- Volume 58, Issue 10, 2008

Phytoplasmas are cell wall-less bacteria that cause numerous diseases in several hundred plant species. During adaptation to transkingdom parasitism in diverse plant and insect hosts, phytoplasma evolution has given rise to widely divergent lineages. Since phytoplasmas cannot be cultured in a cell-free medium, measurable phenotypic characters suitable for conventional microbial classification are mostly inaccessible. Currently, phytoplasma differentiation and classification are mainly dependent on restriction fragment length polymorphism (RFLP) analysis of 16S rRNA gene sequences. Extending our recent efforts in the exploitation of computer-simulated 16S rRNA gene RFLP analysis and virtual gel plotting for rapid classification of phytoplasmas, we have developed a Perl program for automated RFLP pattern comparison and similarity coefficient calculation. This program streamlines virtual RFLP pattern analysis and has led to the establishment of a criterion for phytoplasma 16Sr subgroup classification and to the delineation of new and distinct subgroup lineages in the clover proliferation phytoplasma group (16SrVI).

An examination of the results of phylogenetic analyses based on the sequences of fragments of the 16S rRNA, gyrB and rpoD genes, and the discrimination of genomovars based on siderophore diversity within the genus Pseudomonas, has added important taxonomic tools in the characterization of Pseudomonas stutzeri. Eighteen reference strains, nine newly identified hydrocarbon-degrading strains and three strains showing relevant physiological characteristics of P. stutzeri, together with the type strains of four related species, were included in the study. A novel genomovar within the species is described. A summary of the methodology used in these studies and the results of our attempts to define a solid internal subdivision of this important species within the genus Pseudomonas are presented and discussed.