Microbacterium elymi sp. nov., Isolated from the Rhizospheric Soil of Elymus tsukushiensis, a Plant Native to the Dokdo Islands, Republic of Korea

Microbacterium elymi KUDC0405^T was isolated from the rhizosphere of Elymus tsukushiensis from the Dokdo Islands. The KUDC0405^T strain was Gram-stain-positive, non-spore forming, non-motile, and facultatively anaerobic bacteria. Strain KUDC0405^T was a rod-shaped bacterium with size dimensions of 0.3-0.4 × 0.7-0.8 μm. Based on 16S rRNA gene sequences, KUDC0405^T was most closely related to Microbacterium bovistercoris NEAU-LLE^T (97.8%) and Microbacterium pseudoresistens CC-5209^T (97.6%). The dDDH (digital DNA-DNA hybridization) values between KUDC0405^T and M. bovistercoris NEAU-LLE^T and M. pseudoresistens CC-5209^T were below 17.3% and 17.5%, respectively. The ANI (average nucleotide identity) values among strains KUDC0405^T, M. bovistercoris NEAU-LLE^T, and M. pseudoresistens CC-5209^T were 86.6% and 80.7%, respectively. The AAI (average amino acid identity) values were 64.66% and 64.97%, respectively, between KUDC0405^T and its closest related type strains. The genome contained 3,596 CDCs, three rRNAs, 46 tRNAs, and three non-coding RNAs (ncRNAs). The genomic DNA GC content was 70.4%. The polar lipids included diphosphatydilglycerol, glycolipid, phosphatydilglycerol, and unknown phospholipid, and the major fatty acids were anteiso-C_17:0 and iso-C_16:0. Strain KUDC0405^T contained MK-12 as the major menaquinone. Based on genotypic, phylogenetic, and phenotypic properties, strain KUDC0405^T should be considered a novel species within the genus Microbacterium, for which we propose the name M. elymi sp. nov., and the type strain as KUDC0405^T (=KCTC 49411^T, =CGMCC1.18472^T).

Mycolicibacterium baixiangningiae sp. nov. and Mycolicibacterium mengxianglii sp. nov., two new rapidly growing mycobacterial species

Four bacterial strains (LJ126^T/S18 and Z-34^T/S20) recovered from faecal samples of Tibetan antelopes on the Qinghai-Tibet Plateau of China were analysed using a polyphasic approach. All four isolates were aerobic, short rod-shaped, non-motile, Gram-stain-positive, acid-fast and fast-growing. Phylogenetic analyses based upon 16S rRNA and whole-genome sequences showed that the two pair of strains formed two distinct branches within the evolutionary radiation of the genus Mycolicibacterium. Strains LJ126^T/S18 and Z-34^T/S20 were most closely related to Mycolicibacterium austroafricanum CCUG 37667^T, Mycobacterium aurum NCTC 10437^T, Mycobacterium pyrenivorans DSM 44605^T, Mycobacterium monacense JCM 15658^T, Mycolicibacterium sarraceniae JCM 30395^T, Mycolicibacterium tokaiense JCM 6373^T and Mycobacterium murale JCM 13392^T, but readily distinguished from the known species by a combination of chemotaxonomic and phenotypic features and by low average nucleotide identity values (74.4-84.9 %). Consequently, the two strain pairs are considered to represent different novel species of Mycolicibacterium for which the names Mycolicibacterium baixiangningiae sp. nov. and Mycolicibacterium mengxianglii sp. nov. are proposed, with LJ126^T (=CGMCC 1.1992^T=KCTC 49535^T) and Z-34^T (=CGMCC 1.1993^T=DSM 106172^T) as the respective type strains.

Metabacillus elymi sp. nov., isolated from the Rhizosphere of Elymus tsukushiensis, a plant native to the Dokdo Islands, Republic of Korea

Dokdo islands in Republic of Korea, is not suited to survive plant because strong wind, low organic content and high salinity. Nevertheless, 64 taxa of plants have a symbiotic relationship with microbe. The Metabacillus elymi KUDC1714^T was isolated from the rhizosphere of Elymus tsukushiensis collected from Dokdo Islands. This bacterial strain was Gram-stain positive, non-motile, non-spore forming, aerobic and rod-shape bacteria with 0.4-0.5 × 2.5-3.0 μm in size. Colonies were smooth, yellowish-white circular and 2.0-3.0 mm in diameter. KUDC1714^T was capable of growing at 10-45 °C (optimum, 30 °C), pH 7-11 (optimum, pH 8) and 0-8.0% (w/v) NaCl (optimum, 1.0-2.0%). Flagella were not observed by transmission electron microscopy. Phylogenetic analyses, based on 16S rRNA gene sequences, showed that KUDC1714^T belonged to the genus Metabacillus formed a phyletic lineage within the genus Metabacillus of the family Bacillaceae. The strain KUDC1714^T was most closely related to Metabacillus sediminilitoris DSL-17 ^T (98.2%), Metabacillus litoralis SW-211 ^T (98.2%) and Metabacillus halosaccharovorans E33^T (97.7%) based on 16S rRNA gene sequence. In silico DNA-DNA hybridization using genome-to-genome distance calculator were analysed at 25.8% and 23.5% in strain KUDC1714^T and Metabacillus sediminilitoris DSL-17 ^T, and strain KUDC1714^T and Metabacillus litoralis SW-211 ^T, respectively. Strain KUDC1714^T and its closet type strain were all below cut-off point of the average nucleotide identity and average amino acid identity values. The genome contains 5197 CDSs, 3 rRNAs, 118 tRNAs, 5 ncRNAs. The genomic DNA G + C content was 34.8 mol%. Its polar lipids were diphosphatidylglycerol, phosphatidylglycerol and its major fatty acids were anteiso-C_15:0 and iso-C_15:0. The strain KUDC1714^T contained menaquinone-7 as major isoprenoid quinone. Based on its genetic data, physiological and biochemical characteristics, strain KUDC1714^T should be considered a novel species of the genus Metabacillus, for which we propose the name Metabacillus elymi sp. nov. the type strain is KUDC1714^T (= KCTC 33222 ^T, = DSM 27608 ^T).

Paenibacillus roseus sp. nov., a ginsenoside-transforming bacterium isolated from forest soil

A novel, pink-pigmented, Gram-stain-positive, aerobic, motile, rod-shaped and ginsenoside-converting bacterium, designated strain MAHUQ-46^T, was isolated from soil of a forest. Strain MAHUQ-46^T grew in the pH range 6.0-9.0 (optimum, 7.5), at temperatures between 10 and 37 °C (optimum, 30 °C) and at 0-3% (w/v) NaCl (optimum, 0.5%). 16S rRNA gene sequence analysis showed that strain MAHUQ-46^T was closely related to Paenibacillus pinihumi S23^T (97.3% similarity), followed by Paenibacillus elymi KUDC6143^T (96.7%). The draft genome of strain MAHUQ-46^T had a total length of 5,367,904 base pairs. A total of 4,857 genes were identified, in which 4,629 were protein-coding genes and 137 were RNA genes. The genome annotation of MAHUQ-46^T showed 172 carbohydrate genes, some of them may be responsible for the biosynthesis of ginsenoside Rd from major ginsenoside Rb1. The DNA G + C content was 48.4 mol% and the major quinone was MK-7. Main fatty acids of strain MAHUQ-46^T were C_{15: 0 anteiso}, C_16: 0 and C_{17: 0 anteiso}. The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyl-N-methylethanolamine, two unidentified aminophospholipids and five unidentified phospholipids. Diagnostic diamino acid of peptidoglycan was meso-diaminopimelic acid. The novel strain MAHUQ-46^T was able to rapidly synthesize ginsenoside Rd from major ginsenoside Rb1. The synthesized ginsenoside was confirmed by TLC and HPLC analysis. According to the phenotypic, genetic and chemotaxonomic evidence, strain MAHUQ-46^T was clearly distinguishable from validly published species of genus Paenibacillus and should, therefore, be categorized as a novel species for which the name Paenibacillus roseus sp. nov. is proposed. The type strain is MAHUQ-46^T (= KACC 21242^T = CGMCC 1.17353^T).

Adhaeribacter radiodurans sp. nov., isolated from the rhizospheric soil of Elymus tsukushiensis, a plant native to the Dokdo Islands, Republic of Korea

KUDC8001^T was isolated from the rhizosperic soil of Elymus tsukushiensis in the Dokdo Islands, Republic of Korea. Strain KUDC8001^T was Gram-stain-negative, non-motile and rod-shaped. KUDC8001^T was catalase- and oxidase-positive. This strain is capable of growing at 4-37 °C and pH 7.0-8.0 and exhibited optimal growth at 25 °C and pH 7.0. It could be grown in R2A, nutrient agar and ISP2 agar plates. The cell width ranged from 0.7 to 1.0 µm, and length ranged from 2.5 to 5.5 µm. The genomic G+C content was 40.8 mol%. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that the strain KUDC8001^T belongs to the genus Adhaeribacter, which is most closely related to the strain A. pallidiroseus HMF7616^T (97.5%). The DNA relatedness of KUDC8001^T with the type strains of A. pallidiroseus HMF7616^T, A. swui 17 mud1-7^T and A. arboris HMF7605^T was ≤80.3 % based on average nucleotide identity calculations and ≤86.9 % based on average amino acid identity calculations. In silico DNA-DNA hybridization values of the strain KUDC8001^T with the most closely related strains were 22.1, 24.0 and 24.4 %. Based on its phenotypic, phylogenetic, genetic and chemotaxonomic features, the strain KUDC8001^T should be considered as a novel species in the genus Adhaeribacter, for which we have proposed the name Adhaeribacter radiodurans sp. nov. The type strain is KUDC8001^T (=KCTC 82078^T=CGMCC 1.18475^T).

Nocardioides sambongensis sp. nov., isolated from Dokdo Islands soil

Strain KUDC5002^T was isolated from soil sampled on the Dokdo Islands, Republic of Korea. This bacterial strain was Gram stain-positive, non-motile, rod-shaped, capable of growing at 25-37°C and pH 5.0-12.0, and showed optimal growth at 30 °C and pH 7.0-8.0. Strain KUDC5002^T could be grown in tryptic soy broth containing less than 7.0 % NaCl (w/v). The cell width ranged from 0.5 to 0.6 µm and length ranged from 0.8 to 1.0 µm. Strain KUDC5002^T was catalase- and oxidase-positive. Its genomic G+C content was 72.2 mol%. Its major fatty acids were C_18 : 1 ω9c (17.3 %), iso-C_16 : 0 (16.0 %) and iso-C_17 : 0 (11.4 %). Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain KUDC5002^T belongs to the genus Nocardioides and is most closely related to strain Nocardioides humi DCY24^T (97.0 %). Based on its phenotypic, phylogenetic, genetic and chemotaxonomic features, strain KUDC5002^T should be considered a novel species in the genus Nocardioides, for which we have proposed the name Nocardioides sambongensis sp. nov. The type strain is KUDC5002^T (=KCTC 39855^T=DSM 106604^T).