Genotypic and phenotypic diversity of culturable rhizobacteria from field-grown crops in Mahikeng, South Africa

The rhizosphere is a result of the interactions between roots and microorganisms. Thus, it was hypothesized that native rhizobacteria would best act as indigenous biofertiliser. In this study bacteria from the rhizospheric soil around Mahikeng were isolated and characterized. The culturable isolates were characterized using different morphological and biochemical tests. A confirmatory Analytic Profile Index test was used to identify the isolates. Out of the 17 isolates that were confirmed from the soil samples, 5 were Bacillus spp., 4 were Brevibacillus spp., 3 were Aeromonas hydrophila/caviae, and the others were Pseudomonas luteola, Burkholderia gladioli, Burk. cepacia, Citrobacter freundii, and Pantoea spp. The DNAs of the isolates were extracted using cetyltrimethyl ammonium bromide method and amplified by polymerase chain reaction and RAPD. However, among all isolates, only 6 were amplified when bands were visualized on an agarose gel. DNAs that were amplified were for Brevibacillus spp., A. hydrophila/caviae, Bacillus spp. and Burk. cepacia. Bacillus was the dominant genus found from the soil samples. This may be because of their ability to produce endospores that can withstand extreme conditions that make this genus to handle the stress of the change in conditions, from their natural habitats to media in the laboratory. Genetic distances between the isolate genotypes ranged from 0.167 to 0.917. Bacillus spp. and Burk. gladioli S2 are most closely related of the isolates. This study broadens understanding of bacteria community composition in terms of commonality and peculiarity in Mahikeng locality and indicates possible isolates for use as indigenous biofertiliser.