Survey of soil fungal and oomycete diversity from maize field soils in the Eastern Cape, South Africa

Abstract

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.