Comprehensive Genome Analysis of a Novel Actinobacterium With High Potential for Biotechnological Applications, Nonomuraea aridisoli sp. nov., Isolated From Desert Soil

Abstract

During a study to isolate such actinobacteria with unique metabolic potential, a novel actinobacterium, designated KC333(T), was isolated from a soil sample collected from the Karakum Desert, Turkmenistan. The taxonomic position of the strain was investigated using a polyphasic approach. Phylogenetic analysis of the 16S rRNA gene sequence showed that the strain was most closely related to Nonomuraea terrae CH32(T) (99.0% sequence similarity), Nonomuraea maritima FXJ7.203( T) (98.9%), Nonomuraea candida HMC10(T) (98.7%) and Nonomuraea gerenzanensis ATCC 39727( T) (98.6%), and is therefore considered to represent a member of the genus Nonomuraea. However, the average nucleotide identity and digital DNA-DNA hybridization based on whole-genome sequences between strain KC333(T) and close relatives demonstrated that it represents a novel species of the genus Nonomuraea. The major cellular fatty acids of strain KC333(T) were iso-C-16: 0, C-17:0 10-methyl and iso-C-16: 0 2OH. Strain KC333(T) contained meso-diaminopimelic, mannose, madurose and ribose in the cell-wall peptidoglycan. The predominant menaquinones were MK-9(H-4) and MK-9(H-6). The genome size of strain KC333(T) is approximately 9.86 Mb, and the genomic DNA G + C content of the strain is 71.3%. In addition to the polyphasic characterisation, comprehensive genome analysis for gene clusters encoding carbohydrate-active enzymes and bioactive secondary metabolites as well as CRISPR-associated sequences revealed the high biotechnological potential of the strain. Based on evidence collected from the genotypic, phenotypic, and phylogenetic analyses, a novel species, Nonomuraea aridisoli sp. nov. is proposed with KC333(T) (= DSM 107062( T) = JCM 32584( T) = KCTC 49111( T)) as the type strain.