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Department of Microbiology & Plant Pathology

PhD Students

Nazareth Siyoum
PhD Plantpathology
Promoter: Prof Lise Korsten

Microbial Dynamics of Different Mushroom Casing Materials in the Production of Button Mushrooms (Agaricus bisporus)
In the commercial production of button mushrooms (Agaricus bisporus), spawn run compost is covered by a layer of soil called casing soil to initiate transformation of mushroom mycelium into fruiting bodies. A naturally occurring, non-renewable resource, peat, is commonly used for this purpose worldwide. However, peat mining from the wetlands is restricted in South Africa due to environmental concerns. Hence fi nding an easily available replacement for this valuable resource is crucial for the South African mushroom industry.This project aims at contributing useful knowledge in the finding of a partial or complete replacement for peat by: 1) studying the microbial dynamics of peat and other selected materials 2) setting standards for biological parameters of a good casing material.

Noncy Gomba

PhD Crop Protection
Promoter: Prof Lise Korsten

Microbial dynamics of citrus fruit and the development of innovative disease control strategies to ensure product safety and quality
The total microbial population on a fruit comprises different physiological groups of microorganisms and during the farm-to-consumer continuum further microbial contamination that impact on the growth dynamics of the population can occur from a variety of sources. The citrus fruit can be contaminated by postharvest pathogens and potentially human bacterial pathogens at any point compromising the microbial quality of the fruit. Increased pressure to produce high quality fruit and numerous headlines about foodborne illnesses associated with the consumption of unpasteurised orange juice present challenges for the South African citrus industry. The primary goal to achieving and maintaining the safety and quality of fresh produce is to reduce contamination in the fi rst place because once the produce is contaminated it may be extremely difficult to remove all the pathogens. The objectives of this research are to determine the microbial ecology of the citrus fructoplane during harvesting and the potential changes to this population through postharvest handling and storage that may affect the microbial stability of the fruit, to identify potential sources of foodborne pathogens in citrus production and their prevalence along the supply chain, to assess the survival and /or growth of foodborne pathogens on citrus fruit and their survival under simulated export conditions and development of postharvest and foodborne pathogen control strategies.

Venessa van der Merwe

PhD Microbiology
Promoter: Prof Lise Korsten

Characterization of biofilm’s that develop in pre-harvest environments when using contaminated irrigation water
A potential problem in the extent of contamination of South Africa’s water sources has been identified and thus the Water Research Commission (WRC) solicited research in this regard. This study aims to investigate the links between water quality and the microbiological content of biofi lm’s that form as a result in: irrigation systems and irrigation water storage containers. The presence of Escherichia coli genus, Escherichia coli O157:H7, Salmonella genus and Salmonella enterica subsp. enterica serovar Typhimurium within these pre- and post harvest environments will be monitored based on biofilm formation and their presence in the bulk fl uid. Detachment from biofilm’s containing Salmonella enterica subsp. enterica serovar Typhimurium will also be considered.

Maz Sakupwanya
PhD Plant Pathology
Promoter: Prof N. Labuschagne
Co-Promoter: Prof Z. Apostolidis

Elucidating the Biochemical Mechanisms of Disease Tolerance in Citrus Rootstocks to the Pathogen Phytophthora nicotianae
Phytophthora root rot of citrus is still responsible for serious losses in commercial citrus production worldwide. Use of resistant rootstocks is considered by far, the most effective, environmentally safe and economically sound method of combating this disease. Previous work conducted at the University of Pretoria has conclusively determined several facts regarding the interactions between the various citrus rootstocks and the pathogen, providing example data on the varying levels of tolerances or susceptibility among varieties. The objectives of the current study involve a novel approach of melding techniques, theories and philosophies from biochemistry, microbiology and plant pathology to elucidate the means by which tolerant rootstocks resist sustained infection by the pathogen. This will involve an in-depth analysis of the spectrum of phytochemical found to accumulate in roots of infected plants as opposed to uninoculated plants,specifi cally targeting phytochemical with anti-fungal properties. The current study aims to characterize and determine the role of any such secondary metabolites in citrus rootstock tolerance to the pathogen Phytophthora nicotianae. Such an endeavor should provide the basis for new genetics based research aiming to fi nd more durable resistance in citrus.

Masters Students

Ilonka Scholtz
MSc(Agric) Plant Pathology
Promoter: Prof Lise Korsten

Impact and population dynamics of Penicillium species present within the deciduous fruit
export chain

A contributing factor for the economic losses experienced by the deciduous fruit export industry is postharvest decay. Penicillium species are common postharvest pathogens of various fruit types
and are prevalent decay agents along the supply chain. Spores of the Penicillium species are highly resistant structures, which have the ability to survive sub-optimal conditions such as those found in the export chain. Critical areas along the supply chain, where Penicillium inoculums level are high need to be identified. By identifying the critical control points the necessary precautions and suggested hygiene practices may be implemented in order to decrease decay incidence of the fruit.

The aim of this study is to focus on identifying potential inoculums sources of Penicillium species by monitoring environments throughout the export chain. Local fresh produce markets, wholesalers and retailers will also be sampled. Data obtained will be used to map the dominance and population dynamics of Penicillium species occurring throughout the deciduous fruit supply chain.

Nicole Rudolph
MSc Plant Pathology
Promoter: Prof Terry Aveling

Plant Growth Promoting Rhizobacteria as biofertilizers for maize
Plant growth promoting rhizobacteria (PGPR) are a group of beneficial bacteria that colonize plant roots and promote plant growth. Recently there has been an increasing interest in the agricultural industry in the use of PGPR as biofetilizers to replace chemical fertilizers. Biofetilizers provide plants with the necessary nutrients, increase soil quality, improve productivity and can serve as an inoculant carrier for PGPR. The objectives of this study is to develop a novel inocultant PGPR carrier in the form of a
biofetilizer that will ensure long term survival of the benefi cial bacteria in the soil and will promote growth of the most important staple crop, maize in South Africa. Sixteen potential PGPR isolates will be screened using the paper towel method to select for eight effective growth promoting isolates which will be tested in greenhouse trials on maize. The three most promising PGPR isolates will be selected to be applied to a novel inoculant carrier (biofertilizer) in four different formulations and longevity of the product will be determined at 25 and 37¢ªC over a six month period. The novel PGPR inoculant carrier will then be compared to other PGPR soil application methods under greenhouse conditions with maize as a crop. The potential of PGPR isolates to act as biological control agents against a common maize pathogen (yet to be selected) will also be tested in the greenhouse.

Pieter Louw
MSc (Agric) Plant Pathology
Promoter: Prof L. Korsten
Co-promoter: Ms R. Jacobs

Examining the Pathogenicity and Verifying the Virulence of Problematic Penicillium spp. on Market Dominating Citrus and Deciduous Fruit Cultivars

The citrus and deciduous fruit industries in South Africa are exceptional in size and compete at the top of the world fruit export markets. These markets are although constantly under pressure and are suffering hefty economic losses due to Penicillium spoilage. This project will firstly aim to benefit the industries by identifying the pathogenic Penicillium spp. on citrus, apples, nectarines, plums, and table grapes. The most efficient inoculation methods will also be evaluated for Penicillium research. With this will the most pathogenic Penicillium spp. with the most effective inoculation method be utilized in cultivar trials to differentiate between Penicillium pathogenicity and host susceptibility in the different market dominating fruit cultivars. Cold storage trials will also be conducted to indicate temperature based disease sensitivity. Lastly will the Penicillium-host interactions be illustrated via Scan Electron Microscopy. These experiments will thus help to identify the current Penicillium resistance status of the major cultivars in each fruit group, verify which Penicillium spp. are the most pathogenic under normal and cold storage environments, hopefully help to indicate were Penicillium mainly come into contact with the fruit, and illustrate how the host-pathogen interactions take place. This information will be useful in helping to answering industry problem related to postharvest Penicillium decay.