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Pathogen-free seeds are important for the establishment of young seedlings, prevention of health problems upon consumption by animals and livestock, and inadvertent movement of pathogens into and out of countries. However, testing for the presence of fungi, including pathogens from seeds is a time consuming and difficult process. In this study, we characterized the seed fungal microbiome (mycobiome) of six commercial sorghum cultivars from South Africa using a deep amplicon next generation sequencing approach based on the Internal Transcribed Spacer (ITS) region of the ribosomal operon. Sorghum is the fifth most important crop in the world, and widely used by African farmers. We found that the fungi present in each of the seedlots were similar to those reported by cultural studies. By comparing phylotypes of certain key families and genera to phylotypes used in established phylogenies and reputed sequences from public databases, the diagnostic value of the NGS method was also investigated. We showed that a number of molecular operational taxonomic units (MOTUs) could be identified at the species level and established that certain known pathogens are not present in the tested seeds, for instance in the Aspergillus group. Other groups could not be identified, not even to genus level. While acknowledging the shortcomings of using partial ITS data, we demonstrated that deep amplicon sequencing is a valuable diagnostic tool for seed disease control and prevention in some cases.

Endophytic seed mycobiome of six sorghum (Sorghum bicolor) cultivars from commercial seedlots using an Illumina sequencing approach