Paenibacillus aceris sp. nov., isolated from the rhizosphere of Acer okamotoanum, a plant native to Ulleungdo Island, Republic of Korea

Paenibacillus hexagrammi sp. nov., a novel bacterium isolated from the gut content of Hexagrammos agrammus

A Gram-stain-positive, aerobic bacterium, designated as YPD9-1T, was isolated from the gut contents of a spotty belly greenling, Hexagrammos agrammus, collected near Dokdo island, South Korea. The rod-shaped cells were oxidase-positive, and catalase-negative. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C16 : 0, iso-C16 : 0 and iso-C17: 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and two unidentified lipids. The DNA G+C content was 47.6 mol% and the predominant respiratory quinone was menaquinone MK-7. The 16S rRNA gene sequence of YPD9-1T showed low sequence similarities to species of the genus Paenibacillus, Paenibacillus pocheonensis Gsoil 1138T (97.21 % of sequence similarity), Paenibacillus aestuarii CJ25T (97.12 %) and Paenibacillus allorhizoplanae JJ-42T (96.89 %). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that YPD9-1T formed a distinct branch among other species of the genus Paenibacillus. The digital DNA-DNA hybridisation, average nucleotide identity, and average amino acid identity values between YPD9-1T and the related species were in the ranges of 15.3-16.2 %, 74.1-78.4 %, and 71.1-71.9 %, respectively, which are below the species cutoff values. On the basis of the results of the polyphasic analysis, we conclude that strain YPD9-1T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus hexagrammi sp. nov. is proposed. The type strain of Paenibacillus hexagrammi is YPD9-1T (=KCTC 43424T =LMG 32988T).

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).

Paenibacillus hamazuiensis sp. nov., a bacterium isolated from Hamazui hot spring in Yunnan province, south-west China

A bacterial strain, Gram-positive, aerobic, rod-shaped, motile, designated YIM B00624^T which was isolated from a Hamazui hot spring in Tengchong, Yunnan province, south-west China. The strain grew well on International Streptomyces Project (ISP) 2 medium and colonies were creamy yellow, flat and circular. The results of 16S rRNA gene sequence similarity analysis showed that strain YIM B00624^T was closely related to the type strain of Paenibacillus filicis S4^T (95.9%). The main menaquinone of strain YIM B00624^T was menaquinone-7 (MK-7) and major fatty acids were anteiso-C_15:0, anteiso-C_17:0 and C_16:0. The isolate contained meso-diaminopimelic acid as the diagnostic diamino acid and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine and four unidentified glycolipids. The DNA G+C content of strain YIM B00624^T was 53.4 mol%. Based on physiological, phenotypic and chemotaxonomic data, strain YIM B00624^T belongs to a novel species of the genus Paenibacillus, for which the name Paenibacillus hamazuiensis sp. nov. is proposed. The type strain is YIM B00624^T (= CGMCC 1.19245^T = KCTC 43365^T).

Paenibacillus albicereus sp. nov. and Niallia alba sp. nov., isolated from digestive syrup

Two aerobic, Gram-stain variable, catalase-positive and oxidase-negative rods named strain UniB2^T and UniB3^T, were isolated from digestive syrup containing fungal diastase (10 mg/ml), pepsin (2 mg/ml) and sugar base containing polyethylene glycol. Based on 16S rRNA gene sequence analysis, strain UniB2^T has the highest sequence similarity with Paenibacillus humicus NBRC 102415^T (98.3%) and strain UniB3^T showed the highest sequence similarity with Niallia circulans DSM 11^T (98.9%). The DNA G + C content of UniB2^T was 63.7 mol %. The dDDH and ANI values between the strain UniB2^T and its phylogenetically close relative were < 38.3% and < 89.5%, respectively. The major fatty acids of the strain UniB2^T were C_16:0 (13.9%), C_15:0 anteiso (39.7%), C_17:0 anteiso (15.5%). The DNA G + C content of UniB3^T was 35.6 mol %. The dDDH and ANI values between the strain UniB3^T and its close relatives were < 29.1% and 84.6%, respectively. The major fatty acids of strain UniB3^T were C_16:0 (13.5%), C_15:0 anteiso (40.1%) and C_17:0 anteiso (16.0%). Major polar lipids for both strains were Diphosphatidylglycerol and phosphatidylethanolamine. Both strains showed unique carbon utilization and assimilation pattern that differentiated them from their phylogenetically related neighbours. These phenotypic, genotypic and chemotaxonomic characters indicated the strains UniB2^T and UniB3^T represent two novel species for which the names Paenibacillus albicereus sp. nov. (Type strain UniB2^T = MCC 3997^T = KCTC 43095^T = JCM34513^T) and Niallia alba sp. nov. (Type strain UniB3^T = MCC 3998^T = KCTC 43235^T = JCM 34492^T) are proposed.

Paenibacillus silvestris sp. nov., Isolated from Forest Soil

A bacterial strain, designated 5J-6^T, was isolated from soil in Cheongnyeongpo, Republic of Korea. Cells were Gram-stain-positive, strictly aerobic, and motile rods and their catalase and oxidase activities were positive. Strain 5J-6^T grew at 10-30 °C, pH 6.0-9.0, and 0-0.8% (w/v) NaCl concentration, with optimum growth at 25 °C, pH 6.5, and 0.4% NaCl concentration. Anteiso-C_15:0 and iso-C_16:0 were detected as the predominant fatty acids and menaquinone-7 was the sole isoprenoid quinone detected. Strain 5J-6^T contained phosphatidylethanolamine, phosphatidylglycerol and an unidentified phospholipid as major polar lipids. The peptidoglycan belonged to the type A1γ meso-diaminopimelic acid. The G+C content of the genomic DNA calculated from the whole genomic sequence was 46.1 mol%. Phylogenetic analysis of strain 5J-6^T based on 16S rRNA gene sequences placed the isolate into a member of the genus Paenibacillus. Sequence similarity analysis of 16S rRNA gene sequences revealed that strain 5J-6^T was most closely related to Paenibacillus aceris KUDC4121^T and Paenibacillus chondroitinus DSM 5051^T with 98.76% and 98.42% similarities, respectively. Average nucleotide identity and in silico DNA-DNA hybridization values between strain 5J-6^T and the type strain of P. aceris were 83.97% and 28.60%, respectively. Based on the phylogenetic and phenotypic characteristics and genomic data, strain 5J-6^T could be considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus silvestris sp. nov. is proposed. The type strain is 5J-6^T (= KACC 21430^T = JCM 33812^T).

Penicillium ulleungdoense sp. nov. from Ulleung Island in Korea

In a study of the fungal diversity on Ulleung Island in Korea, three novel strains of Penicillium were isolated. Different sites on Ulleung Island were selected for collecting endophytic fungi, and three endophytic fungal strains showed unique morphological characteristics. DNA sequence of the internal transcribed spacer, β-tubulin, calmodulin, and RNA polymerase II second largest subunit regions of the strains were analyzed and they showed unique taxonomic position from the other species of Penicillium section Sclerotiora. The new strains were named Penicillium ulleungdoense sp. nov. As the novel endophytic Penicillium taxa were discovered in a unique environment, the data could be meaningful for understanding the geographical distribution of Ascomycetes on Ulleung Island.

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).

Comparative genomic analysis reveals metabolic diversity of different Paenibacillus groups

The genus Paenibacillus was originally recognized based on the 16S rRNA gene phylogeny. Recently, a standardized bacterial taxonomy approach based on a genome phylogeny has substantially revised the classification of Paenibacillus, dividing it into 23 genera. However, the metabolic differences among these groups remain undescribed. Here, genomes of 41 Paenibacillus strains comprising 25 species were sequenced, and a comparative genomic analysis was performed considering these and 187 publicly available Paenibacillus genomes to understand their phylogeny and metabolic differences. Phylogenetic analysis indicated that Paenibacillus clustered into 10 subgroups. Core genome and pan-genome analyses revealed similar functional categories among the different Paenibacillus subgroups; however, each group tended to harbor specific gene families. A large proportion of genes in the subgroups A, E, and G are related to carbohydrate metabolism. Among them, genes related to the glycoside hydrolase family were most abundant. Metabolic reconstruction of the newly sequenced genomes showed that the Embden-Meyerhof-Parnas pathway, pentose phosphate pathway, and citric acid cycle are central pathways of carbohydrate metabolism in Paenibacillus. Further, the genomes of the subgroups A and G lack genes involved in glyoxylate cycle and D-galacturonate degradation, respectively. The current study revealed the metabolic diversity of Paenibacillus subgroups assigned based on a genomic phylogeny and could inform the taxonomy of Paenibacillus. KEY POINTS: • Paenibacillus clustered into 10 subgroups. • Genomic content variation and metabolic diversity in the subgroup A, E, and G were described. • Carbohydrate transport and metabolism is important for Paenibacillus survival.

Paenibacillus anseongense sp. nov. a Silver Nanoparticle Producing Bacterium Isolated from Rhizospheric Soil

A silver nanoparticle (AgNP) producing, Gram stain-positive, aerobic, motile, and rod-shaped novel bacterial strain, designated as MAH-34 ^T was isolated from rhizospheric soil of magnolia tree. The colonies were creamy white, smooth, circular, and 0.9-2.0 mm in diameter when grown on R2A agar. Strain MAH-34 ^T was found to be able to grow at 10-37 °C, at pH 6.0-9.5, and at 0-1% NaCl. The strain showed activity for both catalase, and oxidase tests, and was able to rapid synthesis of AgNPs. The TEM image revealed the spherical shape of biosynthesized AgNPs, and the size was 5 to 15 nm. Based on 16S rRNA gene sequence comparisons, the isolate was shown to be a member of genus Paenibacillus, and the close type strains were Paenibacillus chondroitinus DSM 5051 ^T (98.3%), Paenibacillus aceris KUDC4121^T (98.2%), Paenibacillus nebraskensis JJ-59 ^T (97.8%), Paenibacillus alginolyticus DSM 5050 ^T (97.6%), Paenibacillus ferrarius CY1^T (97.4%), Paenibacillus frigoriresistens YIM 016 ^T (97.3%), and Paenibacillus pocheonensis Gsoil 1138 ^T (97.3%). Strain MAH-34 ^T had a genome size of 8,647,010 bp. The genomic G + C content was 46.0 mol %. The major isoprenoid quinone was determined as menaquinone-7 (MK-7). The major cellular fatty acids were determined as C_{15:0 anteiso}, and C_{16:0 iso}. Based on the DNA-DNA hybridization results, genotypic analysis, chemotaxonomic, and physiological data, strain MAH-34 ^T represents a novel species, for which the name Paenibacillus anseongense sp. nov. is proposed, with MAH-34 ^T as the type strain (= KACC 19974 ^T = CGMCC1.16610 ^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).