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

Abstract

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, gyrB and alkB genes was used to compare our strains with type strains of Rhodococcus . For most of our strains, sequence similarity of the 16S rDNA, gyrB and alkB 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 gyrB sequences provided a more precise classification of our strains to species level than 16S rDNA sequences, whereas analysis of alkB sequences was unable to identify strains with orange-coloured colonies to species level.

Isolation and Characterization of Rhodococcus spp. from Pistachio and Almond Rootstocks and Trees in Tunisia

“…Since the identification based on 16S rDNA and vicA genes of our strains was insufficient in discriminating between species, a previous study [57] on concatenated gene sequence comparisons identified several of our strains as R. fascians and others as R. kroppenstedtii, while some remained unclassified and may represent novel species. The vicA gene has been reported to be implicated in R. fascians pathogenicity [35,64], but it was recently detected in red-orange Rhodococcus isolates associated with Pistachio Bushy Top Syndrome [36,37] and diseased ornamentals [38,39].…”

“…One commercial nursery in Kasserine governorate propagating fruit tree rootstocks had bushy almond rootstocks with stunted shoot growth with multiple shoots and considerable compact growth. The one endophytic strain obtained from these almond rootstocks, identified as R. fascians strain GS6 [57], caused severe growth effect on peas. However, the original cause of the symptoms observed on almond rootstocks is yet to be determined.…”

“…The detection of fas and att genes was also determined from the whole genome sequences of three Rhodococcus strains. The selection of these three Rhodococcus strains, identified as R. fascians GS6, R. fascians SB10, and R. kroppenstedtii K5 [40,57], was based on their high pathogenicity effect during pea bioassay (this study). Each virulence gene from pFiD188 plasmid (GenBank accession number JN093097) was used to identify homologs of genes on GS6, SB10, and K5 genomes.…”