Baseline Data of the Fungal Phytobiome of Three Sorghum (Sorghum bicolor) Cultivars in South Africa using Targeted Environmental Sequencing

Abstract

Plant-associated fungi, or the mycobiome, inhabit plant surfaces above ground, reside in plant tissues as endophytes, or are rhizosphere in the narrow zone of soil surrounding plant roots. Studies have characterized mycobiomes of various plant species, but little is known about the sorghum mycobiome, especially in Africa, despite sorghum being one of the most important indigenous and commercial cereals in Africa. In this study, the mycobiome associated with above- and below-ground tissues of three commercial sorghum cultivars, as well as from rhizosphere and surrounding bulk soil samples, were sequenced using targeted sequencing with the Illumina MiSeq platform. Relative abundance differences between fungal communities were found between above-ground and below-ground niches, with most differences mostly in the dominant MOTUs, such as Davidiellaceae sp. (Cladosporium), Didymellaceae sp. 1 (Phoma), Fusarium, Cryptococcus and Mucor. Above-ground communities also appeared to be more diverse than below-ground communities, and plants harboured the most diversity. A considerable number of MOTUs were shared between the cultivars although, especially for NS5511, their abundances often differed. Several of the detected fungal groups include species that are plant pathogens of sorghum, such as Fusarium, and, at low levels, Alternaria and the Ustilaginomycetes. Findings from this study illustrate the usefulness of targeted sequencing of the ITS rDNA gene region (ITS2) to survey and monitor sorghum fungal communities and those from associated soils. This knowledge may provide tools for disease management and crop production and improvement.

Chemical Characterization and Metagenomic Identification of Endophytic Microbiome from South African Sunflower (Helianthus annus) Seeds

“…Additionally, Ascomycota was also largely represented or abundant (58.74%) in the roots of South Africa Vigna unguiculata (Cowpea) [62], followed by Basidiomycota. In reports [63,64] where fungi diversity of maize seed and sorghum cultivars (respectively) were studied, a higher abundance of Ascomycota in the two studies followed by Basidiomycota (in the maize study) was also established. The abundance of Ascomycota, particularly in selected cultivars from Agricol, Pannar, and LimaGrain may be indicative of their strongest capacity to build a community within the plant's endosphere, arising from their ability to decompose plant biomass, maintenance of soil stability, carbon, nitrogen cycling (especially in arid regions) [65], and fermentation of foods [66], particularly in alcoholic beverages [67].…”

Plant and Soil Core Mycobiomes in a Two-Year Sorghum–Legume Intercropping System of Underutilized Crops in South Africa

“…1 varied between the plant tissues and soils, albeit the plant tissues possibly showing dominance. This MOTU was assigned in the pipeline as Nectriaceae but shown in [ 37 ] to represent Fusarium . Cryptococcus was relatively balanced between the substrates.…”

“…MOTUs named by the pipeline with synonymous names—such as Giberrella, currently known under Fusarium —were changed to the current name with the distinction indicated as sp. “x”, with x being a number based on the number of MOTUs for that genus [ 37 ].…”

“…The software was used for additional analyses to visualize fungal diversity indices in different samples (rarefaction curves and bar charts). The statistical significances of detected differences between plant niches and year were compared using permutational multivariate analysis of variance (PERMANOVA) using the function “adonis2” in the vegan package [ 37 ] Unidentified MOTUs were not discarded and were included in the analysis. The core fungal communities for plant tissues and soils from year one and two were based on the concepts used by [ 22 ], which required that genera must be present in all samples to be part of the core.…”