Aeromicrobium stalagmiti sp. nov., isolated from a lava cave

Abstract

A Gram-reaction-positive, strictly aerobic, non-sporulating, non-motile, rod-shaped bacterium, designated YC3-14T, was isolated from pieces of stalagmite collected in a lava cave in Jeju, Republic of Korea. Cells showed growth at 15–35 °C, pH 6.0–9.0 and with 0–3 % (w/v) NaCl. Colonies of the cells were circular, smooth, convex and cream in colour. A 16S rRNA gene-based neighbour-joining tree indicated that the organism belonged to the genus Aeromicrobium and formed a sublineage between an Aeromicrobium endophyticum–Aeromicrobium fastidiosum cluster and an Aeromicrobium yanjiei–Aeromicrobium chenweiae cluster. The highest 16S rRNA gene similarity values of strain YC3-14T were with the type strains of A. yanjiei (99.2 %), A. endophyticum (99.1 %), A. fastidiosum (98.8 %), A. ginsengisoli (98.8 %) and A . chenweiae (98.7 %). The cell-wall peptidoglycan contained ll-diaminopimelic acid as the diagnostic diamino acid. The major menaquinone was MK-9(H4). The predominant fatty acids were C18 : 0.10-methyl, C18 : 1  ω9c and C16 : 0. The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, an unidentified phospholipid and two unidentified lipids. The G+C content of the genome DNA was 69.9 mol%. These chemotaxonomic features of the isolate were typical for the genus Aeromicrobium . The genome-based phylogeny showed the same tree topology as the 16S rRNA gene phylogeny. The average nucleotide identity (≤84.5 %) and digital DNA–DNA hybridization (≤27.5 %) values supported that the isolate belongs to a novel species of the genus Aeromicrobium . On the basis of data obtained by a polyphasic approach, strain YC3-14T (=KCTC 49469T=NBRC 114653T) represents a novel species of the genus Aeromicrobium , for which the name Aeromicrobium stalagmiti sp. nov. is proposed.