Theses and Dissertations (Forestry and Agricultural Biotechnology Institute (FABI))

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    Survey of soil fungal and oomycete diversity from maize field soils in the Eastern Cape, South Africa
    (University of Pretoria, 2024-04-04) Visagie, Cobus; Yilmaz, Neriman; alice.mthembu@up.ac.za; Mthembu, Alice
    Maize plays a crucial role as a staple food and feed grain in South Africa and globally. Fungal diseases pose a significant threat to maize yields in South Africa, particularly in the Eastern Cape where fungal and oomycete diversity in maize rhizosphere soils is limited. The first chapter presents a comprehensive literature review focused on soilborne diseases affecting maize, with a particular emphasis on those prevalent in South Africa. It covers their distribution, symptoms, and commonly employed management strategies. Additionally, the chapter delves into maize production in the Eastern Cape, addressing the challenges encountered by the emerging farmers in this region. Chapter 2 (first research chapter) focuses on a survey of fungal and oomycete diversity in rhizosphere soils from maize farms in the Eastern Cape. Our goal was to isolate and culture fungi and oomycetes from these soils and identify the isolates using both morphological characteristics and DNA sequence data. Isolation resulted in 421 fungal and 16 oomycete strains The most dominant fungal genera from the soil collected were Penicillium (n=98), Fusarium (n=90), Cladosporium (n=46), and Trichoderma (n=103), with Fusarium oxysporum sensu lato (n=64), Trichoderma gamsii (n=29), and Penicillium cremeogriseum (n=18) among the most common species. Several pathogenic fungal species like A. alternata, F. graminearum, Beauveria amorpha, S. maydis, G. irregulare and G. ultimum, were isolated from this study and have been reported to cause root and stalk rot in maize. There is a large variation in the distribution of fungal and oomycete species across all farms. The fungal and oomycete communities that were dominant in the soils belonged to the genera Fusarium, Penicillium, Trichoderma, and Globisporangium. None of the isolated Penicillium and Trichoderma species have been reported to cause diseases in maize in South Africa. Notably, Globisporangium irregulare was the predominant oomycete species identified. Several strains belonged to species known to cause maize diseases, such as Fusarium stalk rot, Diplodia stalk rot, and Pythium root and stalk rot. Chapter 3 (second research chapter) of this study provided the description of a newly proposed Penicillium species in the section Canescentia series Atrovenata. We described the species based on its unique DNA sequences and provide morphological evidence for its formal description. Overall this study shows that the fungal communities detected in the maize rhizosphere soils are relatively diverse and some have been reported to cause important maize diseases.
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    Taxonomy, mating type distribution and population biology of Calonectria species
    (University of Pretoria, 2020) Chen, ShuaiFei; Wingfield, Michael J.; Barnes, Irene; jieqiong.li@fabi.up.ac.za; Li, JieQiong
    the promovendus investigated species diversity, mating strategies and population diversity of the plant pathogen Calonectria species. An extensive disease surveys and multigene phylogenetic analyses discovered six novel and seven known Calonectria species associated with Eucalyptus plantations in South China. Mating strategies study of Calonectria species revealed the mating type structure of both homothallic and heterothallic, and provided an improved understanding of the evolutionary history of sexual reproduction in Calonectria. The results of Calonectria pauciramosa population study showed that a single dominant genotype and mating type of the pathogen widely distributed in multiple countries and on different hosts, this related with the international trade of asymptomatic plant germplasm and contaminated soil. The results from this study provide a valuable aid towards understanding the biology and managing diseases caused by these pathogens.
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    Important pests and diseases of plantation grown Pinus and Eucalyptus in Colombia and their control
    (University of Pretoria, 2013-01-13) Wingfield, Michael J.; Rodas Pelaez, C.A. (Carlos Alberto)
    Colombia covers an area of approximately 114 million hectares (ha) of which the potential forestly land has been estimated at 60.7 million ha, about 53% of the total area. Only 54 million ha are considered as natural forest, leaving approximately 29 million ha to be used for livestock and agriculture. In order to provide an alternative source of timber, Colombian groups have planted approximately 327 000 ha to different species of Pinus, Eucalyptus and native species. This clearly represents only a small proportion of the total area that might be used for forestry, which is set to grow in the future. In general, trees established in plantations have been grown as monocultures that allow for substantial productivity per management unit. But this is also a homogeneous genetic resource that is highly susceptible to damage caused by insect pests and diseases. It is therefore, surprising that relatively little work has been conducted on pests and pathogens negatively affecting plantation foresty in Colombia. In this regard, the studies presented in this thesis present the first comprehensive treatment of the topic for the country. It is consequently hoped that these will form a basis for the future management and sustainability of forestry in Colombia. In the first Chapter of this thesis, I provide a historical background and the current pest and disease situation for the forestry sector in Colombia. This includes an overview of the main pest and diseases affecting commercial nonnative trees, especially species of Pinus and Eucalyptus. A wide range of sites occurring in Colombia were considered and the document also includes the impact of different climatic conditions on the incidence and management of the various pests and diseases treated. Some of the most important defoliators in Colombia reside in the order Phasmatodea and one of these, Litosermyle ocanae, was treated in studies presented in chapter two. The overall aim was to contribute basic knowledge of L. ocanae including an understanding of the biology, egg population dynamics, and potential biological control assessments based on early detection of the insect. vi Chapter three includes the discovery of one of the members of the Geometridae that causes serious damage due to defoliation of Pinus and Eucalyptus plantations. This pest, known as Chrysomima semiluteraria, has been known in Colombia for many years and this study included a comprehensive evaluation of its biology and field monitoring contributing to an Integrated Pest Management strategy for it. The insect was studied under field and laboratory conditions and a special emphasis was placed on its biological control using the egg parasitoid Telenomus alsophilae. Pinus plantations in Colombia have been affected by numerous pests, including recently, the adelgid Pineus sp. To establish management strategies to assist commercial forestry operations, the life cycle of this insect and the susceptibility of different Pinus species were determined in Chapter four. In addition, the possible role of a Ceraeochrysa sp. as a biological control agent was investigated. In chapter five, Fusarium circinatum is recorded for the first time on Pinus spp. in Colombia. The discovery of this fungus, known to cause the disease Pitch Canker has had an important impact on forestry, especially with regard to management strategies aimed at reducing its impact. Studies in this chapter included those to evaluate the susceptibility of families and provenances of Pinus spp., which are currently used in forestry planting programs in Colombia. The first emergence of the foliage pathogen Dothistroma septosporum as an important constraint to pine forestry in Colombia is treated in chapter six. This fungus is a serious pathogen of many species of Pinus around the world. It was, however, not recognised as a serious threat to forestry in Colombia until it emerged as a serious source of damage to Pinus tecunumanii. In this chapter, the aim was firstly to confirm the identity of the pathogen based on DNA sequence data. Subsequently, the host range and distribution of the pathogen was established in different Colombian forestry areas. The impact of the disease and the susceptibility of different provenances of P. tecunumanii was also assessed. In chapter seven, the main objective was to described the susceptibility of E. grandis clones to a new species of Ceratocystis and to identify clones resistant to it. The fungus was described as Ceratocystis neglecta and management strategies are suggested for it. This thesis includes two Appendices treating new reports of insect pests and an important Eucalyptus pathogen. In Appendix 1, I report on the importance of three different pest insects. Appendix 2 includes a description of a new disease, as well as the potential risks that this disease poses for the Colombian forestry sector.
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    Ceratocystis species on timber harvested for export in Ghana
    (University of Pretoria, 2011-08-08) felix.fru@fabi.up.ac.za; Fru, Felix Fon; Prof J Roux; Dr G K Nkuekam
    There has been an increase in research on the genus Ceratocystis, particularly in Africa, in the past ten years. This is due to the fact that these fungi represent economically important pathogens of agricultural and forestry crops, causing diseases of, for example, coffee, cacao, sweet potato, taro, oak and eucalypt trees globally. Despite this, little is known about the genus in Ghana. During studies of wood rot and other fungi in Ghana, the oak wilt pathogen, C. fagacearum, was reported from native Ghanaian trees. Previous to this report from Ghana, C. fagacearum was only known from oak trees and only from the United States of America, making this report from unrelated hosts in Ghana, highly significant. However, some doubt exists as to the accuracy of this identification since the fungus was identified based only on morphological observations. This study aims to try and confirm the occurrence of C. fagacearum in Ghana by identifying Ceratocystis isolates collected from the same hosts and from the same areas in the country, using modern molecular techniques. Chapter one deals with an overview of the genus Ceratocystis, with a particular focus on its taxonomy and identification of species in the genus. The ecology and importance of Ceratocystis spp. is covered, including its movement and dispersal. A particular focus is also placed on information regarding the species that are known to occur in Africa, since this forms an important component of any quarantine system. The importance of Ceratocystis species as quarantine pests is, therefore, also discussed. This chapter concludes with a discussion of the features that enable Ceratocystis species to be listed as pests of quarantine interest. Generally, the specific identity of a pathogen is a pre-requisite for proper classification and an understanding of its ecology and impact. Chapter two aims to identify isolates of Ceratocystis collected from logs of native trees in Ghana, using DNA sequence data and multiple-gene phylogenies. In using sequence data, three gene regions, the internal transcription spacer regions (ITS), including the 5.8S gene, the Beta-tubulin (BT) and transcription elongation factor-1α (TEF), are considered to compare isolates from Ghana with previously described Ceratocystis species to determine their identity. This work was done over a period of five months using a collection of isolates from Ghana. Since the project was designed as a mini-thesis and was based only on a pilot study in Ghana, more research is needed to clarify the morphology, ecology, distribution and impact of Ceratocystis spp. on both native and non-native plants in that country. This is especially important since vast quantities of native timber are exported to Europe and other regions, forming an important basis of the economy of Ghana. Copyright