Sequence analysis of 16S rDNA, gyrB and alkB genes of plant-associated Rhodococcus species from Tunisia

The genus Rhodococcus contains several species with agricultural, biotechnological and ecological importance. Within this genus, many phyllosphere, rhizosphere and endosphere strains are plant growth promoting bacteria, whereas strains designated as R. fascians are plant pathogens. In this study, we isolated 47 Rhodococcus strains from a range of herbaceous and woody plant species. Phylogenetic analysis based on 16S rDNA, gyr B and alk B genes was used to compare our strains with type strains of Rhodococcus . For most of our strains, sequence similarity of the 16S rDNA, gyr B and alk B regions to type strains ranged from 98–100 %. Results of the concatenated gene sequence comparisons identified 18 strains of R. fascians and three strains of R. kroppenstedtii . The remaining strains were unclassified, and may represent novel species of Rhodococcus . Phylogenetic analysis based on gyr B sequences provided a more precise classification of our strains to species level than 16S rDNA sequences, whereas analysis of alk B sequences was unable to identify strains with orange-coloured colonies to species level.