Streptacidiphilus alkalitolerans sp. nov., Streptacidiphilus cavernicola sp. nov. and Streptacidiphilus jeojiensis sp. nov. isolated from a cave, and an emended description of the genus Streptacidiphilus.

Abstract

Six Gram-reaction-positive, strictly aerobic, mycelium-forming actinobacteria were isolated from soils collected from a natural cave in Jeju, Republic of Korea. The isolates produced well-developed, branched, substrate mycelia and white aerial mycelia that differentiated into straight or flexuous chains of smooth-surfaced spores. Cells showed growth at 15-30 °C, pH 3.5-8.0 and 0-1% (w/v) NaCl. Most of the isolates also grew at pH 10.0. The cell-wall peptidoglycan in common contained ll-diaminopimelic acid, galactose, glucose, mannose and rhamnose. The major menaquinone was MK-9(H₆) and MK-9(H₈). The polar lipids in common contained phosphatidylglycerol, phosphatidylinositol and an unidentified phospholipid, with the presence of diphosphatidylglycerol and phosphatidylethanolamine in some strains. The predominant fatty acids in common were anteiso-C_15 : 0, iso-C_16 : 0 and C_16 : 0. Strains N1-1^T, N1-3 and N1-12 contained genomes of 8.44-8.77 Mbp, and strains N1-5 and N1-10^T consisted of genomes of 9.00-9.17 Mbp, while strain N8-3^T contained the smallest genome (7.33 Mbp) among the isolates. The genomic DNA G+C contents of the isolates were 71.5-72.2%. Three representatives of the isolates encompassed 16-29 biosynthetic gene clusters predicted to encode for secondary metabolites. The core genome-based phylogenomic tree showed that they formed three distinct clusters within the genus Streptacidiphilus, with the closest relative, the type strain of Streptacidiphilus carbonis, which was also supported by 16S rRNA gene phylogeny. The orthologous average nucleotide identity (≤88.2%) and digital DNA-DNA hybridization (≤30.3%) between three representatives of the isolates and members of the genus Streptacidiphilus and among them supported that the isolates represent three new species of the genus Streptacidiphilus, for which the names Streptacidiphilus alkalitolerans [type strain, N1-1^T (=KCTC 19224^T=DSM 45080^T)], Streptacidiphilus cavernicola [type strain, N8-3^T (=KCTC 29470^T=DSM 117389^T)] and Streptacidiphilus jeojiensis sp. nov. [type strain, N1-10^T (=KCTC 19257^T=DSM 117391^T=NRRL B-24556^T)] are proposed.