Re-Evaluation of the Relationship Between Average Nucleotide Identity and dDDH Values in the Genus Micromonospora, and Description of Micromonospora cynarisoli sp. nov., a Novel Actinobacterium from the Rhizosphere Soil of Cynara scolymus

It is widely accepted in prokaryotic systematics that a 95–96% ANI (average nucleotide identity) value is equivalent to 70% dDDH (digital DNA–DNA hybridization) value in prokaryotic systematics. However, we recently found that a 70% dDDH value was equivalent to an approximately 96.7% ANIm value in the genus Micromonospora based on a correlation analysis between dDDH and ANIm from a total of 1770 pairs of type Micromonospora strains (60 type strains). Therefore, we proposed that 96.7% ANIm (ANI based on the MUMmer algorithm) value could act as the threshold value in delineating Micromonospora species. Meanwhile, the taxonomic status of an actinobacterial strain HUAS LYJ1T, isolated from the rhizosphere soil of Camellia oleifera, was determined by using a polyphasic method. A 16S rRNA gene sequence analysis indicated that strain HUAS LYJ1T shared the highest similarity to Micromonospora wenchangensis CCTCC AA 2012002T (99.3%). Phylogenetic trees based on 16S rRNA gene and whole-genome sequences demonstrated that strain HUAS LYJ1T was most closely related to M. wenchangensis CCTCC AA 2012002T. However, the ANIm value between them was 95.77%, below the 96.7% cut-off point recommended above; the dDDH value between them was 63.2%, also far below the 70% threshold value in delineating bacterial species. Based on these molecular data, as well as phenotypic and chemotaxonomical features, it is concluded that strain HUAS LYJ1T represents a novel Micromonospora species, for which the name Micromonospora cynarisoli sp. nov. is proposed. In addition, it was found that the ANIm and dDDH values of Micromonospora haikouensis DSM 45626T, Micromonospora harpali NEAU-JC6T and Micromonospora oryzae DSM 102119T were 97.21–97.86% and dDDH 73.9–79.6%, respectively, above the 96.6% ANIm and 70% dDDH threshold value in delineating Micromonospora species. Consequently, according to rule 42 of the International Committee on Systematics of Prokaryote Code, we propose that M. harpali Fang et al. 2015 and M. oryzae Kittiwongwattana et al. 2015 are later heterotypic synonyms of M. haikouensis Xie et al. 2012.