Unveiling three novel actinobacterial species (Streptomyces cavernicola sp. nov., Streptomyces solicavernae sp. nov. and Streptomyces luteolus sp. nov.) in soil samples in Phu Pha Phet Cave, Thailand.

Three strains of actinobacteria, designated as B-S-A6^T, B-S-A8^T and B-S-A12^T, were isolated from soil samples collected in the Phu Pha Phet Cave located in the Satun UNESCO Global Geopark, Satun Province, Thailand. A comprehensive polyphasic approach was used to describe these strains. Strains B-S-A6^T, B-S-A8^T and B-S-A12^T were identified within the genus Streptomyces based on a comparative examination of 16S rRNA gene sequences. Strains B-S-A8^T and B-S-A12^T showed a high genetic similarity to Streptomyces spectabilis NBRC 13424^T (99.0%, for both) and to Streptomyces deserti C63^T (98.6 and 98.7 %, respectively). Meanwhile, strain B-S-A6^T exhibited 98.6% sequence similarity with S. spectabilis NBRC 13424^T and Streptomyces koyangensis VK-A6 ^T. However, upon further comparison, the 16S rRNA gene sequence of strain B-S-A6^T showed a similarity of 99.6% to B-S-A8^T and 99.7% to B-S-A12^T. Contrastingly, B-S-A8^T showed a very high similarity of 99.8% with B-S-A12^T. The use of digital DNA-DNA hybridization, along with the analysis of average nt identities and aa identities, comparing the three strains to their closest known type strains, validated that each of these strains represents a new and distinct species. Three newly identified strains exhibited phenotypic characteristics and chemotaxonomic properties consistent with the members of the genus Streptomyces. The primary menaquinones identified in these strains were MK-9(H₆) and MK-9(H₈). The major fatty acids were iso-C_15 : 0 and anteiso-C_15 : 0. Their polar lipid profiles included diphosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The comprehensive phenotypic and genomic analyses of the Streptomyces strains strongly suggest that strains B-S-A6^T, B-S-A8^T and B-S-A12^T represent three new species for which the names Streptomyces cavernicola sp. nov. (type strain B-S-A6^T =TBRC 17074^T =NBRC 116118^T), Streptomyces solicavernae sp. nov. (type strain B-S-A8^T =TBRC 17072^T =NBRC 116117^T) and Streptomyces luteolus sp. nov. (type strain B-S-A12^T =TBRC 17060^T =NBRC 116116^T) are proposed.