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Phylogenetic relationship of 22 FLPs was  revealed on the basis of polymorphism in three genes namely 16S rDNA,  Pseudomonas -specific and  rpo D gene regions. The primers for 16S rDNA,  Pseudomonas -specific region and  rpo D gene region were amplifying a region of 1492, 990 and 760 bp, respectively, from all the isolates investigated. The RFLP analysis of the PCR products resulted in a classification of these fluorescent pseudomonads which was best answered by  rpo D-based RFLP analysis. The 22 FLPs were placed in two major clusters and seven subclusters suggesting that these were genotypically heterogenous and might belong to several species within  Pseudomonas  sensu stricto. Sequence analysis of these three genes for three selected isolates AS5, AS7 and AS15 showed 16S rDNA and  Pseudomonas -specific gene region phylogenies were generally similar, but  rpo D gene phylogeny was somewhat different from these two genes. These results were also congruent with the results of RFLP of these three genes.  rpo D provided comparable phylogenetic resolution to that of the 16S rRNA and  Pseudomonas -specific genes at all taxonomic levels, except between closely related organisms (species and subspecies levels), for which it provided better resolution. This is particularly relevant in the context of a growing number of studies focusing on subspecies diversity, in which single-copy protein-encoding genes such as  rpo D could complement and better justify the information provided by the 16S rRNA gene. Hence  rpo D can be used further as an evolutionary chronometer for species-level identification.

Phylogenetic relationships of fluorescent pseudomonads deduced from the sequence analysis of 16S rRNA, Pseudomonas-specific and rpoD genes