Molecular identification and assessment of genetic diversity of fluorescent pseudomonads based on different polymerase chain reaction (PCR) methods

A total of 66 fluorescent pseudomonads strains isolated from diverse Tunisian environmental biotypes (wastewater, compost, wastewater treatment plant, etc.) were analysed by two polymerase chain reaction (PCR)-based methods, 16S-23S intergenic spacer regions (ITS)-PCR and repetitive extragenic palindromic (BOX)-PCR. These typing techniques were evaluated to assess their usefulness as tool to study the Pseudomonas diversity within this complex group. Genetic analysis using ITSand BOX-PCR generated respectively 12 and 45 distinct profiles. Phylogenetic relationships within fluorescent pseudomonads were examined by analyzing partial 16S rRNA and rpoB genes sequences. The phylogenetic resolution of the rpoB tree was higher than that of the 16S rRNA tree. Moreover, the sequencing of the rpoB gene has recognized 13 different species and sub-species, while the 16 rRNA gene sequencing differentiated only 9 species.