Genome-based classification of Micromonospora craterilacus sp. nov., a novel actinobacterium isolated from Nemrut Lake

Antonie Van Leeuwenhoek. 2020 Jun;113(6):791-801. doi: 10.1007/s10482-020-01390-w. Epub 2020 Feb 14.

Abstract

A novel actinobacterial strain, designated NA12T, was isolated from coastal sediment sample of Nemrut Lake, a crater lake in eastern Anatolia, Turkey. The taxonomic position of the strain was established using a polyphasic approach. Cultural and chemotaxonomic characteristics of the strain were consistent with its classification within the family Micromonosporaceae. The 16S rRNA gene sequence analysis of strain NA12T showed that the strain closely related to M. radicis AZ1-13T, M. zingiberis PLAI 1-1T, M. craniella LHW63014T and M. endophytica 202201T with pairwise sequence identity values ranging from 99.4 to 99.3%. Digital DNA-DNA hybridization values between strain NA12T and the closely related type strains were ranged from 41.0 to 18.3% while the average nucleotide identity values were between 87.3 and 86.5%, which are well below the designed cut-off points of 70 and 95%, respectively. The G + C content of genomic DNA was 71.5%. Whole-cell hydrolysates of strain NA12T contained 3-hydroxydiaminopimelic acid and meso-diaminopimelic acid. Cell-wall sugars were composed of arabinose, fucose, glucose, mannose, rhamnose and xylose. The polar lipid profile contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylglycerol, glycophospholipid, amino-phospholipid and two unidentified phospholipids. The predominant menaquinones were MK-9(H6) and MK-9(H4). Major fatty acids were iso-C16:0 and C17:1ω8c. Based upon the consensus of phenotypic and phylogenetic analyses as well as whole genome comparisons, strain NA12T (DSM 100982T = KCTC 39647T) is proposed to represent the type strain of a novel species, Micromonospora craterilacus sp. nov.

Keywords: Nemrut Lake; Phylogenomics; Polyphasic taxonomy.

MeSH terms

  • Actinobacteria / classification
  • Cell Wall / chemistry
  • DNA, Bacterial / genetics
  • Fatty Acids / analysis
  • Lakes / microbiology
  • Micromonospora* / classification
  • Micromonospora* / genetics
  • Micromonospora* / isolation & purification
  • Phospholipids / analysis
  • Phylogeny
  • RNA, Ribosomal, 16S / genetics
  • Turkey

Substances

  • DNA, Bacterial
  • Fatty Acids
  • Phospholipids
  • RNA, Ribosomal, 16S