Molecular characters of Pandoraea, a bacterium associated with tomato (Solanum lycopersicum) using 16S rDNA from Limpopo Province, South Africa

Abstract

Tomato is one of the premier vegetables in the world and is widely cultivated for higher yield and economic importance; thus, the area under cultivation is increasing. Pandoraea species can be a risky pathogenic bacterium to tomato plants, impacting the yield. They are gram-negative, motile, and rod-shaped. In 2022, the University of Limpopo conducted a study to identify and name the Pandoraea bacterium found in a tomato field located in Limpopo Province, South Africa. Molecular methods were employed, and the Chelex approach was utilized to extract the 16S rDNA marker, enabling the identification of bacteria present in the soil of tomato fields in South Africa. After conducting tests using specific primers to amplify the 16S rDNA, we have identified the bacterium as Pandoraea. Our analysis indicates that the strain of Pandoraea found in South Africa shares a 90% similarity with a population from Belgium (LR536859). Furthermore, maximum likelihood phylogenetic analysis indicates that this species is grouped with other Pandoraea species, with highly supported (100) bootstrap values. While the 16S rDNA method successfully identified this species, we recommend utilizing other DNA markers for a more comprehensive understanding of the Pandoraea phylogeny.