Nocardia glycosmidis, Nocardia aegles and Nocardia citri spp. nov., three novel endophytic actinomycetes isolated from the roots of Rutaceae plants.

In this study, three novel actinomycete strains, designated R6R-6ᵀ, R7R-8ᵀ and R16R-3ᵀ, were isolated from the roots of Glycosmis pentaphylla (Retz.) DC., Aegle marmelos (L.) Corrêa ex Roxb. and Citrus × aurantiifolia, respectively. The taxonomic status of these strains was evaluated using a polyphasic taxonomic approach. All three strains produced short spore chains (three to five spores) with cylindrical spores on aerial mycelia and exhibited chemotaxonomic characteristics consistent with members of the genus Nocardia. These features included the presence of meso-diaminopimelic acid and mycolic acids in the cell wall peptidoglycan, a polar lipid profile of type PII characterized by phosphatidylethanolamine, and cellular fatty acids (>1%) comprising C14 : 0, C16 : 0, C17 : 0, C18 : 0, C18 : 0 10-methyl, C16 : 1 ω11c, C18 : 1 ω9c and C16 : 1 ω6c and/or C16 : 1 ω7c. Based on 16S rRNA gene sequence analysis, strains R6R-6ᵀ and R7R-8ᵀ showed the highest sequence similarities of 98.9 and 99.1%, respectively, to Nocardia xestospongiae ST01-07ᵀ, while strain R16R-3ᵀ exhibited the highest similarity (98.5%) to Nocardia anaemiae NBRC 100462ᵀ. Genome-based comparisons using digital DNA-DNA hybridization and average nucleotide identity revealed that all three strains shared values below the established species delineation thresholds when compared with their closest phylogenetic relatives. Based on the combined phenotypic, phylogenetic and genomic evidence, strains R6R-6ᵀ, R7R-8ᵀ and R16R-3ᵀ represent three novel species of the genus Nocardia, for which the names Nocardia glycosmidis sp. nov. (type strain R6R-6ᵀ=TBRC 14548T, =NBRC 115197T), Nocardia aegles sp. nov. (type strain R7R-8ᵀ=TBRC 14549T, =NBRC 115198T) and Nocardia citri sp. nov. (type strain R16R-3ᵀ=TBRC 14550T, =NBRC 115199T) are proposed.