Rathayibacter rhapontici sp. nov., Isolated from Leaf Gall Induced by the Knapweed Nematode Mesoanguina picridis on Rhaponticum repens

A novel aerobic, gram-stain-positive, nonmotile, coryneform actinobacterium, strain VKM Ac-2630T, was isolated in 2016 from a leaf gall induced by the knapweed nematode Mesoanguina picridis (family Anguinidae) on a plant Rhaponticum repens (family Asteraceae) collected in the Kyzylkum Desert (Uzbekistan) in 1992. Analysis of the 16S rRNA gene sequence showed that the strain belonged to the genus Rathayibacter (family Microbacteriaceae), and had the highest similarity to R. rubneri ZW T2_19T (100%) and R. caricis VKM Ac-1799T (99.79%). Analysis of the genome sequence revealed that the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values did not exceed 93.73 and 56.4%, respectively. These values fall below the established thresholds for species delineation. The strain exhibited the key chemotaxonomic properties characteristic of most Rathayibacter species, including the DAB-based peptidoglycan, rhamnose and mannose as the predominant cell wall sugars, MK-10 as the major menaquinone, and fatty acids of the iso-anteiso type, with prevalence of anteiso-15:0. Based on the results obtained in this study and the data on genome sequence published previously, we provide description of novel species Rathayibacter rhapontici sp. nov. with the type strain DL-579T (=VKM Ac-2630T = LMG 33115T).