Phytoplasma classification: Taxonomy based on 16S ribosomal gene, is it enough?

The discovery in 1967, of a new group of plant pathogens related to bacteria led to the finding of pleomorphic, wall-less prokaryotes in the phloem of many plant species affected by yellows-type diseases. Following the application of molecular technologies the phylogeny of these prokaryotes was resolved and led to the new trivial name of “phytoplasma” and to the designation of a new taxon named ‘Candidatus phytoplasma’. The first comprehensive phytoplasma classification scheme was based on RFLP analysis of PCR-amplified 16S rDNA, providing a reliable means for the differentiation of a broad array of phytoplasmas and has become the most comprehensive and widely accepted phytoplasma classification system. This approach using RFLP analyses of PCR amplified 16S rDNA provides a simple, reliable and rapid mean for differentiation and identification of known phytoplasmas. A consensus for naming novel phytoplasmas was recommended by the IRPCM Phytoplasma/Spiroplasma Working Team-Phytoplasma Taxonomy Group that a ‘Candidatus Phytoplasma’ species description should refer to a single, unique 16S rRNA gene sequence that has <97.5% similarity to that of any previously described ‘Ca. Phytoplasma’ species. Because of the highly conserved nature of the 16S rDNA, many biologically or ecologically distinct phytoplasma strains, which may warrant designation of a new taxon may fail to meet the requirement. In this case, additional unique biological properties such as antibody specificity, host range and vector transmission specificity as well as other molecular criteria (gene) need to be included for speciation. However, because of the highly conserved nature of the 16S rDNA and of the not uncommon presence of 16S rDNA interoperon sequence heterogeneity, the classification based on ‘Candidatus’ or on 16S ribosomal group does not always provide the molecular distinction necessary for phytoplasma strain characterization. Moreover, some additional tools for phylogenetic analyses and finer strain differentiation of phytoplasmas such as rp, secY, tuf, groEL genes, and the 16S-23S rRNA intergenic spacer region sequences have been used as supplementary tools selecting those providing the most useful and reliable taxonomic information in combination with 16SrDNA.