Fungal diversity and community composition of wheat rhizosphere and non-rhizosphere soils from three different agricultural production regions of South Africa

Understanding complex interactions among plant genotypes, environmental conditions and microbiome structure provides crucial information for sustainable farming practices towards disease control in agriculture. In this study, fungal diversity and composition in wheat rhizosphere and non-rhizosphere soils were investigated. Special emphasis was placed on pathogenic and beneficial genera. Wheat rhizosphere and non-rhizosphere soil from three different wheat growing regions were analyzed using Illumina high-throughput sequencing. The analysis showed a significant decline in the fungal diversity and richness from non-rhizosphere to rhizosphere soils. Ascomycota and Basidiomycota were the dominant fungal phyla detected in both rhizosphere and non-rhizosphere soils across the three test sites. Genera known to include wheat pathogens detected included Fusarium, Phoma and Colletotrichum genera while, beneficial groups included Trichoderma, Aureobasidium and Acaulospora. The presence of Fusarium was observed to be inversely proportional to that of Aureobasidium, a well-known antagonist of the Fusarium spp. This information could provide new opportunities to explore the potential of manipulating natural fungal antagonistic microorganisms for use in controlling soil-borne pathogenic fungi in wheat.