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

Abstract

A novel actinobacterial strain, designated NA12(T), 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 NA12(T) showed that the strain closely related to M. radicis AZ1-13(T), M. zingiberis PLAI 1-1(T), M. craniella LHW63014(T) and M. endophytica 202201(T) with pairwise sequence identity values ranging from 99.4 to 99.3%. Digital DNA-DNA hybridization values between strain NA12(T) 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 NA12(T) 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(H-6) and MK-9(H-4). Major fatty acids were iso-C-16:0 and C-17:1 omega 8c. Based upon the consensus of phenotypic and phylogenetic analyses as well as whole genome comparisons, strain NA12(T) (DSM 100982(T) = KCTC 39647(T)) is proposed to represent the type strain of a novel species, Micromonospora craterilacus sp. nov.