Streptomyces mabaensis sp. nov., isolated from karst cave samples of ancient Ma'ba remains.

Abstract

Caves are generally considered to be natural subterranean spaces with nutrient-deficient conditions and represent a particular source of uncharacterized microbial diversity. During a culturable actinomycetes diversity research, 84 Streptomyces spp. strains were harvested from the karst cave of the Maba hominins (one of the most important representatives of archaic Homo sapiens in China) in Shaoguan City. Among these culturable Streptomyces strains, two novel strains, SYSU K21746^T and SYSU K217416, were identified and characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences and genomes indicated that strains SYSU K21746^T and SYSU K217416 were closely related to Streptomyces hiroshimensis NBRC 12785^T (98.2%/98.1% sequence similarity), Streptomyces abikoensis NBRC 13860^T (98.1%/98.0%) and Streptomyces genisteinicus CRPJ-33^T (98.0%/97.9%). The two strains showed nearly identical 16S rRNA gene sequences (99.5%), and the average nucleotide identity and digital DNA-DNA hybridization relatedness values were 98.6% and 85.8%, respectively, suggesting that these strains are affiliated with the same species. Furthermore, the major polar lipids of the two strains were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The MK-9(H₈) and MK-9(H₆) were the main isoprenoid quinones of the two strains. The major fatty acids of the two strains were iso-C_16:0 and anteiso-C_15:0. In addition, the chemotaxonomic and culture characteristics of both strains were also consistent with the genus Streptomyces, while phenotypic properties, genome-based comparisons and phylogenomic analyses distinguished strains SYSU K21746^T and SYSU K217416 from their closest phylogenetic relatives. According to these results, two isolates from the karst cave niche represent a novel species of the genus Streptomyces, for which the name Streptomyces mabaensis sp. nov. is proposed, with SYSU 21746^T (=NBRC 115001^T=CGMCC 4.7690^T) as the type strain.