Nocardia cavernae sp. nov., a novel actinobacterium isolated from a karst cave sample

A novel actinobacterial strain, designated YIM A1135T, was isolated from a soil sample collected from a karst cave in Xingyi county, Guizhou province, south-western China. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of the strain were aerobic, Gram-stain-positive and partially acid-alcohol-fast. Strain YIM A1135T shared 98.3 % 16S rRNA gene sequence similarity with Nocardia jejuensis NBRC 103114T and 97.6 % with Nocardia alba YIM 30243T. DNA-DNA hybridization values between strain YIM A1135T and related type strains of the genus Nocardia were less than 70 %. In addition, meso-diaminopimelic acid was the diagnostic diamino acid in cell-wall peptidoglycan. The whole-cell sugars were fructose, mannose, galactose and glucose. The major isoprenoid quinone was MK-8(H4,ω-cycl), while the major fatty acids (>10 %) were C16 : 0, C18 : 1ω9c, C18 : 0 10-methyl and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. Mycolic acids were present. The genomic DNA G+C content of strain YIM A1135T was 66.7 mol%. Based on the results of the molecular studies supported by its morphological, physiological, chemotaxnomic and other differential phenotypic characteristics, strain YIM A1135T is considered to represent a novel species within the genus Nocardia, for which the name Nocardia cavernae sp. nov. is proposed. The type strain is YIM A1135T (=KCTC 39595T=CCTCC AA 2017030T).