Streptomyces Spinosus Sp. Nov. And Streptomyces Shenzenensis Subsp. Endophyticus Subsp. Nov. Endophytic Actinobacteria Isolated From Jasmine Rice and Their Genome Mining Correlate With Potential as Antibiotic Producers and Plant Growth Promoters

Abstract Two endophytic actinobacteria, strains SBTS01T and W18L9T, were isolated from leaf sheath tissue and leaf sample of Jasmine rice (Oryza sativa KDML 105), respectively, grown in a rice paddy field in Roiet Province, Thailand. The polyphasic study showed that both strains belonged to the genus Streptomyces; they are aerobe, with well-developed substrate mycelia and aerial mycelia to form long chains of spores. Strain SBTS01T shared the highest 16S rRNA gene sequence similarity with Streptomyces rochei NRRL B-2410T (99.0%) and Streptomyces naganishii NRRL ISP-5282T (99.0%). Strain W18L9T shared the highest 16S rRNA gene sequence similarity with Streptomyces shenzhenensis DSM 42034T. The genotypic and phenotypic data of strains SBTS01T and W18L9T distinguished these two strains with the closely related species with valid names. The genome analysis showed the dDDH, ANIb and ANIm values of the draft genome between strain SBTS01T and its related species; S. rochei NRRL B-2410T (29.4, 81.1, 86.5%) and W18L9T and its closest species; S. shenzhenensis DSM 42034T (72.5, 95.1, 97.0%). The name proposed for the new species of type strain SBTS01T is Streptomyces spinosus (=NRRL B-65636T =TBRC 15052T). The name proposed for the novel subspecies of strain W18L9T is Streptomyces shenzenensis subsp. endophyticus (=NRRL B-65635T =TBRC 15051T). Both strains could produce antibiotics to inhibit pathogens and contained plant growth promoting (PGP) traits. Genome mining of these two strains revealed that they comprised many Biosynthesis Gene Clusters (BGCs); terpene, type 1, 2 and 3 polyketide synthase, Non-ribosomal peptide synthetase (NRPS), and lanthipeptide including genes encoding PGP traits; nitrogen fixation, ACC (1-aminocyclopropane-1-carboxylate) deaminase and siderophore production.