Micromonospora radicis sp. nov., isolated from roots of Azadirachta indica var. siamensis Valenton, and reclassification of Jishengella zingiberis as Micromonospora zingiberis comb. nov

Int J Syst Evol Microbiol. 2019 Sep;69(9):2884-2891. doi: 10.1099/ijsem.0.003574.


A novel endophytic actinomycete strain AZ1-13T was isolated from roots of Azadirachta indica, and its taxonomic position was investigated using a polyphasic approach. Pairwise 16S rRNA gene sequence similarities of strain AZ1-13T and its closest species, Jishegella zingiberis PLAI1-1T and Micromonospora endophytica 202201T, were 99.7 and 99.2 %, respectively. Phylogenetic analyses of the family Micromonosporaceae based on 16S rRNA gene sequences indicated strains AZ1-13T and J. zingiberis PLAI1-1Tare located within the genus Micromonospora. The approximate genome size of the strain was 5.96 Mb with 71.9 mol% of G+C content. The strain AZ1-13T exhibited ANIb values of 87.4 % with J. zingiberis PLAI1-1T and 85.1 % with M. endophytica 202201T. Chemotaxonomic characteristics of strain AZ1-13T were consistent within the genus Micromonospora: cell-wall peptidoglycan of the strain contained meso-diaminopimelic acid; glucose, mannose, ribose and xylose are presented as the whole-cell sugars; the predominant menaquinones were MK-9(H4) and MK-9(H6); major cellular fatty acids were iso-C15 : 0, 10-methyl C17 : 0, C17 : 0, anteiso-C17 : 0 and iso-C17 : 1ω8c; diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol were detected as distinguished phospholipids. Based on phenotypic properties, phylogeny and genomic data, the strain AZ1-13T could be distinguished from its closest neighbours, representing a novel species of the genus Micromonospora, for which the name Micromonospora radicis sp. nov. is proposed. The type strain is AZ1-13T (=KCTC 39786T=NBRC 112324T=JCM 32147T = TISTR 2404T). This study also proposed that J. zingiberisis transferred to the genus Micromonospora as Micromonospora zingiberis comb. nov. (type strain PLAI1-1T=TBRC 7644T=NBRC 113144T=JCM 32592T).

Keywords: Azadirachta indica; Micromonospora; average nucleotide identity; digital DNA-DNA hybridisation; draft genome sequences.

MeSH terms

  • Azadirachta / microbiology*
  • Bacterial Typing Techniques
  • Base Composition
  • Cell Wall / chemistry
  • DNA, Bacterial / genetics
  • Diaminopimelic Acid / chemistry
  • Fatty Acids / chemistry
  • Micromonospora / classification*
  • Micromonospora / isolation & purification
  • Peptidoglycan / chemistry
  • Phospholipids / chemistry
  • Phylogeny*
  • Plant Roots / microbiology*
  • RNA, Ribosomal, 16S / genetics
  • Sequence Analysis, DNA
  • Thailand
  • Vitamin K 2 / analogs & derivatives
  • Vitamin K 2 / chemistry


  • DNA, Bacterial
  • Fatty Acids
  • Peptidoglycan
  • Phospholipids
  • RNA, Ribosomal, 16S
  • Vitamin K 2
  • menaquinone 9
  • Diaminopimelic Acid