Streptomyces tagetis sp. nov., a chromomycin producing bacteria isolated from the roots of Tagetes patula.

A novel halotolerant actinobacterium, designated as RG38T, capable of producing black extracellular melanin pigment on SP2 agar, was isolated from the roots of Tagetes patula. Comparative analysis of the 16S rRNA gene sequence revealed the highest similarity to Streptomyces collinus NBRC 12759T (99.3%). Phylogenetic analysis showed that strain RG38T clustered within the genus Streptomyces forming a monophyletic cluster with its close relatives. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and amino-acid identity (AAI) values between strain RG38T and related species within the genus Streptomyces were below the standard threshold for prokaryotic species delineation. The DNA G + C content of the strain RG38T was determined to be 73.3%. The genome size measured 7,150,598 bp comprising 17 contigs and encompassed 6,053 protein coding genes. AntiSMASH analysis of the whole genome revealed 35 putative biosynthetic gene clusters (BGCs) responsible for various secondary metabolites. Among these clusters, two gene clusters exhibited 100% similarity to the chromomycin A3, albaflavenone, and anthracimycin, respectively. These compounds were reported to possess significant anticancer and antibacterial activities. LC-MS-based analysis, coupled with further isolation studies, confirmed the production of chromomycins A2 (1), A3 (2), and their derivatives, along with their antibiotic activities. These findings underscore the potential of this novel strain as a novel resource for the discovery of diverse antimicrobial compounds. This study is the first to report an antimicrobial compound producing Streptomyces species isolated from medicinal plant T. patula. Based on a polyphasic study, the strain RG38T isolated from an unexplored habitat with a high potential for new natural products represents a novel species within the genus Streptomyces. Accordingly, we propose the name Streptomyces tagetis sp. nov. for this novel species, with the type strain is RG38T (=KCTC 49624T = TBRC 15113T).

Mesorhizobium liriopis sp. nov., isolated from the fermented fruit of Liriope platyphylla a medicinal plant.

A facultative anaerobic and Gram-negative strain, designated RP14T, was isolated from the fruit of Liriope platyphylla fermented for 60 days at 25°C. Strain RP14T showed 98.0 % 16S rRNA similarity to Mesorhizobium huakuii IFO 15243T, but in the phylogenetic tree, Mesorhizobium terrae NIBRBAC000500504T was its closest neighbour. The average nucleotide identity and digital DNA-DNA hybridization values between strain RP14T and 15 genomes of type strains of Mesorhizobium, were 73.8-74.4% and 16.4-20.2 %, respectively, which were lower than the recommended thresholds for species delineation. The strain grew at 25-32°C (optimum, 28°C), at pH 7.0-12.0 (optimum, pH 9.0) and with 0-2% NaCl (optimum, 0 %; w/v). Cells of strain RP14T were catalase-positive, oxidase-negative, rod-shaped and formed yellow-coloured colonies. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major fatty acid were C16 : 0, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The DNA G+C content was 62.8 mol%. Based on polyphasic evidence, we propose Mesorhizobium liriopis sp. nov as a novel species within the genus Mesorhizobium. The type strain is RP14T (=KACC 22720T=TBRC 16341T).

Chryseobacterium tagetis sp. nov., a plant growth promoting bacterium with an antimicrobial activity isolated from the roots of medicinal plant (Tagetes patula).

A novel plant growth-promoting and indole acetic acid (IAA) producing strain designated RG1T was isolated from the roots of Tagetes patula (marigold) collected from Goyang, South Korea. The cells of strain RG1T is aerobic, yellow, Gram-stain-negative, pleomorphic and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain RG1T belongs to the genus Chryseobacterium and is closely related to Chryseobacterium gwangjuense THG-A18T (98.6%). The strain produced IAA (70.5 µg ml-1) in the presence of L-tryptophan and showed antimicrobial activity against Gram-negative bacterium Xanthomonas campestris pv. campestris KACC 10377T. The isolate had a significant positive effect on rice plant shoot and root growth. The novel strain RG1T had a draft genome size of 4,430,189 bp, with ten scaffolds and 3969 protein-coding genes. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain RG1T and other closely related members ranged from 21.5 to 36.6% and from 79.2 to 86.6%, respectively. The genomic DNA G + C content was 34.8 mol%. Furthermore, anti-SMASH analysis of the whole genome revealed six putative biosynthetic gene clusters responsible for various secondary metabolites. The major respiratory quinone was MK-6 and the major fatty acids were iso-C15:0, summed feature 3 (comprising C16: 1ω7c and/or C16: 1ω6c) and summed feature 9 (comprising iso-C17: 1 ω9c and/or 10-methyl C16:0). The major polar lipid is phosphatidylethanolamine. Based on the genotypic, chemotaxonomic and physiological data, strain RG1T represents a novel species, for which the name Chryseobacterium tagetis sp. nov. is proposed. The type strain is designated as RG1T ( = KCTC 82696T = NBRC 115057T).