Paenibacillus brassicae sp. nov., isolated from cabbage rhizosphere in Beijing, China

A novel Gram-positive, rod-shaped, motile, spore-forming, nitrogen-fixing bacterium, designated strain 112^T, was isolated from cabbage rhizosphere in Beijing, China. The strain was found to grow at 10–40 °C and pH 4–11, with an optimum of 30 °C and pH 7.0, respectively. Phylogenetic analysis based on a fragment of the full-length 16S rRNA gene sequence revealed that strain 112^T is a member of the genus Paenibacillus. High levels of 16S rRNA gene similarities were found between strain 112^T, Paenibacillus sabinae DSM 17841^T (97.82 %) and Paenibacillus forsythiae DSM 17842^T (97.22 %). However, the DNA–DNA hybridization values between strain 112^T and the type strains of these two species were 10.36 and 6.28 %, respectively. The predominant menaquinone was found to be menaquinone 7 (MK-7). The major fatty acids were determined to be anteiso-C_15:0 and C_16:0. The major polar lipids were found to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and unknown aminophospholipids. The cell wall peptidoglycan was found to contain meso-diaminopimelic acid. The DNA G+C content was determined to be 55.4 mol%. On the basis of its phenotypic characteristics, 16S rRNA gene sequence analysis and the value of DNA–DNA hybridization, strain 112^T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus brassicae sp. nov. is proposed. The type strain is 112^T (= ACCC 01125^T = DSM 24983^T).     

Paenibacillus beijingensis sp. nov., a nitrogen-fixing species isolated from wheat rhizosphere soil

A novel nitrogen-fixing bacterium, BJ-18^T, was isolated from wheat rhizosphere soil. Strain BJ-18^T was observed to be Gram-positive, facultatively anaerobic, motile and rod-shaped (0.4–0.9 μm × 2.0–2.9 μm). Phylogenetic analysis based on a partial nifH gene sequence and an assay for nitrogenase activity showed its nitrogen-fixing capacity. Phylogenetic analysis based on full 16S rRNA gene sequences suggested that strain BJ-18^T is a member of the genus Paenibacillus. High similarity of 16S rRNA gene sequence was found between BJ-18^T and Paenibacillus peoriae DSM 8320^T (99.05 %), Paenibacillus jamilae DSM 13815^T (98.86 %), Paenibacillus brasiliensis DSM 13188^T (98.55 %), Paenibacillus polymyxa DSM 36^T (98.74 %), Paenibacillus terrae DSM 15891^T (97.99 %) and Paenibacillus kribbensis JCM 11465^T (97.92 %), whereas the similarity was below 96.0 % between BJ-18^T and the other Paenibacillus species. DNA–DNA relatedness between strain BJ-18^T and P. peoriae DSM 8320^T, P. jamilae DSM 13815^T, P. brasiliensis DSM 13188^T, P. polymyxa DSM 36^T, P. kribbensis JCM 11465^T and P. terrae DSM 15891^T was determined to be 43.6 ± 2.7, 34.2 ± 5.3, 47.9 ± 6.6, 36.8 ± 3.5, 27.4 ± 4.3 and 23.6 ± 4.1 % respectively. The DNA G+C content of BJ-18^T was determined to be 45.8 mol %. The major fatty acid was identified as anteiso-C_15:0 (67.1 %). The polar lipids present in strain BJ-18^T were identified as diphosphatidylglycerol, phosphatidyl methylethanolamine, phosphatidylethanolamine and phosphatidylglycerol. The phenotypic and genotypic characteristics, and DNA–DNA relatedness data, suggest that BJ-18^T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus beijingensis sp. nov. (Type strain BJ-18^T=DSM25425^T=CGMCC 1.12045^T) is proposed.     

Paenibacillus pinihumi sp. nov., a cellulolytic bacterium isolated from the rhizosphere of Pinus densiflora

A novel cellulolytic bacterium, strain S23^T, was isolated from the rhizosphere of the pine trees in Daejeon, Republic of Korea. This isolate was Gram-positive, strictly aerobic, rod-shaped, catalase-negative, oxidase-positive, motile by means of peritrichous flagella, and tested positive for alkaline phosphatase, esterase lipase, leucine arylamidase, α-galactosidase, and β-galactosidase activities. The DNA G+C content was 49.5 mol%. The main cellular fatty acids were anteiso-C_15:0 (51.9%), iso-C_16:0 (14.7%), and iso-C_15:0 (13.2%). The major isoprenoid quinone was menaquinone 7 (MK-7). Diagnostic diamino acid in the cell-wall pepti-doglycan was meso-diaminopimelic acid. Comparative 16S rRNA gene sequence analysis showed that this strain clustered with Paenibacillus species. The 16S rRNA gene sequence similarity values between S23^T and other Paenibacillus species were between 89.9% and 95.9%, and S23^T was most closely related to Paenibacillus tarimensis SA-7-6^T. On the basis of phylogenetic and phenotypic properties of strain S23^T, the isolate is considered as a novel species belonging to the genus Paenibacillus. Therefore, the name, Paenibacillus pinihumi sp. nov., is proposed for the rhizosphere isolate; the type strain is S23^T (=KCTC 13695^T =KACC 14199^T =JCM 16419^T)     

Paenibacillus nicotianae sp. nov., isolated from a tobacco sample

A Gram-stain positive, facultative anaerobic endospore-forming bacterium, designated strain YIM h-19^T, was isolated from a tobacco sample. Cells were observed to be motile rods by means of peritrichous flagella and colonies were observed to be convex, yellow, circular and showed catalase-positive and oxidase-negative reactions. Strain YIM h-19^T was able to grow at 4–45 °C, pH 6.0–8.0 and 0–3 % NaCl (w/v). The predominant respiratory quinone was identified as MK-7. Major fatty acids were identified as anteiso-C_15:0, anteiso-C_17:0 and C_16:0. The polar lipids were found to be phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and two unidentified polar lipids. The genomic DNA G+C content was determined to be 54 mol%. 16S rRNA gene sequence analysis showed the strain YIM h-19^T was most closely related to Paenibacillus hordei RH-N24^T and Paenibacillus hunanensis FeL05^T with similarities of 98.30 and 94.64 % respectively. However, DNA–DNA hybridization data indicated that the isolate represented a novel genomic species with the genus Paenibacillus. All data from genotypic and phenotypic analyses support the conclusion that strain YIM h-19^T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus nicotianae sp. nov. is proposed. The type strain is YIM h-19^T (=CGMCC1.12819^T = NRRL B-59112^T).     

Paenibacillus swuensis sp. nov., a bacterium isolated from soil

Strain DY6^T, a Gram-positive endospore-forming motile rod-shaped bacterium, was isolated from soil in South Korea and characterized to determine its taxonomic position. Phylogenetic analyses based on the 16S rRNA gene sequence of strain DY6^T revealed that strain DY6^T belongs to the genus Paenibacillus in the family Paenibacillaceae in the class Bacilli. The highest degree of sequence similarities of strain DY6^T were found with Paenibacillus gansuensis B518^T (97.9%), P. chitinolyticus IFO 15660^T (95.3%), P. chinjuensis WN9T (94.7%), and P. rigui WPCB173^T (94.7%). Chemotaxonomic data revealed that the predominant fatty acids were anteiso-C_15:0 (38.7%) and C_16:0 (18.0%). A complex polar lipid profile consisted of major amounts of diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. The predominant respiratory quinone was MK-7. Based on these phylogenetic, chemotaxonomic, and phenotypic data, strain DY6^T (=KCTC 33026^T =JCM 18491^T) should be classified as a type strain of a novel species, for which the name Paenibacillus swuensis sp. nov. is proposed.     

Paenibacillus hordei sp. nov., isolated from naked barley in Korea

A Gram-staining positive, facultative aerobic bacterium, designated strain RH-N24^T, was isolated from naked barley in South Korea. Cells of the isolate were observed to be motile rods by means of peritrichous flagella and showed catalase-positive and oxidase-negative reactions. Growth of strain RH-N24^T was observed at 4–40 °C (optimum: 35–37 °C) and at pH 5.0–9.0 (optimum: pH 6.0–7.0). Chemotaxonomic data (major isoprenoid quinone: MK-7; DNA G + C content: 53.5 mol %; cell wall type: A1γ-meso-diaminopimelic acid; major fatty acids: anteiso-CB_15:0 and CB_16:0B) supported the affiliation of the isolate to the genus Paenibacillus. The major cellular polar lipids were identified as phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and two unidentified polar lipids. Phylogenetic analysis based on 16S rRNA gene sequences also supported the conclusion that strain RH-N24^T belonged to the genus Paenibacillus. Comparative 16S rRNA gene sequence analysis showed that strain RH-N24^T was most closely related to Paenibacillus hunanensis FeL05^T and Paenibacillus illinoisensis NRRL NRS-1356^T with similarities of 94.64 and 94.54 %, respectively. On the basis of phenotypic and molecular properties, strain RH-N24^T represents a novel species within the genus Paenibacillus for which the name Paenibacillus hordei sp. nov. is proposed. The type strain is RH-N24^T (=KACC 15511^T = JCM 17570^T).     

生境对啮齿动物介导下锐齿槲栎种子命运的影响

干扰作为森林演替的驱动力,在改变森林结构和地表植被的同时也对林内动物介导下的种子扩散过程产生影响.本研究采用塑料标签标记法,选取秦岭林区不同人为干扰后形成的3种类型生境(未抚育林分、抚育3年后林分、裸地),研究啮齿动物扩散行为对不同生境类型锐齿槲栎种子命运的响应.结果表明:抚育3年后林分的种子扩散速率最大,裸地扩散速率最小.裸地的种子原地取食率显著低于未抚育(25.0%)和抚育3年后林分(36.3%),而抚育3年后林分的种子搬运后取食率显著高于未抚育林分(17.3%)和裸地(5.0%),且抚育3年后的林分中被啮齿动物分散埋藏的种子比例最高(4.3%).种子扩散距离以抚育3年后林分最大(26 m),且扩散距离显著大于裸地和未抚育林分.锐齿槲栎种子的初次扩散过程在不同生境中表现不同,其种子后期成苗率也存在差异.不同类型生境在一定程度上影响啮齿动物的觅食策略,最终导致不同的种子扩散模式和森林天然更新格局的形成.     

Paenibacillus marinisediminis sp. nov., a bacterium isolated from marine sediment

A Gram-negative, nonmotile, endospore-forming, rod-shaped bacterial strain LHW35^T, which belonged to the genus Paenibacillus, was isolated from marine sediment collected from the south coast of the Republic of Korea. A phylogenetic analysis of 16S rRNA gene sequences indicated that strain LHW35^T was most closely related to Paenibacillus taiwanensis G-soil-2-3^T (97.2% similarity). The optimal growth conditions for strain LHW35^T were 37°C, pH 6.0, and 0% (w/v) NaCl. The main isoprenoid quinone was menaquinone-7 (MK-7) and the major polyamine was spermidine. The diamino acid present in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major fatty acids were anteiso-C_15:0 and C_16:0. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, unidentified amino-hospholipids, unidentified phospholipids, and unidentified polar lipids. A DNA-DNA hybridization experiment using the type strain of P. taiwanensis indicated <40% relatedness. The DNA G+C content was 45.0 mol%. Based on these phylogenetic, genomic, and phenotypic analyses, strain LHW35^T should be classified as a novel species within the genus Paenibacillus, for which the name Paenibacillus marinisediminis sp. nov. is proposed. The type strain is LHW35^T (=KACC 16317^T =JCM 17886^T).     

Lysobacter telluris sp. nov., isolated from Korean rhizosphere soil

Archives of Microbiology - A Gram-stain-negative, aerobic, non-motile, non-spore-forming light-yellow-coloured rod-shaped bacterial strain, designated YJ15T, was isolated from soil at Bigeum island...     

Chryseobacterium zeae sp. nov., Chryseobacterium arachidis sp. nov., and Chryseobacterium geocarposphaerae sp. nov. isolated from the rhizosphere environment

Four yellow pigmented strains (91A-561^T, 91A-576, 91A-593^T, and JM-1085^T) isolated from plant materials, showed 97.2–98.7 % 16S rRNA gene sequence similarities among each other and were studied in a polyphasic approach for their taxonomic allocation. Cells of all four isolates were rod-shaped and stained Gram-negative. Comparative 16S rRNA gene sequence analysis showed that the four bacteria had highest sequence similarities to Chryseobacterium formosense (97.2–98.7 %), Chryseobacterium gwangjuense (97.1–97.8 %), and Chryseobacterium defluvii (94.6–98.0 %). Sequence similarities to all other Chryseobacterium species were below 97.5 %. Fatty acid analysis of the four strains showed Chryseobacterium typical profiles consisting of major fatty acids C_15:0 iso, C_15:0 iso 2-OH/C_16:1 ω7c, C_17:1 iso ω9c, and C_17:0 iso 3-OH, but showed also slight differences. DNA–DNA hybridizations with type strains of C. gwangjuense, C. formosense, and C. defluvii resulted in values below 70 %. Isolates 91A-561^T and 91A-576 showed DNA–DNA hybridization values >80 % indicating that they belonged to the same species; but nucleic acid fingerprinting showed that the two isolates represent two different strains. DNA–DNA hybridization results and the differentiating biochemical and chemotaxonomic properties showed, that both strains 91A-561^T and 91A-576 represent a novel species, for which the name Chryseobacterium geocarposphaerae sp. nov. (type strain 91A-561^T=LMG 27811^T=CCM 8488^T) is proposed. Strains 91A-593^T and JM-1085^T represent two additional new species for which we propose the names Chyrseobacterium zeae sp. nov. (type strain JM-1085^T=LMG 27809^T, =CCM 8491^T) and Chryseobacterium arachidis sp. nov. (type strain 91A-593^T=LMG 27813^T, =CCM 8489^T), respectively.     

Paenibacillus sinensis sp. nov., a nitrogen-fixing species isolated from plant rhizospheres

Two strains HN-1^T and 39 were isolated from rhizospheres of different plants grown in different regions of PR China. The two strains exhibited high nitrogenase activities and possessed almost identical 16S rRNA gene sequences. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the two strains were 99.9 and 99.8%, respectively, suggesting that they belong to one species. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strains HN-1^T and 39 are the members of the genus Paenibacillus and both strains exhibited 99.5% similarity to Paenibacillus stellifer DSM 14472^T and the both strains represented a separate lineage from all other Paenibacillus species. However, the ANI of type strain HN-1^T with P. stellifer DSM 14472^T was 90.69, which was below the recommended threshold value (<?95–96% ANI). The dDDH showed 42.1% relatedness between strain HN-1^T and P. stellifer DSM 14472^T, which was lower than the recommended threshold value (dDDH?<?70%). The strain HN-1^T contain anteiso-C_15:0 as major fatty acids and MK-7 as predominant isoprenoid quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four aminophospholipids and an unidentified glycolipid. Unlike the most closely related P. stellifer DSM 14472^T, strain HN-1^T or 39 was positive for catalase reaction. Distinct phenotypic and genomic characterisations from previously described taxa support the classification of strains HN-1^T or 39 as representatives of a novel species of the genus Paenibacillus, for which the name Paenibacillus sinensis is proposed, with type strains HN-1^T (=CGMCC 1.18902, JCM 34,620), and reference strain 39 (=CGMCC 1.18879, JCM 34,616), respectively.

     

Paenibacillus taohuashanense sp. nov., a nitrogen-fixing species isolated from rhizosphere soil of the root of Caragana kansuensis Pojark

A nitrogen-fixing bacterium, designated strain gs65^T, was isolated from a rhizosphere soil sample of Caragana kansuensis Pojark. Phylogenetic analysis based on a fragment of the nifH gene and the full-length 16S rRNA gene sequence revealed that strain gs65^T is a member of the genus Paenibacillus. High levels of 16S rRNA gene similarity were found between strain gs65^T and Paenibacillus borealis DSM 13188^T (97.5 %), Paenibacillus odorifer ATCC BAA-93^T (97.3 %), Paenibacillus durus DSM 1735^T (97.0 %) and Paenibacillus sophorae DSM23020^T (96.9 %). Levels of 16S rRNA gene sequence similarity between strain gs65^T and the type strains of other recognized members of the genus Paenibacillus were below 97.0 %. Levels of DNA–DNA relatedness between strain gs65^T and P. borealis DSM 13188^T, P. odorifer ATCC BAA-93^T (97.3 %), P. durus DSM 1735^T and P. sophorae DSM23020^T were 35.9, 38.0, 34.2 and 35.5 % respectively. The DNA G+C content of strain gs65^T was determined to be 51.6 mol%. The major fatty acids were found to be iso-C_14:0, anteiso-C_15:0 and iso-C_16:0. On the basis of its phenotypic characteristics and levels of DNA–DNA hybridization, strain gs65^T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus taohuashanense sp. nov. is proposed. The type strain is gs65^T (=CGMCC 1.12175^T = DSM 25809^T).     

河南宝天曼锐齿栎林群落学特征

锐齿栎群落是我国暖温带地区主要植物群落类型之一,广泛分布于各山区的阳坡,同时它也是我国暖温带地区重要的用材资源之一。我国暖温带地区人口密集,开发较早而且强度较高,研究认识该区锐齿栎群落特征和物种多样性,对有计划地发展、保护和合理开发利用其资源以及区域林业可持续发展具有重要意义。陈灵芝等[1]对北京山区的栎林进行了研究,河南宝天曼保护区锐齿栎群落的研究尚未见报道,我们于1994年～1995年对该区锐齿栎群落进行了初步研究。1　研究地区概况宝天曼自然保护区位于河南省西南部内乡县境内,伏牛山南麓,地理坐标为北纬33°25′～3…     

Paenibacillus cucumis sp. nov. isolated from greenhouse soil

Strain CO 4–7^T was isolated from greenhouse soil used for cultivation of cucumbers in Korea. The 16S rRNA gene sequence of strain CO 4–7^T showed the highest sequence similarity with Paenibacillus contaminans CKOBP-6^T (94.2%) among the type strains. Strain CO 4–7^T was a strictly aerobic, Gram-staining-positive, endospore-forming, and motile rodshaped bacterium. Strain CO 4–7^T grew at 10–45°C (optimum, 30°C), at pH 6.0–7.5 (optimum, pH 6.5) and in the presence of 0–5% NaCl (optimum, 0.5%). The DNA G+C content of strain CO 4–7^T was 48.5 mol%. It contained MK-7 as the major isoprenoid quinone and anteiso-C15:0 (51.8%), C16:0 (12.7%), and iso-C16:0 (8.6%) as the major fatty acids. The cell wall contained meso-diaminopimelic acid. Based on evidence from our polyphasic taxonomic study, it was concluded that strain CO 4-7T should be classified as a novel species of the genus Paenibacillus, for which, the name Paenibacillus cucumis sp. nov. is proposed. The type strain is CO 4–7^T (=KACC 17444^T=JCM 19515^T).