Comparative genomics reveals environmental adaptability and antimicrobial activity of a novel Streptomyces isolated from soil under black Gobi rocks

A novel Streptomyces strain, designated 3_2(T), was isolated from soil under the black Gobi rock sample of Northwest China. The taxonomic position of this strain was revealed by a polyphasic approach. Comparative analysis of the 16S rRNA gene sequences indicated that 3_2(T) was closely related to the members of the genus Streptomyces, with the highest similarity to Streptomyces rimosus subsp. rimosus CGMCC 4.1438 (99.17%), Streptomyces sioyaensis DSM 40032 (98.97%). Strain 3_2(T) can grow in media up to 13% NaCl. The genomic DNA G + C content of strain 3_2(T) was 69.9%. We obtained the genomes of 22 Streptomyces strains similar to strain 3_2(T), compared the average nucleotide similarity, dDDH and average amino acid identity, and found that the genomic similarity of the new isolate 3_2(T) to all strains was below the threshold for interspecies classification. Chemotaxonomic data revealed that strain 3_2(T) possessed MK-9 (H-6) and MK-9 (H-8) as the major menaquinones. The cell wall contained LL-diaminopimelic acid (LL-DAP) and the whole-cell sugars were ribose and glucose. The major fatty acid methyl esters were iso-C-16:0 (23.6%) and anteiso-C-15:0 (10.4%). The fermentation products of strain 3_2(T) were inhibitory to Staphylococcus aureus and Bacillus thuringiensi. The genome of 3_2(T) was further predicted using anti-smash and the strain was found to encode the production of 41 secondary metabolites, and these gene clusters may be key to the good inhibitory activity exhibited by the strain. Genomic analysis revealed that strain 3_2(T) can encode genes that produce a variety of genes in response to environmental stresses, including cold shock, detoxification, heat shock, osmotic stress, oxidative stress, and these genes may play a key role in the harsh environment in which the strain can survive. Therefore, this strain represents a novel Streptomyces species, for which the name Streptomyces halobius sp. nov. is proposed. The type strain is 3_2(T) (= JCM 34935(T) = GDMCC 4.217(T)).