Paenibacillus kyungheensis sp. nov., isolated from flowers of magnolia

Complete genome sequences of the Paenibacillus kyungheensis KACC 18744T, Sphingomonas naphthae KACC 18716T, and Novosphingobium humi KACC 19094T

We report the whole genome sequences of Paenibacillus kyungheensis KACC 18744T, Sphingomonas naphthae KACC 18716T, and Novosphingobium humi KACC 19094T, to investigate the genomic diversity of bacterial type strains distributed in Korea.

Paenibacillus glufosinatiresistens sp. nov., a glufosinate-resistant bacterium isolated from sludge

A Gram-stain-positive bacterium capable of resisting 5.0 mM glufosinate, designated strain YX-27T, was isolated from a sludge sample collected from a factory in Wuxi, Jiangsu, PR China. Cells were rod-shaped, facultatively anaerobic, endospore-forming, and motile by peritrichous flagella. Growth was observed at 15-42 °C (optimum at 30 °C), pH 4.0-8.0 (optimum pH 7.0-7.5) and with 0-2.5% NaCl (w/v; optimum, 0.5 %). Strain YX-27T could tolerate up to 6.0 mM glufosinate. Strain YX-27T showed the highest 16S rRNA gene sequence similarity to Paenibacillus tianjinensis TB2019T (96.17 %), followed by Paenibacillus odorifer DSM 1539T (96.15 %), Paenibacillus sophorae S27T (96.04 %), Paenibacillus apii 7124T (96.02 %) and Paenibacillus stellifer DSM 14472T (95.87 %). The phylogenetic tree based on genome and 16S rRNA gene sequences indicated that strain YX-27T was clustered in the genus Paenibacillus but formed a separate clade. The genome size of YX-27T was 5.22 Mb with a G+C content of 57.5 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between the genomes of strain YX-27T and 12 closely related type strains ranged from 70.8 to 74.8% and 19.8 to 23.0 %, respectively. The major cellular fatty acids were C16 : 0, anteiso-C15 : 0 and iso-C16 : 0. The major polar lipids were one diphosphatidylglycerol, one phosphatidylethanolamine, one phosphatidylglycerol, one phospholipid, four aminophospholipids and four unidentified lipids. The predominant respiratory quinone was MK-7. Based on phylogenetic, genomic, chemotaxonomic and phenotypic data, strain YX-27T was considered to represent a novel species for which the name Paenibacillus glufosinatiresistens sp. nov. is proposed, with YX-27T (=MCCC 1K08803T= KCTC 43611T) as the type strain.

Comparative genomic and functional analyses of Paenibacillus peoriae ZBSF16 with biocontrol potential against grapevine diseases, provide insights into its genes related to plant growth-promoting and biocontrol mechanisms

Paenibacillus peoriae is a plant growth-promoting rhizobacteria (PGPR) widely distributed in various environments. P. peoriae ZBFS16 was isolated from the wheat rhizosphere and significantly suppressed grape white rot disease caused by Coniella vitis. Here, we present the complete genome sequence of P. peoriae ZBFS16, which consists of a 5.83 Mb circular chromosome with an average G + C content of 45.62%. Phylogenetic analyses showed that ZBFS16 belongs to the genus P. peoriae and was similar to P. peoriae ZF390, P. peoriae HS311 and P. peoriae HJ-2. Comparative analysis with three closely related sequenced strains of P. peoriae identified the conservation of genes involved in indole-3-acetic acid production, phosphate solubilization, nitrogen fixation, biofilm formation, flagella and chemotaxis, quorum-sensing systems, two-component systems, antimicrobial substances and resistance inducers. Meanwhile, in vitro experiments were also performed to confirm these functions. In addition, the strong colonization ability of P. peoriae ZBFS16 was observed in soil, which provides it with great potential for use in agriculture as a PGPR. This study will be helpful for further studies of P. peoriae on the mechanisms of plant growth promotion and biocontrol.

Paenibacillus tianjinensis sp. nov., isolated from corridor air

A Gram-stain-positive, facultatively anaerobic, non-motile, endospore-forming and rod-shaped bacterium, occurring singly or in pairs, designated TB2019^T, was isolated from environmental monitoring samples of corridor air collected at the Tianjin Institute for Drug Control, Tianjin Province (PR China). The isolate was able to grow at 15-40 °C (optimum growth at 37 °C), pH 6.0-8.0 (pH 7.0) and in the presence of 0-2% (w/v) NaCl (0% NaCl). Comparison of 16S rRNA gene sequences indicated that TB2019^T was most closely related to Paenibacillus typhae CGMCC 1.11012^T (98.63%), Paenibacillus albidus Q4-3^T (98.19%), Paenibacillus borealis DSM 13188^T (97.55%), Paenibacillus helianthi P26E^T (97.33%) and Paenibacillus odorifer DSM 15391^T (97.19%). The digital DNA-DNA hybridization and the average nucleotide identity values between TB2019^T and the five type strains mentioned above ranged from 20.7 to 25.0% and 75.2 to 81.3%, respectively, and the genomic DNA G+C content was 49.52 mol%. The diagnostic cell-wall sugar was ribose, and the diagnostic amino acid was meso-diaminopimelic acid. The polar lipids of TB2019^T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified aminophospholipids and one unidentified phospholipid. MK-7 was the predominant menaquinone, and anteiso-C_15:0 (30.6%) was the major fatty acid. Based on the polyphasic taxonomic data, strain TB2019^T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus tianjinensis sp. nov. is proposed. The type strain is TB2019^T (=CICC 25065^T=JCM 34610^T).

Epiphytic PGPB Bacillus megaterium AFI1 and Paenibacillus nicotianae AFI2 Improve Wheat Growth and Antioxidant Status under Ni Stress

The present study demonstrates the Ni toxicity-ameliorating and growth-promoting abilities of two different bacterial isolates when applied to wheat (Triticum aestivum L.) as the host plant. Two bacterial strains tolerant to Ni stress were isolated from wheat seeds and selected based on their ability to improve the germination of wheat plants; they were identified as Bacillus megaterium AFI1 and Paenibacillus nicotianae AFI2. The protective effects of these epiphytic bacteria against Ni stress were studied in model experiments with two wheat cultivars: Ni stress-tolerant Leningradskaya 6 and susceptible Chinese spring. When these isolates were used as the inoculants applied to Ni-treated wheat plants, the growth parameters and the levels of photosynthetic pigments of the two wheat cultivars both under normal and Ni-stress conditions were increased, though B. megaterium AFI1 had a more pronounced ameliorative effect on the Ni contents in plant tissues due to its synthesis of siderophores. Over the 10 days of Ni exposure, the plant growth promotion bacteria (PGPB) significantly reduced the lipid peroxidation (LPO), ascorbate peroxidase (APX), superoxide dismutase (SOD) activities and proline content in the leaves of both wheat cultivars. The PGPB also increased peroxidase (POX) activity and the levels of chlorophyll a, chlorophyll b, and carotenoids in the wheat leaves. It was concluded that B. megaterium AFI1 is an ideal candidate for bioremediation and wheat growth promotion against Ni-induced oxidative stress, as it increases photosynthetic pigment contents, induces the antioxidant defense system, and lowers Ni metal uptake.

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).

Paenibacillus lycopersici sp. nov. and Paenibacillus rhizovicinus sp. nov., isolated from the rhizosphere of tomato (Solanum lycopersicum)

Two Gram-stain-positive, rod-shaped, endospore-forming bacteria, designated 12200R-189^T and 14171R-81^T were isolated from the rhizosphere of tomato plants. The 16S rRNA gene sequence similarity between strains 12200R-189^T and 14171R-81^T were 97.2%. Both strains showed the highest 16S rRNA gene sequence similarities to Paenibacillus sacheonensis SY01^T (96.3% and 98.0%, respectively). The genome of strain 12200R-189^T was approximately 6.7 Mb in size with 5,750 protein-coding genes (CDSs) and the G + C content was 58.1 mol%, whereas that of strain 14171R-81^T comprised one chromosome of 7.0 Mb and two plasmids (0.2 Mb each) with 6,595 CDSs and the G + C content was 54.5 mol%. Comparative genome analysis revealed that average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among 12200R-189^T, 14171R-81^T, and other closely related species were below the cut-off levels 95% and 70%, respectively. Strain 12200R-189^T grew at a temperature range of 15-40°C, pH 6.0-9.0, and 0-3% NaCl (w/v), whereas strain 14171R-81^T grew at a temperature range of 10-37°C, pH 6.0-8.0, and 0-1% NaCl (w/v). Menaquinone-7 (MK-7) was the only isoprenoid quinone detected in both strains. The predominant cellular fatty acids (> 10%) were iso-C_15:0, anteiso-C_15:0, and iso-C_16:0. The polar lipids of strain 12200R-189^T were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), aminophospholipid (APL), phospholipid (PL), phosphatidylglycolipid (PGL), and four aminophosphoglycolipids (APGLs) and those of strain 14171R-81^T were DPG, PG, PE, APL, three PLs, two PGLs, and three APGLs. Based on phylogenetic, genomic, phenotypic, and chemotaxonomic analyses, strains 12200R-189^T and 14171R-81^T represent two novel species of the genus Paenibacillus, for which the names Paenibacillus lycopersici sp. nov. and Paenibacillus rhizovicinus sp. nov. are proposed. The type strains are 12200R-189^T (= KACC 19916^T = CCTCC AB 2020027^T) and 14171R-81^T (= KACC 19915^T = CCTCC AB 2020026^T).

Paenibacillus nuruki sp. nov., isolated from Nuruk, a Korean fermentation starter

A Gram-stain-positive, rod-shaped, non-endospore-forming motile by means of peritrichous flagella, facultatively anaerobic bacterium designated TI45-13ar^T was isolated from Nuruk, a Korean traditional Makgeolli fermentation starter. It grew at 4-35°C (optimum, 28-30°C), pH 5.0-9.0 (optimum, pH 7.0) and NaCl concentrations up to 5% (w/v). Phylogenetic trees generated using 16S rRNA gene sequences revealed that strain TI45-13ar^T belonged to the genus Paenibacillus and showed the highest sequence similarities with Paenibacillus kyungheensis DCY88^T (98.5%), Paenibacillus hordei RH-N24^T (98.4%) and Paenibacillus nicotianae YIM h-19^T (98.1%). The major fatty acid was anteiso-C_15:0. The DNA G+C content was 39.0 mol%, and MK-7 was the predominant isoprenoid quinone. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified glycolipids, and one unidentified aminoglycolipid. The cell-wall peptidoglycan contained meso-diaminopimelic acid. On the basis of polyphasic taxonomy study, it was suggested that strain TI45-13ar^T represents a novel species within the genus Paenibacillus for which the name Paenibacillus nuruki sp. nov. is proposed. The type strain was TI45-13ar^T (= KACC 18728^T = NBRC 112013^T).

Paenibacillus konkukensis sp. nov., isolated from animal feed

A Gram-stain-positive, oxidase- and catalase-positive, aerobic, rod-shaped bacterium, designated strain SK-3146T, was isolated from animal feed. Phylogenetic analysis, based on 16S rRNA gene sequence comparisons, revealed that the strain formed a distinct lineage within the genus Paenibacillus that was closely related to Paenibacillusyunnanensis JCM 30953T (98.6 %), Paenibacillusvulneris CCUG 53270T (98.0 %) and Paenibacilluschinjuensis DSM 15045T (96.9 %). Cells were non-motile, endospore-forming and formed milky colonies on NA and R2A agar media. Growth of strain SK-3146T occurred at temperatures of 18-45 °C, at pH 6.0-9.5 and between 0.5-3.0 % NaCl (w/v). The major menaquinone was MK-7, with lesser amounts of MK-6 present. The cell wall peptidoglycan of strain SK-3146T contained meso-diaminopimelic acid. The major fatty acids were anteiso-C15 : 0 and iso-C16 : 0. The major polar lipids were diphosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 53.8 mol% and the DNA-DNA hybridization relatedness values between strain SK-3146T and P.yunnanensis JCM 30953T and P.vulneris CCUG 53270T were 26.13±0.8 % and 38.7±0.6 %, respectively. The phenotypic, phylogenetic and chemotaxonomic results indicate that strain SK-3146T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus konkukensis sp. nov. is proposed. The type strain is SK-3146T (=KACC 18876T=LMG 29568T).