Isolation and Characterization of <i>Rhodococcus</i> spp. from Pistachio and Almond Rootstocks and Trees in Tunisia

The purpose of this study was to isolate and identify <i>Rhodococcus</i> spp. strains from almond and pistachio rootstocks and trees in Tunisia. Twenty-eight strains were identified through 16S rDNA and <i>vic</i>A genes amplification and sequencing. Pea bioassay was performed to determine the pathogenicity of the strains. Representative 16S rDNA and <i>vic</i>A sequences of eight strains from pistachio and seven strains from almond were closely related (>98% similarity) to <i>Rhodococcus</i> spp. accessions in GenBank. Phylogenetic analysis based on 16S rDNA sequences revealed that the yellow-colored strains clustered with phytopathogenic <i>Rhodococcus</i><i>fascians</i>. The red and orange-colored strains were separated into a different group with <i>R. kroppenstedtii</i> and <i>R. corynebacteiroides</i> isolates. Eleven strains affected the pea seedlings’ growth and exhibited different levels of virulence. The number of shoots was significantly higher in seedlings inoculated with four <i>Rhodococcus</i> strains, whereas the other three strains caused up to 80% of plant height reduction and reduced root secondary growth compared to non-inoculated pea seedlings. These strains, most of which are epiphytes from asymptomatic hosts, showed strong pathogenicity during pea bioassay and were established endophytically in pea tissues. Ten <i>att</i> and five <i>fas</i> genes were detected in four strains and may represent a novel model of plant pathogenic <i>Rhodococcus</i> virulence. The results of our survey showed that <i>Rhodococcus</i> is present but not prevalent in all visited orchards of almond and pistachio rootstocks and trees. Our surveys complemented the investments being made on ornamental species in Tunisia and unveiled the presence of undocumented plant-associated <i>Rhodococcus</i> spp. on economically important crops.