Antrihabitans stalagmiti sp. nov., isolated from a larva cave and a proposal to transfer Rhodococcus cavernicola Lee et al. 2020 to a new genus Spelaeibacter as Spelaeibacter cavernicola gen. nov. comb. nov

• Published in: Antonie van Leeuwenhoek 2022-04, Vol.115 (4), p.521-532
• Main Authors: Kim, Sung-Min, Lee, Soon Dong, Koh, Young Sang, Kim, In Seop
• Format: Article
• Language: English
• Subjects: Amino acids; Biomedical and Life Sciences; Clusters; Genomes; Life Sciences; Medical Microbiology; Microbiology; Morphology; New genera; New species; Nucleotides; Original Paper; Phylogeny; Physical characteristics; Plant Sciences; Rhodococcus; Roncocreagris cavernicola; rRNA 16S; Similarity; Sodium chloride; Soil Science & Conservation; Taxonomic revision
• ISSN: 0003-6072; 1572-9699
• DOI: 10.1007/s10482-022-01718-8

An actinobacterial strain, designated YC3-6 T , was isolated from a larva cave in Jeju, Republic of Korea. The novel isolate was found to grow at 10–30 °C, pH 5.0–10.0 and 0–4% (w/v) NaCl. The 16S rRNA gene phylogeny showed that the novel isolate formed a distinct subline within the family Nocardiaceae . Levels of 16S rRNA gene similarity indicated that the close relatives are Rhodococcus cavernicola (98.4% sequence similarity) and “ Rhodococcus psychrotolerans ” (98.2%) followed by Antrihabitans stalactiti (96.8%). However, the core gene-based phylogeny revealed that the novel isolate formed a tight cluster with A. stalactiti and was separated from R. cavernicola and other members of the family Nocardiaceae. The morphological and chemotaxonomic characteristics of strain YC3-6 T are in line with those of the genus Antrihabitans . Strain YC3-6 T showed an average nucleotide identity of 75.5% and a digital DDH of 20.3% with A. stalactiti. In addition, the core gene analysis showed that R. cavernicola formed a distinct subline between an Antrihabitans cluster and Aldersonia kunmingensis , and well separated from members of the genus Rhodococcus . The average amino acid identity values of R. cavernicola to closely related neighbours were 69.3–69.4% with members of the genus Antrihabitans and 67.3% with Ald. kunmingensis , while the POCP values ranged from 56.9 to 63.6%. On the basis of results obtained here, strain YC3-6 T is concluded to represent a novel species of the genus Antrihabitans , for which the name Antrihabitans stalagmiti sp. nov. (type strain, YC3-6 T  = KACC 19963 T  = DSM 107561 T ) is proposed. Based on overall genome relatedness and chemotaxonomic differences, it is also proposed that R. cavernicola Lee et al. 2020 be transferred to a new genus Spelaeibacter as Spelaeibacter cavernicola gen. nov., comb. nov.