Streptomyces mahasarakhamensis sp. nov., an Endophytic Actinobacterium Isolated from Jasmine Rice and its Potential as plant Growth Promoter.

Two endophytic actinobacteria, strains MK5T and MK7, were isolated from the surface-sterilized root of Jasmine rice (Oryza sativa KDML 105). These strains were aerobic actinobacteria with a well-developed substrate and aerial mycelia that formed spiral spore chains. The type strains that shared the high 16S rRNA gene sequence similarity with both strains were Streptomyces naganishii NBRC 12892T (99.4%), "Streptomyces griseicoloratus" TRM S81-3T (99.2%), and Streptomyces spiralis NBRC 14215T (98.9%). Strains MK5T and MK7 are the same species sharing a digital DNA-DNA hybridization (dDDH) value of 95.3% and a 16S rRNA gene sequence similarity of 100%. Chemotaxonomic data confirmed the affiliation of strains MK5T and MK7 to the genus Streptomyces. Strains MK5T and MK7 contained MK-9(H4) as a major menaquinone; the whole-cell sugar of both strains was galactose and glucose. The strain MK5T shared 93.4% average nucleotide identity (ANI)-Blast, 95.5% ANI-MUMmer, 93% average amino acid identity, and 61.3% dDDH with S. spiralis NBRC 14215T. The polyphasic approach confirmed that strain MK5T represents a novel species, and the name Streptomyces mahasarakhamensis sp. nov. is proposed. The type strain is MK5T (= TBRC 17754 = NRRL B-65683). Genome mining, using an in silico approach and searching biosynthesis gene clusters of strains MK5T and MK7, revealed that the genomes contained genes encoding proteins relating to plant growth promotion, bioactive compounds, and beneficial enzymes. Strains MK5T and MK7 could produce indole acetic acid and solubilize phosphate in vitro.

Streptomyces spinosus sp. nov. and Streptomyces shenzhenensis subsp. oryzicola subsp. nov. endophytic actinobacteria isolated from Jasmine rice and their genome mining for potential as antibiotic producers and plant growth promoters.

Two endophytic actinobacteria, strains SBTS01T and W18L9T, were isolated from leaf sheath and leaf tissue, respectively, of Jasmine rice (Oryza sativa KDML 105) grown in a rice paddy field in Roi Et Province, Thailand. A polyphasic taxonomic study showed that both strains belong to the genus Streptomyces; they are aerobic, forming well-developed substrate mycelia and aerial mycelia with long chains of spores. Strain SBTS01T shares high 16S rRNA gene sequence similarity with Streptomyces rochei NRRL B-2410 T (99.0%) and Streptomyces naganishii NRRL ISP-5282 T (99.0%). Strain W18L9T shares high 16S rRNA gene sequence similarity with Streptomyces shenzhenensis DSM 42034 T (99.7%). The genotypic and phenotypic properties of strains SBTS01T and W18L9T distinguish these two strains from the closely related species with validly published names. The genome analysis showed the dDDH, ANIb and ANIm values of the draft genome between strain SBTS01T and its close neighbour in the phylogenomic tree, Streptomyces corchorusii DSM 40340T to be 54.1, 92.6, and 94.3%, respectively; similarly for strain W18L9T and the closely related species S. shenzhenensis DSM 42034 T values were 72.5, 95.1 and 97.0%. The name proposed for the new species represented by the type strain SBTS01T is Streptomyces spinosus (= NRRL B-65636 T = TBRC 15052T). The name proposed for the novel subspecies of strain W18L9T is Streptomyces shenzhenensis subsp. oryzicola (= NRRL B-65635 T = TBRC 15051T). Recognition of this subspecies also permits the description of Streptomyces shenzhenensis subsp. shenzhenensis. Strains SBTS01T and W18L9T can produce antibiotic against rice and human pathogens and showed plant growth promoting properties such as production of indole acetic acid, cytokinin, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, siderophores and cellulase. Genomic data mining of these two strains confirmed their potential as antibiotic producers and plant growth promoters. Their genomes contain multiple biosynthetic gene clusters including those for terpene, type 1, 2 and 3 polyketide synthase, Non-ribosomal peptide synthetase and lanthipeptides. Genes encoding plant growth promoting traits such; nitrogen fixation, ACC deaminase, siderophore production and stress-related adaption may have ecological significance.

Description of Streptomyces naphthomycinicus sp. nov., an endophytic actinobacterium producing naphthomycin A and its genome insight for discovering bioactive compounds.

Endophytic actinobacteria are a group of bacteria living inside plant tissue without harmful effects, and benefit the host plant. Many can inhibit plant pathogens and promote plant growth. This study aimed to identify a strain of Streptomyces as a novel species and study its antibiotics production. An endophytic actinobacterium, strain TML10T was isolated from a surface-sterilized leaf of a Thai medicinal plant (Terminalia mucronata Craib and Hutch). As a result of a polyphasic taxonomy study, strain TML10T was identified as a member of the genus Streptomyces. Strain TML10T was an aerobic actinobacterium with well-developed substrate mycelia with loop spore chains and spiny surface. Chemotaxonomic data, including cell wall components, major menaquinones, and major fatty acids, confirmed the affiliation of strain TML10T to the genus Streptomyces. The results of the phylogenetic analysis, including physiological and biochemical studies in combination with a genome comparison study, allowed the genotypic and phenotypic differentiation of strain TML10T and the closest related type strains. The digital DNA-DNA hybridization (dDDH), Average nucleotide identity Blast (ANIb), and ANIMummer (ANIm) values between strain TML10T and the closest type strain, Streptomyces musisoli CH5-8T were 38.8%, 88.5%, and 90.8%, respectively. The name proposed for the new species is Streptomyces naphthomycinicus sp. nov. (TML10T = TBRC 15050T = NRRL B-65638T). Strain TML10T was further studied for liquid and solid-state fermentation of antibiotic production. Solid-state fermentation with cooked rice provided the best conditions for antibiotic production against methicillin-resistant Staphylococcus aureus. The elucidation of the chemical structures from this strain revealed a known antimicrobial agent, naphthomycin A. Mining the genome data of strain TML10T suggested its potential as a producer of antbiotics and other valuable compounds such as ε-Poly-L-lysine (ε-PL) and arginine deiminase. Strain TML10T contains the arcA gene encoding arginine deiminase and could degrade arginine in vitro.