Identification of endophytic bacterial communities associated with South African crops: sorghum bicolor (L. Moench), pennisetum glaucum and arachis villosulicarpa

Abstract

In this study, the diversity of endophytic bacteria associated with food crops, sorghum (Sorghum bicolor L. Moench), pearl millet (Pennisetum glaucum L.) and groundnut (Arachis villosulicarpa) is investigated using culture-independent techniques: terminal retriction fragment length polymorphism (t- RFLP) and next generation sequencing (NGS). The first objective of this study was to investigate the effect of different DNA extraction protocols on mDNA yield and quality, as well as the diversity of endophytic bacteria retrieved from root and stem tissues (0.1g or 0.3g) of sorghum, pearl millet and groundnut. Protocols used include two classical methods (CTAB- and SDS-based) and five commercial kits: MoBio PowerPlant Pro® DNA Isolation Kit, Qiagen DNeasyR Plant Mini Kit, Fermentas GeneJET Plant Genomic DNA Purification Kit, MoBio PowerSoilTM DNA Purification Kit and MoBio UltraClean® Soil DNA Isolation Kit. Eletrophoresis and the Nanodrop were used to determine DNA yield and purity