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Sanfeng Chen - One of the best experts on this subject based on the ideXlab platform.
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Paenibacillus strains with nitrogen fixation and multiple beneficial properties for promoting plant growth.
PeerJ, 2019Co-Authors: Xiaomeng Liu, Guohua Guan, Sanfeng ChenAbstract:Paenibacillus is a large genus of Gram-positive, facultative anaerobic, endospore-forming bacteria. The genus Paenibacillus currently comprises more than 150 named species, approximately 20 of which have nitrogen-fixation ability. The N2-fixing Paenibacillus strains have potential uses as a bacterial fertilizer in agriculture. In this study, 179 bacterial strains were isolated by using nitrogen-free medium after heating at 85 °C for 10 min from 69 soil samples collected from different plant rhizospheres in different areas. Of the 179 bacterial strains, 25 Paenibacillus strains had nifH gene encoding Fe protein of nitrogenase and showed nitrogenase activities. Of the 25 N2-fixing Paenibacillus strains, 22 strains produced indole-3-acetic acid (IAA). 21 strains out of the 25 N2-fixing Paenibacillus strains inhibited at least one of the 6 plant pathogens Rhizoctonia cerealis, Fusarium graminearum, Gibberella zeae, Fusarium solani, Colletotrichum gossypii and Alternaria longipes. 18 strains inhibited 5 plant pathogens and Paenibacillus sp. SZ-13b could inhibit the growth of all of the 6 plant pathogens. According to the nitrogenase activities, antibacterial capacities and IAA production, we chose eight strains to inoculate wheat, cucumber and tomato. Our results showed that the 5 strains Paenibacillus sp. JS-4, Paenibacillus sp. SZ-10, Paenibacillus sp. SZ-14, Paenibacillus sp. BJ-4 and Paenibacillus sp. SZ-15 significantly promoted plant growth and enhanced the dry weight of plants. Hence, the five strains have the greater potential to be used as good candidates for biofertilizer to facilitate sustainable development of agriculture.
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Phylogeny of 16S rRNA and nifH genes and regulation of nitrogenase activity by oxygen and ammonium in the genus Paenibacillus.
Microbiology, 2012Co-Authors: Jianbo Xie, L. Q. Bai, L. Y. Wang, Sanfeng ChenAbstract:All Paenibacillus 16S rDNA sequences, except for that of Paenibacillus massiliensis T7, formed a coherent cluster, distinct from gram-positive nitrogen-fixing Clostridium pasteurianum and Heliobacterium chlorum. All Paenibacillus NifH sequences formed two main clusters. Cluster I encompassing the NifH sequences from most of members of Paenibacillus spp., such as Paenibacillus azotofixans NifH1 and NifH2, Paenibacillus polymyxa and Paenibacillus macerans. Cluster II including only P. azotofixans NifH3. Curiously, three copies of nifH genes of Paenibacillus sabine T27 clustered within P. azotofixans cluster I (NifH1 and NifH2). The effect of O2 and ammonium on nitrogenase activity was studied with 14 different nitrogenfixing Paenibacillus strains. The optimal oxygen concentration level for all Paenibacillus strains is in the 0 to 0.05% range, similar to that for Klebsiella pneumoniae. In all Paenibacillus strains, the highest nitrogenase activity is obtained in the condition of 0–0.1 mM NH4Cl and the increase of NH4Cl from 0.1 to 5 mM caused a rapid inhibition of nitrogenase activity. However, the inhibition was reversible in the presence of 200 mM NH4Cl in some Paenibacillus strains. It is the first time to use almost all of the recognized nitrogen-fixing Paenibacilus spp. to investigate the phylogeny of 16S rRNA and nifH genes. The data that the inhibition of O2 and ammonium on nitrogenase acitivity will provide a base for studying the molecular regulatory mechanism of nitrogen fixation in the genus Paenibacillus.
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Paenibacillus jilunlii sp nov a nitrogen fixing species isolated from the rhizosphere of begonia semperflorens
International Journal of Systematic and Evolutionary Microbiology, 2011Co-Authors: Haojie Jin, Yu-guang Zhou, Hongcan Liu, Sanfeng ChenAbstract:A nitrogen-fixing bacterium, designated strain Be17T, was isolated from rhizosphere soil of Begonia semperflorens planted in Beijing Botanical Garden, PR China. Phylogenetic analyses based on a segment of the nifH gene sequence and a full-length 16S rRNA gene sequence revealed that strain Be17T was a member of the genus Paenibacillus. High levels of 16S rRNA gene sequence similarity were found between strain Be17T and Paenibacillus graminis RSA19T (97.9 %), Paenibacillus sonchi LMG 24727T (97.8 %), Paenibacillus riograndensis CECT 7330T (96.2 %) and Paenibacillus borealis DSM 13188T (96.1 %), respectively. Levels of 16S rRNA gene sequence similarity between strain Be17T and the type strains of other recognized members of the genus Paenibacillus were below 96.0 %. However, the DNA–DNA hybridization values between strain Be17T and P. graminis RSA19T, P. sonchi LMG 24727T and P. riograndensis CECT 7330T were 47.9 %, 38.7 % and 37.5 %, respectively. The DNA G+C content of strain Be17T was 52.9 mol%. The major fatty acid component of strain Be17T was anteiso-branched C15 : 0 (30.92 %). The major isoprenoid quinone was MK-7. The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. On the basis of its phenotypic characteristics, 16S rRNA gene sequences, DNA G+C content, DNA–DNA relatedness, chemotaxonomic properties and nifH gene sequence, strain Be17T represents a nitrogen-fixing strain of a novel species of the genus Paenibacillus, for which the name Paenibacillus jilunlii sp. nov. is proposed. The type strain is Be17T ( = CGMCC 1.10239T = DSM 23019T).
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Paenibacillus sophorae sp nov a nitrogen fixing species isolated from the rhizosphere of sophora japonica
International Journal of Systematic and Evolutionary Microbiology, 2011Co-Authors: Jing Lv, Sanfeng ChenAbstract:A nitrogen-fixing bacterium, designated strain S27T, was isolated from rhizosphere soil of Sophora japonica. Phylogenetic analysis based on a fragment of the nifH gene and the full-length 16S rRNA gene sequence revealed that strain S27T is a member of the genus Paenibacillus. High levels of 16S rRNA gene sequence similarity were found between strain S27T and Paenibacillus durus DSM 1735T (97.3 %), Paenibacillus sabinae DSM 17841T (96.9 %), Paenibacillus forsythiae DSM 17842T (96.7 %) and Paenibacillus zanthoxyli DSM 18202T (96.6 %). However, DNA–DNA hybridization values between strain S27T and the four type strains were 37.64 %, 23.12 %, 25.6 % and 34.99 %, respectively. Levels of 16S rRNA gene sequence similarity between strain S27T and the type strains of other recognized members of the genus Paenibacillus were below 96.5 %. The DNA G+C content of strain S27T was 46.0 mol%. The major fatty acids were anteiso-C15 : 0, C16 : 0 and iso-C16 : 0. The major isoprenoid quinone was MK-7. On the basis of its phenotypic characteristics and DNA–DNA hybridization results, strain S27T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus sophorae sp. nov. is proposed. The type strain is S27T ( = CGMCC 1.10238T = DSM 23020T).
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Paenibacillus forsythiae sp nov a nitrogen fixing species isolated from rhizosphere soil of forsythia mira
International Journal of Systematic and Evolutionary Microbiology, 2008Co-Authors: Sanfeng ChenAbstract:A nitrogen-fixing bacterium, designated strain T98(T), was isolated from rhizosphere soil of Forsythia mira. Phylogenetic analysis based on a fragment of the nifH gene and the full-length 16S rRNA gene sequence revealed that strain T98(T) was a member of the genus Paenibacillus. High levels of 16S rRNA gene similarity were found between strain T98(T) and Paenibacillus durus ATCC 35681(T) (97.0 %), Paenibacillus sabinae DSM 17841(T) (98.3 %) and Paenibacillus zanthoxyli DSM 18202(T) (96.8 %). Levels of 16S rRNA gene sequence similarity between strain T98(T) and the type strains of other recognized members of the genus Paenibacillus were below 97.0 %. Levels of DNA-DNA relatedness between strain T98(T) and P. durus ATCC 35681(T), P. sabinae DSM 17841(T) and P. zanthoxyli DSM 18202(T) were 27.6, 30.0 and 32.1 %, respectively. The DNA G+C content of strain T98(T) was 50.4 mol%. The major fatty acids were anteiso-C(15 : 0), C(16 : 0) and iso-C(16 : 0). On the basis of its phenotypic characteristics and levels of DNA-DNA hybridization, strain T98(T) is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus forsythiae sp. nov. is proposed. The type strain is T98(T) (=CCBAU 10203(T) =DSM 17842(T)).
Meng Zhao - One of the best experts on this subject based on the ideXlab platform.
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Paenibacillus yunnanensis sp. nov., isolated from Pu'er tea.
International journal of systematic and evolutionary microbiology, 2015Co-Authors: Lili Niu, Tianyi Tang, Lei Song, Kegui Zhang, Yuanyuan Chen, Ziyi Hua, Meng ZhaoAbstract:A novel Gram-staining-positive, aerobic, endospore-forming, rod-shaped bacterial strain, YN2T, was isolated from ripened Pu'er tea. Phylogenetic analysis of 16S rRNA gene sequences showed that the strain represented a novel species of the genus Paenibacillus. The strains most closely related to strain YN2T were Paenibacillus vulneris JCM 18268T and Paenibacillus rigui JCM 16352T, with 16S rRNA similarities of 98.6 and 95.5 %, respectively. Chemotaxonomic data supported the affiliation of the new isolate to the genus Paenibacillus, including MK-7 as the major menaquinone, DNA G+C content of 51 mol%, cell-wall type A1γ (meso-diaminopimelic acid as the diagnostic diamino acid) and anteiso-C15 : 0 and iso-C16 : 0 as the major fatty acids. Major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine and phospholipid. Strain YN2T could be differentiated from recognized species of the genus Paenibacillus based on phenotypic characteristics, chemotaxonomic differences, phylogenetic analysis and DNA-DNA hybridization data. On the basis of evidence from this polyphasic study, Paenibacillus yunnanensis sp. nov., is proposed, with strain YN2T ( = CGMCC 1.12968T = JCM 30953T) as the type strain.
Pierre-edouard Fournier - One of the best experts on this subject based on the ideXlab platform.
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Noncontiguous finished genome sequences and descriptions of 'Paenibacillus bouchesdurhonensis,' 'Paenibacillus rubinfantis,' 'Paenibacillus senegalimassiliensis' and 'Paenibacillus tuaregi' identified by culturomics.
New Microbes and New Infections, 2017Co-Authors: T.-p.-t. Pham, S.i. Traore, Souleymane Brah, A. Diallo, Emeline Baptiste, Anthony Levasseur, M. Tidjani Alou, B. Ali Diallo, C. Sokhna, Pierre-edouard FournierAbstract:Microbial culturomics represents a completely new approach to investigate microbial diversity by using different optimized culture conditions, mass spectrometry, genome sequencing and annotation and phenotypic description that allow for an extensive characterization of new species and the study of the human microbiome. Here we present four new species within the genus Paenibacillus: 'Paenibacillus bouchesdurhonensis' strain Marseille-P3071(T), 'Paenibacillus rubinfantis' strain MT18(T), 'Paenibacillus senegalimassiliensis' strain SIT18(T) and 'Paenibacillus tuaregi' strain Marseille-P2472(T), which are all facultatively aerobic and Gram-positive bacilli.
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Noncontiguous finished genome sequences and descriptions of ‘Paenibacillus bouchesdurhonensis,’ ‘Paenibacillus rubinfantis,’ ‘Paenibacillus senegalimassiliensis’ and ‘Paenibacillus tuaregi’ identified by culturomics
New microbes and new infections, 2017Co-Authors: T.-p.-t. Pham, M. Tidjani Alou, S.i. Traore, Souleymane Brah, B. Ali Diallo, A. Diallo, Sokhna, Emeline Baptiste, Anthony Levasseur, Pierre-edouard FournierAbstract:Microbial culturomics represents a completely new approach to investigate microbial diversity by using different optimized culture conditions, mass spectrometry, genome sequencing and annotation and phenotypic description that allow for an extensive characterization of new species and the study of the human microbiome. Here we present four new species within the genus Paenibacillus: 'Paenibacillus bouchesdurhonensis' strain Marseille-P3071T, 'Paenibacillus rubinfantis' strain MT18T, 'Paenibacillus senegalimassiliensis' strain SIT18T and 'Paenibacillus tuaregi' strain Marseille-P2472T, which are all facultatively aerobic and Gram-positive bacilli.
Fernando Hayashi Sant'anna - One of the best experts on this subject based on the ideXlab platform.
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Genome-based reclassification of Paenibacillus panacisoli DSM 21345T as Paenibacillus massiliensis subsp. panacisoli subsp. nov. and description of Paenibacillus massiliensis subsp. massiliensis subsp. nov.
International journal of systematic and evolutionary microbiology, 2020Co-Authors: Fabiana Tonial, Felipe Guella, Luciane Maria Pereira Passaglia, Fernando Hayashi Sant'annaAbstract:Bacteria of the genus Paenibacillus are relevant to humans, animals and plants. The species Paenibacillus massiliensis and Paenibacillus panacisoli are Gram-stain-positive and endospore-forming bacilli isolated from a blood culture of a leukemia patient and from soil of a ginseng field, respectively. Comparative analyses of their 16S rRNA genes revealed that the two Paenibacillus species could be synonyms (99.3% sequence identity). In the present study we performed different genomic analyses in order to evaluate the phylogenetic relationship of these micro-organisms. Paenibacillus massiliensis DSM 16942T and P. panacisoli DSM 21345T presented a difference in their G+C content lower than 1 mol%, overall genome relatedness index values higher than the species circumscription thresholds (average nucleotide identity, 95.57 %; genome-wide ANI, =96.51 %; and orthologous ANI, 96.25 %), and a monophyletic grouping pattern in the phylogenies of the 16S rRNA gene and the proteome core. Considering that these strains present differential biochemical capabilities and that their computed digital DNA–DNA hybridization value is lower than the cut-off for bacterial subspecies circumscription, we suggest that each of them form different subspecies of P. massiliensis , Paenibacillus massiliensis subsp. panacisoli subsp. nov. (type strain DSM 21345T) and Paenibacillus massiliensis subsp. massiliensis subsp. nov. (type strain DSM 16942T).
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Genomic metrics analyses indicate that Paenibacillus azotofixans is not a later synonym of Paenibacillus durus.
International journal of systematic and evolutionary microbiology, 2019Co-Authors: Felipe Guella, Adriana Ambrosini, Fernando Hayashi Sant'anna, Renan Zanini Porto, Luciane Maria Pereira PassagliaAbstract:Paenibacillus durus and Paenibacillus azotofixans , both Gram-stain-positive and endospore-forming bacilli, have been considered to be a single species. However, a preliminary computation of their average nucleotide identity (ANI) values suggested that these species are not synonyms. Given this, the taxonomic attributions of these species were evaluated through genomic and phylogenomic approaches. Although the identity of 16S rRNA gene sequences of P. durus DSM 1735T and P. azotofixans ATCC 35681T are above the circumscription species threshold, genomic metrics analyses indicate otherwise. ANI, gANI and OrthoANI values computed from their genome sequences were around 92 %, below the species limits. Digital DNA–DNA hybridization and MUMi estimations also corroborated these observations. In fact, in all metrics, Paenibacillus zanthoxyli JH29T seemed to be more similar to Paenibacillus azotofixans . ATCC 35681T than P. durus DSM 1735T. Phylogenetic analyses based on concatenated core-proteome and concatenated gyrB, recA, recN and rpoB genes confirmed that P. zanthoxyli is the closest Paenibacillus species to P. azotofixans . A review of the phenotypic profiles from these three species revealed that their biochemical repertoires are very similar, although P. azotofixans ATCC 35681T can be differentiated from P. durus DSM1735T in 13 among more than 90 phenotypic traits. Considering phylogenetic and genomic analyses, Paenibacillus azotofixans should be considered as an independent species, and not as a later synonym of Paenibacillus durus .
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Reclassification of Paenibacillus riograndensis as a Genomovar of Paenibacillus sonchi: Genome-Based Metrics Improve Bacterial Taxonomic Classification
Frontiers in microbiology, 2017Co-Authors: Fernando Hayashi Sant'anna, Adriana Ambrosini, Rocheli De Souza, Gabriela De Carvalho Fernandes, Luciana Fernandes De Brito, Evelise Bach, Eduardo Balsanelli, Valter A Baura, Volker F. Wendisch, Fábio O. PedrosaAbstract:Species from the genus Paenibacillus are widely studied due to their biotechnological relevance. Dozens of novel species descriptions of this genus were published in the last couple of years, but few utilized genomic data as classification criteria. Here, we demonstrate the importance of using genome-based metrics and phylogenetic analyses to identify and classify Paenibacillus strains. For this purpose, Paenibacillus riograndensis SBR5T, Paenibacillus sonchi X19-5T, and their close relatives were compared through phenotypic, genotypic, and genomic approaches. With respect to P. sonchi X19-5T, P. riograndensis SBR5T, Paenibacillus sp. CAR114, and Paenibacillus sp. CAS34 presented ANI (average nucleotide identity) values ranging from 95.61 to 96.32%, gANI (whole-genome average nucleotide identity) values ranging from 96.78 to 97.31%, and dDDH (digital DNA-DNA hybridization) values ranging from 68.2 to 73.2%. Phylogenetic analyses of 16S rRNA, gyrB, recA, recN, and rpoB genes and concatenated proteins supported the monophyletic origin of these Paenibacillus strains. Therefore, we propose to assign Paenibacillus sp. CAR114 and Paenibacillus sp. CAS34 to P. sonchi species, and reclassify P. riograndensis SBR5T as a later heterotypic synonym of P. sonchi (type strain X19-5T), with the creation of three novel genomovars, P. sonchi genomovar Sonchi (type strain X19-5T), P. sonchi genomovar Riograndensis (type strain SBR5T), P. sonchi genomovar Oryzarum (type strain CAS34T = DSM 102041T; = BR10511T).
Shixue Zheng - One of the best experts on this subject based on the ideXlab platform.
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Paenibacillus flagellatus sp. nov., isolated from selenium mineral soil.
International journal of systematic and evolutionary microbiology, 2018Co-Authors: Xingli Dai, Rui Wang, Shixue Zheng, Kaixiang Shi, Xin Wang, Jun Fan, Gejiao WangAbstract:Strain DXL2T, a Gram-stain-negative, rod-shaped, endospore-forming, motile, aerobic bacterium, was isolated from selenium mineral soil. DXL2T had the highest 16S rRNA gene sequence similarities with those of Paenibacillus ginsengarvi Gsoil 139T (96.8 %), Paenibacillus hemerocallicola DLE-12T (95.5 %) and Paenibacillus hodogayensis SGT (95.4 %). The genome size of DXL2T was 7.24 Mb, containing 6243 predicted protein-coding genes, with a DNA G+C content of 60.2 mol%. DXL2T contained meso-diaminopimelic acid in the cell-wall peptidoglycan. The major cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and iso-C15 : 0. The major quinone was menaquinone 7. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two aminophospholipids, an unidentified aminolipid, phosphatidylmethylethanolamine, an unidentified glycolipid and an unidentified phospholipid. Compared with the other strains, DXL2T had a specific phospholipid and a specific aminolipid, it hydrolyzed Tween 40 and could not assimilate potassium gluconate. On the basis of the phenotypic, chemotaxonomic and phylogenetic results, strain DXL2T represents a novel species within the genus Paenibacillus , for which the name Paenibacillus flagellatus sp. nov. is proposed. The type strain is DXL2T (=KCTC 33976T=CCTCC AB 2018054T).
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Paenibacillus selenii sp. nov., isolated from selenium mineral soil
International Journal of Systematic and Evolutionary Microbiology, 2014Co-Authors: Wanwan Xiang, Gejiao Wang, Yuantao Wang, Rong Yao, Fujun Zhang, Rui Wang, Dan Wang, Shixue ZhengAbstract:Strain W126T, a Gram-reaction-positive, spore-forming, rod-shaped, facultatively anaerobic bacterium, motile by means of peritrichous flagella, was isolated from selenium mineral soil in Hubei province of China. 16S rRNA gene sequence analysis demonstrated that this isolate belonged to the genus Paenibacillus , with 97.9 % sequence similarity to Paenibacillus anaericanus MH21T, while compared with the other species of the genus Paenibacillus , the 16S rRNA gene sequence similarities were less than 96.0 %. DNA–DNA hybridization between strain W126T and Paenibacillus anaericanus DSM 15890T was 24 %. The major isoprenoid menaquinone was menaquinone-7. Anteiso-C15 : 0 was the major fatty acid. The DNA G+C content was 42.3 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown aminophospholipids and an unknown lipid. Strain W126T contained A1γ-meso-diaminopimelic acid in the cell-wall peptidoglycan. The phenotypic, chemotaxonomic and genotypic data indicate that strain W126T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus selenii sp. nov. is proposed. The type strain is W126T ( = KCTC 33420T = CCTCC AB 2014003T).
