Nocardioides antri sp. nov., isolated from soil in a rock cave

Abstract

A Gram-positive, aerobic, rod-shaped, non-spore-forming bacterium, designated as BN140041T, was isolated from cave soil at Gubyeongsan Mountain, Boeun-gun, Chungbuk province in Republic of Korea. Phylogenetic analysis of the 16S rRNA gene sequence showed that the strain is closely related to Nocardioides silvaticus S-34 T, N. pelophilus THG-T63T, and N. immobilis FLL521T with 97.4%, 97.1%, and 96.8% similarity. The draft genome length was 4.27 Mb containing 424 contigs with a DNA G + C content of 70.5 mol%. The ANI value between strain BN140044T and its closely related species N. silvaticus S-34 T was 82.6%. The genome sequence of BN140041T displayed a key enzyme involved in the bioremediation of organic pollutants. The diagnostic diamino acid of peptidoglycan was LL-2,6-diaminopimelic acid. The major respiratory quinone was MK-8(H4), and the major fatty acids (> 5% of the total fatty acids) were iso-C16:0 (55.3%), C18:1ω9c (7.7%) and iso-C17:0 (5.7%). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and phosphatidylinositol. The results of genotypical, physiological, and biochemical characterization allow the phenotypic differentiation of strain BN140041T from related the Nocardioides strains. Therefore, strain BN140041T represents a novel species of the genus Nocardioides, for which we propose the name Nocardioides antri sp. nov. The type strain is BN140041T (= KCTC 49080 T = CCTCC AB 2018226 T).