind, so prevalent in this area. Furthermore, despite producing conspicuous signals for mate attraction and pair formation, katydids were found not to be part of bat-eared fox diet, an insectivorous, nocturnal predator that uses its characteristic large ears to detect sounds made by invertebrate prey. This study shows the value of using acoustic emissions from katydids to identify acoustic diversity patterns across ecological gradients and in response to human impacts on the landscape.
Acridid ecology in the sugarcane agro-ecosystem in the Zululand region of KwaZulu-Natal, South Africa
(Pensoft, 2020-01-10) Bam, Adrian; Addison, Pia; Conlong, Desmond
Grasshoppers and locusts are well known crop and pasture pests throughout the world. Periodically they cause extensive damage to large areas of crops and grazing lands, which often exacerbate food shortage issues in many countries. In South Africa, acridid outbreaks rarely reach economic proportions, but in sugarcane plantations, localized outbreaks of native acridid species have been reported for the last eight years with increasing frequency and intensity in certain areas. This study was undertaken from May 2012 to May 2013 to identify the economically important acridid species in the sugarcane agroecosystem in these outbreak areas, to monitor seasonal activity patterns, to assess sampling methods, and to determine the pest status of the major species through damage ratings. Five acridid species of particular importance were identified: Nomadacris septemfasciata (Serville), Petamella prosternalis (Karny), Ornithacris cyanea (Stoll), Cataloipus zuluensis Sjötedt, and Cyrtacanthacris aeruginosa (Stoll). All species are univoltine. Petamella prosternalis was the most abundant species and exhibited a winter egg diapause, while N. septemfasciata, the second most abundant species, exhibited a winter reproductive diapause. Petamella prosternalis and N. septemfasciata were significantly correlated with the damage-rating index, suggesting that these two species were responsible for most of the feeding damage found on sugarcane. This study, for the first time, identified the acridid species complex causing damage to sugarcane in the Zululand area of KwaZulu-Natal, South Africa, and documented their population characteristics and related damage. These data are important information on which to base sound integrated pest management strategies.
Across flock genetic parameter estimation for yearling body weight and fleece traits in the South African Dohne Merino population
(South African Society for Animal Science, 2008) Van Wyk, J. B.; Swanepoel, J. W.; Cloete, S. W. P. (Schalk Willem Petrus van der Merwe); Olivier, J. J.; Delport, G. J.
Accurate genetic parameter estimates are needed upon which to perform multiple-trait across flock breed analyses. Genetic parameters for yearling body weight (BW), clean fleece weight (CFW) and mean fibre diameter (MFD) were estimated using records of 107 389 individuals (the progeny of 1 530 sires and 45 178 dams) collected between 1992 and 2004 in the South African Dohne Merino population. Fixed effects included in the model were flock-year-season-sex- management group (1 594 classes), type of birth (singles, multiples), age of dam (2 - 7+ years) and age at measurement, fitted as a linear covariate (385 ± 12 days). Six different single-trait animal models were fitted, where different combinations of the following random effects were fitted: direct additive, the sire-flock interaction, the sire-flock-year-season interaction (SFYS), the dam genetic effect, the direct-maternal correlation and the dam permanent environmental effect. These analyses were followed by a three-trait analysis structured according to the log likelihood ratios obtained for the single-trait analysis. This analysis allowed the calculation of relevant correlations among traits together with their respective standard errors. Direct heritability estimates from the three-trait analysis were 0.17 for BW, 0.19 for CFW and 0.45 for MFD. Maternal heritability estimates were 0.01 for BW and 0.006 for CFW, with corresponding dam permanent environmental ratios of respectively 0.03 and 0.02. The genetic correlation between animal effects amounted to 0.48 for BW. Derived proportions of the total phenotypic variance due to SFYS were 0.02, 0.02 and 0.02, respectively. Genetic correlations of BW with CFW and MFD were 0.11 and 0.13, respectively, and of CFW with MFD 0.16. It was concluded that the inclusion of some form of a genotype by environmental interaction as part of the national evaluation is essential, although it controlled only a modest portion of the overall phenotypic variation.
Active modified atmosphere packaging, postharvest physiology, quality attributes and shelf life of minimally processed pomegranate arils (cv. Wonderful)
(Stellenbosch : Stellenbosch University, 2015-03) Banda, Kalenga; Opara, Umezuruike Linus; Caleb, Oluwafemi James; Stellenbosch University. Faculty of Agrisciences. Dept. of Horticulture.
ENGLISH ABSTRACT: Minimally processed fresh products have a short shelf life and marketable period and could therefore benefit from active modified atmosphere packaging (MAP) technology because it allows earlier establishment of suitable equilibrium atmospheres than passive MAP. However, there are limited studies that have explored the application of active MAP in minimally processed pomegranate arils. This study, therefore, investigated the effects of active MAP and storage conditions on postharvest physiology, quality attributes and shelf life of pomegranate arils (cv. Wonderful). In the first part of the study, the effects of storage temperature (5, 10 and 15 °C), relative humidity (76, 86 and 96%) and citric acid pre-treatment on transpiration rate (TR) of minimally processed pomegranate arils were investigated. In addition, the effects of storage temperature (5, 10, 15 and 20 ± 2 °C, and 90 ± 2 % RH) on respiration rate (RR) and quality attributes of citric acid treated and non-treated arils were determined in order to establish best storage conditions. Citric acid pre-treatment was only effective in reducing aril RR at 15 and 20 °C. Aril RRs were lowest at 5 °C throughout the 5 d storage duration and declined from 4.75 to 2.86 mL CO2 kg-1 h-1 and 4.86 to 2.7072 mL CO2 kg-1 h-1 for citric acid treated and non-treated arils, respectively. About twofold increase in RR was observed with increase in storage temperature from 5 to 15 °C and threefold when increased to 20 °C. Storing arils under low temperature condition (5 °C and 96 % RH) maintained the lowest transpiration rates (TR), with arils under these conditions suffering negligible moisture loss (~1%) after 9 d compared to 7 and 12% moisture loss for those stored under 86 and 76 % RH, respectively. The study further showed that citric acid pre-treatment had no significant effects on TR of arils at all the temperature and RH combinations. The effects of active MAP on postharvest physiology, quality attributes and shelf life of minimally processed pomegranate arils at 5 °C and 90 % RH were investigated using two independent experiments. In experiment 1, arils were packed in low barrier bi-axially oriented polyester (BOP) polymeric film under two active MAPs (5% O2 + 10% CO2 + 85% N2; 30% O2 + 40% CO2 + 30% N2), passive MAP and clamshell containers as control. In experiment 2, a high barrier polyethylene polymeric film (polylid) was used with arils packed in three active MAPs (5% O2 + 10% CO2 + 85% N2; 30% O2 + 10% O2 + 60% N2; 100% N2) and passive MAP as the control. Respiration rate, physico-chemical attributes, antioxidant properties (total anthocyanin, total phenolic and ascorbic acid content, and radical scavenging activity), microbial quality and sensory attributes were monitored every third day over a 12 d storage period. Equilibrium O2 (16-18%) and CO2 (7%) atmospheres were established after 3 d in the low barrier BOP in experiment 1; however, the recommended levels of gas composition (2-5 % O2 and 10-20% CO2) for MAP of minimally processed pomegranate arils were not reached. In contrast, O2 levels decreased and CO2 increased continuously, in pomegranate arils packaged in high barrier polylid film in experiment 2. Respiration rate of arils in both low barrier BOP film and high barrier polylid film were significantly affected by MAP and increased significantly (p < 0.05) with storage duration. Arils in clamshell containers maintained lower RR than other MAP treatments, while passive MAP had the highest in experiment 1. Arils in active MAPs with low O2 (5% O2 + 10% CO2 + 85% N2), high O2 (30% O2 + 10% CO2 + 60% N2) and passive MAP in the high barrier polylid film generally maintained similar RR levels throughout the 12 d storage duration. In contrast, RR of arils in 100% N2 was about 40% lower than that in other MAP treatments from day 6 until the end of storage. Furthermore, MAP with 100% N2 was effective in supressing ascorbic acid oxidation from day 6 until the end of storage. Total anthocyanin content (TAC) of arils fluctuated with storage duration across all the MAP treatments. At the end of 12 d storage duration, anthocyanin content of arils in experiment 1 was highest in clamshell packages (30.7 ± 0.9 mg C3gE/ 100ml) and lowest in passive MAP (26.7 ± 1.8 mg C3gE/ 100 ml). In the high barrier polylid film in experiment 2, arils in 100% N2 maintained higher TAC levels than other MAP treatments from day 9 until the end of storage. Similarly, radical scavenging activity of arils in the high barrier polylid film in experiment 2 was highest in 100% N2 while that in passive MAP was lowest from day 6 until the end of storage. Arils in in 100% N2 and high O2 atmospheres in both experiment 1 (30% O2 + 40% CO2 + 30% N2) and 2 (30% O2 + 10% CO2 + 60% N2) maintained lower aerobic mesophilic bacteria counts than other MAP treatments throughout the storage duration. However, shelf life was limited to 9 days for arils in 100% N2 based on overall acceptability and off-odour sensory scores, while arils in active MAP with high O2 scored above the acceptable limit by day 9. Arils in passive MAP in both films also remained acceptable until day 9, while those in clamshell packages were not acceptable beyond day 6.
Actual and predicted performance of broiler chickens
(Stellenbosch : Stellenbosch University, 2004-03) Van Niekerk, S. J. (Sarel Johannes); Ekermans, L. G.; Stellenbosch University. Faculty of AgriSciences. Dept. of Animal Sciences.
ENGLISH ABSTRACT: The aim of this study was to evaluate the performance and profitability of different dietary specifications for broiler chickens slaughtered at 35 days of age. Two trials were performed to evaluate different production parameters. The results of these trials were compared to the predicted results of the EFG broiler model. No carcass data were available for the two trials mentioned above. Therefore, in order to evaluate the accuracy of the broiler model when predicting carcass characteristics, two published data sets (Leeson et al., 1996a) were used. Predicted and actual values were compared, evaluated and discussed. Two broiler trials were performed. In Trial One the amino acid density decreased throughout the range of three treatments from prestarter to finisher diets. In Trial Two the amino acid density decreased only in the four finisher diets. The main difference between predicted and actual results was the response to body weight. The model predicted a steady increase in feed intake to compensate for the lower dietary specifications while body weight did not change significantly. This increase in feed intake seems to be enough to maintain body weight. Trial birds also increased their feed intake as dietary amino acid density decreased, but this compensation seemed to be too low to maintain body weight compared to the control diet. The birds may find it easier to compensate when they have time to adapt to the specification. There is evidence in the literature that birds need seven days to adapt their feed intake to a lower feed specification (Leeson et al., 1996a). It can be speculated that the trial birds started to loose body weight due to a lower amino acid intake in this period. The model seems to adapt feed intake immediately after a change in diet specification. The simulation on literature data lead to the following conclusions: 1) Broilers posses the capacity to increase their feed intake with at least 65% should finisher diets with lower amino acid and energy concentrations be supplied. If only the energy concentration of finisher diets were decreased, the increase in feed intake will be around 30%. (see Table 16 and 23) 2) The accurate prediction of feed intake from the given dietary specification has a major influence on the accuracy of the prediction of broiler performance. 3) Amino acid density and DLys:ME ratio plays a significant role in the control and prediction of feed intake. The EFG broiler model is based on sound scientific principles. The model is comprehensive and can be used for a wide range of environmental and management conditions as well as dietary conditions. The nutritionist can use the model with confidence to assist in practical feed formulation. The actual strength of the model lies in the time and money being saved compared to practical trials.

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