Analysing Pandoraea associated with Brassica oleracea using 16S rDNA from Limpopo Province, South Africa

Abstract

The genus Pandoraea comprises gram-negative, motile, non-spore-forming, rod-shaped, oxidase-positive, and obligate aerobes bacteria with a single polar flagellum. Several species belonging to this genus have been identified as potentially risky pathogenic bacteria, which can adversely impact the yield of white cabbage plants. A study was conducted at the University of Limpopo in 2023 to isolate and identify the Pandoraea bacterium from a white cabbage field and a free-living nematode, Acrobeles complexus, in South Africa. The molecular study used the 16S rDNA marker to identify the bacterium associated with nematode and white cabbage fields from South Africa's soils. The DNA was extracted using the Chelex method, and the bacterium was identified as Pandoraea. Specific primers were used to amplify the 16S rDNA to identify the nematode. The Nblast analysis showed that South African Pandoraea has a 99% similarity with a population from India (AB510957). Phylogenetic analysis using maximum likelihood placed this species with those molecularly identified as Pandoraea in the same clade with highly supported (100) bootstrap values. In conclusion, this study has demonstrated that the 16S rDNA marker can be effectively used to identify Pandoraea species. However, the use of additional DNA markers is recommended to achieve a better understanding of Pandoraea's phylogeny.