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Genome-Wide Transcriptome Analysis of Rice Seedlings after Seed Dressing with Paenibacillus yonginensis DCY84 T and Silicon. Int J Mol Sci 2019; 20:ijms20235883. [PMID: 31771205 PMCID: PMC6928808 DOI: 10.3390/ijms20235883] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/19/2019] [Accepted: 11/19/2019] [Indexed: 02/07/2023] Open
Abstract
Plant-growth-promoting bacteria (PGPB) are beneficial microorganisms that can also protect against disease and environmental stress. Silicon (Si) is the second most abundant element in soil, and is known to increase plant growth, grain yield, resistance to biotic stress, and tolerance to abiotic stress. Combined treatment of PGPB and Si has been shown to further enhance plant growth and crop yield. To determine the global effects of the PGPB and Si on rice growth, we compared rice plants treated with Paenibacillus yonginensis DCY84T (DCY84T) and Si with untreated rice. To identify the genes that respond to DCY84T+Si treatment in rice, we performed an RNA-Seq transcriptome analysis by sampling treated and untreated roots on a weekly basis for three weeks. Overall, 576 genes were upregulated, and 394 genes were downregulated in treated roots, using threshold fold-changes of at least 2 (log2) and p-values < 0.05. Gene ontology analysis showed that phenylpropanoids and the L-phenylalanine metabolic process were prominent in the upregulated genes. In a metabolic overview analysis using the MapMan toolkit, pathways involving phenylpropanoids and ethylene were strongly associated with upregulated genes. The functions of seven upregulated genes were identified as being associated with drought stress through a literature search, and a stress experiment confirmed that plants treated with DCY84T+Si exhibited greater drought tolerance than the untreated control plants. Furthermore, the predicted protein–protein interaction network analysis associated with DCY84T+ Si suggests mechanisms underlying growth promotion and stress tolerance.
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Ripa FA, Tong S, Cao WD, Wang ET, Wang T, Liu HC, Gao JL, Sun JG. Paenibacillus rhizophilus sp. nov., a nitrogen-fixing bacterium isolated from the rhizosphere of wheat ( Triticum aestivum L.). Int J Syst Evol Microbiol 2019; 69:3689-3695. [PMID: 31647399 DOI: 10.1099/ijsem.0.003472] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-variable, endospore-forming, motile, rod-shaped, facultative aerobic bacterium, designated 7197T, was isolated from rhizosphere soil of wheat (Triticum aestivum L.) collected from Yakeshi County, Inner Mongolia, PR China. This isolate was found to have the highest 16S rRNA gene sequence similarity to Paenibacillussabinae T27T (98.0 %), followed by Paenibacillussophorae S27T (97.9 %) and Paenibacillusforsythiae T98T (97.7 %). To ascertain the genomic relatedness of this strain to its phylogenetic neighbours, its genome sequence was determined. The average nucleotide identity values of genome sequences between the novel isolate and the type strains of related species P. sabinae T27T, P. sophorae S27T and P. forsythiae T98T were 87.9 %, 85.8 and 83.9 %, respectively. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unidentified aminophospholipids and one unidentified aminolipid. The major cellular fatty acids were anteiso-C15 : 0 (56.3 %), C16 : 0 (15.7 %) and iso-C15 : 0 (14.1 %).The genome size of strain 7197T was 5.21 Mb, comprising 4879 predicted genes with a DNA G+C content of 51.9 mol%. Menaquinone-7 was reported as the major respiratory quinone. The diamino acid in the cell-wall peptidoglycan was found to be meso-diaminopimelic acid. Based on phylogenetic, genomic, chemotaxonomic and phenotypic characteristics, strain 7197T was classified as a novel species within the genus Paenibacillus, for which the name Paenibacillus rhizophilus sp. nov. is proposed. The type strain of Paenibacillus rhizophilus is 7197T (=DSM 103168T=CGMCC 1.15699T).
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Affiliation(s)
- Farhana Alam Ripa
- Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs/ Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Shuai Tong
- Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs/ Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Wei-Dong Cao
- Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs/ Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D. F. 11340, México
| | - Tianyu Wang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry/Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing 100097, PR China.,Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs/ Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Hong Can Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Jun-Lian Gao
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry/Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing 100097, PR China
| | - Jian-Guang Sun
- Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs/ Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
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Shin SK, Kim E, Yi H. Paenibacillus crassostreae sp. nov., isolated from the Pacific oyster Crassostrea gigas. Int J Syst Evol Microbiol 2017; 68:58-63. [PMID: 29068277 DOI: 10.1099/ijsem.0.002444] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, endospore-forming, rod-shaped, aerobic bacterium, designated LPB0068T, was isolated from a Pacific oyster (Crassostrea gigas) in Korea. This isolate was found to share the highest 16S rRNA gene sequence similarity with Paenibacillus macquariensis subsp. macquariensis DSM 2T (98.1 %) and Paenibacillus macquariensis subsp. defensor JCM 14954T (98.0 %). To establish the genomic relatedness of this isolate to its phylogenetic neighbours, its genome sequence and those of Paenibacillus antarcticus CECT 5836T, P. macquariensis subsp. macquariensis DSM 2T, P. macquariensis subsp. defensor JCM 14954T, and Paenibacillus glacialis DSM 22343T were determined. The low average nucleotide identity and digital DNA-DNA hybridization values exhibited by LPB0068T in relation to the other strains in this analysis revealed that it is distinct from other Paenibacillus species. The genome of strain LPB0068T consists of one chromosome and three circular plasmids, and had a DNA G+C content of 40.0 mol%. The major respiratory quinone was menaquinone-7 and the diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid, one unidentified glycolipid, and two unidentified polar lipids. The major cellular fatty acids were anteiso-C15 : 0, C14 : 0, and C16 : 0. Based on genomic, phylogenetic, and phenotypic characteristics, this strain was clearly distinguished from other Paenibacillus species with validly published names and should therefore be classified as a novel species of the genus. The name Paenibacillus crassostreae sp. nov. is proposed, the type strain of which is LPB0068T (=KACC 18694T=JCM 31183T).
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Affiliation(s)
- Su-Kyoung Shin
- Department of Public Health Sciences, BK21PLUS Program in Embodiment: Health-Society Interaction, Graduate School, Korea University, Seoul, Republic of Korea
| | - Eunji Kim
- Department of Public Health Sciences, BK21PLUS Program in Embodiment: Health-Society Interaction, Graduate School, Korea University, Seoul, Republic of Korea
| | - Hana Yi
- Department of Public Health Sciences, BK21PLUS Program in Embodiment: Health-Society Interaction, Graduate School, Korea University, Seoul, Republic of Korea.,School of Biosystem and Biomedical Science, Korea University, Seoul, Republic of Korea
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Im WT, Yi KJ, Lee SS, Moon HI, Jeon CO, Kim DW, Kim SK. Paenibacillus konkukensis sp. nov., isolated from animal feed. Int J Syst Evol Microbiol 2017; 67:2343-2348. [PMID: 28699880 DOI: 10.1099/ijsem.0.001955] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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).
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Affiliation(s)
- Wan-Taek Im
- Department of Biotechnology, Hankyoung National University, 327 Chungang-no Anseong-si, Kyonggi-do 17579, Republic of Korea
| | - Kwon-Jung Yi
- Department of Animal Science and Technology, Konkuk University, Seoul 05029, Republic of Korea
| | - Sang-Suk Lee
- Department of Animal Science and Technology, Sunchon National University, Jeonnam 57922, Republic of Korea
| | - Hyung In Moon
- Department of Medicinal Biotechnology, Dong-A University, Busan 49315, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Dong-Woon Kim
- National Institute of Animal Science, RDA, Wanju 55365, Republic of Korea
| | - Soo-Ki Kim
- Department of Animal Science and Technology, Konkuk University, Seoul 05029, Republic of Korea
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Lai WA, Hameed A, Lin SY, Hung MH, Hsu YH, Liu YC, Shahina M, Shen FT, Young CC. Paenibacillus medicaginis sp. nov. a chitinolytic endophyte isolated from a root nodule of alfalfa (Medicago sativa L.). Int J Syst Evol Microbiol 2015; 65:3853-3860. [PMID: 28875919 DOI: 10.1099/ijsem.0.000505] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-variable, short-rod-shaped, endospore-forming, strictly aerobic, non-motile, chitinolytic and endophytic bacterium, designated strain CC-Alfalfa-19T, exhibiting unusual bipolar appendages was isolated from a root nodule of alfalfa (Medicago sativa L.) in Taiwan and subjected to a polyphasic taxonomic study. Based on 16S rRNA gene sequence analysis, strain CC-Alfalfa-19T was found to be most closely related to Paenibacillus puldeungensis CAU 9324T (95.2 %), whereas other species of the genus Paenibacillus shared ≤ 95.0 % sequence similarity. The phylogenetic analysis revealed a distinct phyletic lineage established by strain CC-Alfalfa-19T with respect to other species of the genus Paenibacillus. Fatty acids comprised predominantly anteiso-C15 : 0, C16 : 0, anteiso-C17 : 0 and iso-C16 : 0. Menaquinone 7 (MK-7) was identified as the sole respiratory quinone and the genomic DNA G+C content was 42.7 mol%. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, an unidentified glycolipid and an unidentified lipid. The diagnostic diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. Based on the polyphasic taxonomic evidence that was in line with the genus Paenibacillus and additional distinguishing characteristics, strain CC-Alfalfa-19T is considered to represent a novel species, for which the name Paenibacillus medicaginis sp. nov. (type strain CC-Alfalfa-19T = BCRC 80441T = JCM 18446T) is proposed.
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Affiliation(s)
- Wei-An Lai
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung City 402, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City 402, Taiwan, ROC
| | - Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City 402, Taiwan, ROC
| | - Mei-Hua Hung
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City 402, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City 402, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City 402, Taiwan, ROC
| | - Mariyan Shahina
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City 402, Taiwan, ROC
| | - Fo-Ting Shen
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung City 402, Taiwan, ROC
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City 402, Taiwan, ROC
| | - Chiu-Chung Young
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung City 402, Taiwan, ROC
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City 402, Taiwan, ROC
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Paenibacillus yonginensis sp. nov., a potential plant growth promoting bacterium isolated from humus soil of Yongin forest. Antonie van Leeuwenhoek 2014; 106:935-45. [PMID: 25169799 DOI: 10.1007/s10482-014-0263-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 08/14/2014] [Indexed: 10/24/2022]
Abstract
Strain DCY84(T), a Gram-stain positive, rod-shaped, aerobic, spore-forming bacterium, motile by means of peritrichous flagella, was isolated from humus soil from Yongin forest in Gyeonggi province, South Korea. Strain DCY84(T) shared the highest sequence similarity with Paenibacillus barengoltzii KACC 15270(T) (96.86 %), followed by Paenibacillus timonensis KACC 11491(T) (96.49 %) and Paenibacillus phoenicis NBRC 106274(T) (95.77 %). Strain DCY84(T) was found to able to grow best in TSA at temperature 30 °C, at pH 8 and at 0.5 % NaCl. MK-7 menaquinone was identified as the isoprenoid quinone. The major polar lipids were identified as phosphatidylethanolamine, an unidentified aminophospholipid, two unidentified aminolipids and an unidentified polar lipid. The peptidoglycan was found to contain the amino acids meso-diaminopimelic acid, alanine and D-glutamic acid. The major fatty acids of strain DCY84(T) were identified as branched chain anteiso-C15:0, saturated C16:0 and branched chain anteiso-C17:0. The cell wall sugars of strain DCY84(T) were found to comprise of ribose, galactose and xylose. The major polyamine was identified as spermidine. The DNA G+C content was determined to be 62.6 mol%. After 6 days of incubation, strain DCY84(T) produced 52.96 ± 1.85 and 72.83 ± 2.86 µg/ml L-indole-3-acetic acid, using media without L-tryptophan and supplemented with L-tryptophan, respectively. Strain DCY84(T) was also found to be able to solubilize phosphate and produce siderophores. On the basis of the phenotypic characteristics, genotypic analysis and chemotaxonomic characteristics, strain DCY84(T) is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus yonginensis sp. nov. is proposed. The type strain is DCY84(T) (=KCTC 33428(T) = JCM 19885(T)).
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Moon J, Kim J. Isolation of Paenibacillus pinesoli sp. nov. from forest soil in Gyeonggi-Do, Korea. J Microbiol 2014; 52:273-7. [PMID: 24682991 DOI: 10.1007/s12275-014-3622-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 02/21/2014] [Accepted: 02/24/2014] [Indexed: 10/25/2022]
Abstract
Using a new culture method for unculturable soil bacteria, strain NB5(T) was isolated from forest soil at Kyonggi University, and characterized taxonomically on the basis of 16S rRNA gene sequence as well as phenotypic and chemotaxonomic characteristics. The novel strain was a Gram- and catalase-positive, rod-shaped bacterium, which grew in the pH range 6.0-9.5 (optimum, 6.5-9.5) and at temperatures between 15°C and 45°C (optimum, 25-40°C). Growth was possible at 0-5% NaCl (optimum, 0% to 3%) in nutrient, Luria-Bertani, and trypticase soy broths (TSB), as well as R2A medium (with optimal growth in TSB). A phylogenetic analysis of the 16S rRNA gene sequence showed that the novel strain was affiliated with the genus Paenibacillus and had 96.8% and 96.5% similarity to P. nanensis MX2-3(T) and P. agaridevorans DSM 1355(T), respectively. The predominant menaquinone in NB5(T) was MK-7; the major fatty acids were anteiso-C15:0 and iso-C16:0; and the DNA G+C content was 54.5 mol%. We propose this strain as a novel species of the genus Paenibacillus, and suggest the name Paenibacillus pinesoli sp. nov. (type strain, KACC 17472(T)=KEMB 9005-025(T)=JCM 19203(T)).
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Affiliation(s)
- Jeongsuk Moon
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, 443-760, Republic of Korea
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Song HY, Lim HK, Kim DR, Lee KI, Hwang IT. A new bi-modular endo-β-1,4-xylanase KRICT PX-3 from whole genome sequence of Paenibacillus terrae HPL-003. Enzyme Microb Technol 2014; 54:1-7. [DOI: 10.1016/j.enzmictec.2013.09.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 09/04/2013] [Accepted: 09/05/2013] [Indexed: 10/26/2022]
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Paenibacillus xylaniclasticus sp. nov., a xylanolytic-cellulolytic bacterium isolated from sludge in an anaerobic digester. J Microbiol 2012; 50:394-400. [PMID: 22752902 DOI: 10.1007/s12275-012-1480-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 03/11/2012] [Indexed: 10/28/2022]
Abstract
A mesophilic, facultative, anaerobic, xylanolytic-cellulolytic bacterium, TW1(T), was isolated from sludge in an anaerobic digester fed with pineapple waste. Cells stained Gram-positive, were spore-forming, and had the morphology of straight to slightly curved rods. Growth was observed in the temperature range of 30 to 50°C (optimum 37°C) and the pH range of 6.0 to 7.5 (optimum pH 7.0) under aerobic and anaerobic conditions. The strain contained meso-diaminopimelic acid in the cell-wall peptidoglycan. The predominant isoprenoid quinone was menaquinone with seven isoprene units (MK-7). Anteiso-C(15:0), iso-C(16:0), anteiso-C(17:0), and C(16:0) were the predominant cellular fatty acids. The G+C content of the DNA was 49.5 mol%. A phylogenetic analysis based on 16S rRNA showed that strain TW1(T) belonged within the genus Paenibacillus and was closely related to Paenibacillus cellulosilyticus LMG 22232(T), P. curdlanolyticus KCTC 3759(T), and P. kobensis KCTC 3761(T) with 97.7, 97.5, and 97.3% sequence similarity, respectively. The DNA-DNA hybridization values between the isolate and type strains of P. cellulosilyticus LMG 22232(T), P. curdlanolyticus KCTC 3759(T), and P. kobensis KCTC 3761(T) were found to be 18.6, 18.3, and 18.0%, respectively. The protein and xylanase patterns of strain TW1(T) were quite different from those of the type strains of closely related Paenibacillus species. On the basis of DNA-DNA relatedness and phenotypic analyses, phylogenetic data and the enzymatic pattern presented in this study, strain TW1(T) should be classified as a novel species of the genus Paenibacillus, for which the name Paenibacillus xylaniclasticus sp. nov. is proposed. The type strain is TW1(T) (=NBRC 106381(T) =KCTC 13719(T) =TISTR 1914(T)).
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Glaeser SP, Falsen E, Busse HJ, Kämpfer P. Paenibacillus vulneris sp. nov., isolated from a necrotic wound. Int J Syst Evol Microbiol 2012; 63:777-782. [PMID: 22581904 DOI: 10.1099/ijs.0.041210-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive-staining, aerobic, endospore-forming bacterium, isolated from a necrotic wound of a 35-year-old man was studied in detail to determine its taxonomic position. Based on 16S rRNA gene sequence similarity comparisons, strain CCUG 53270(T) was grouped into the genus Paenibacillus, most closely related to the type strains of Paenibacillus rigui (97.2 %), Paenibacillus xylanisolvens (96.3 %) and Paenibacillus chinjuensis (96.1 %). The 16S rRNA gene sequence similarity to strains of other Paenibacillus species was ≤96 %. Chemotaxonomic characterization supported the allocation of the strain to the genus Paenibacillus. The major menaquinones were MK-7 (85 %) and MK-6 (15 %). The polar lipid profile contained the major compounds diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine and phosphatidylglycerol. The polyamine pattern contained predominantly spermidine. The major fatty acids were iso- and anteiso-branched fatty acids. The results of physiological and biochemical tests allowed phenotypic differentiation of strain CCUG 53270(T) from closely related species. Thus, strain CCUG 53270(T) represents a novel species of the genus Paenibacillus, for which the name Paenibacillus vulneris sp. nov. is proposed, with CCUG 53270(T) ( = JCM 18268(T)) as the type strain.
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Affiliation(s)
- Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Enevold Falsen
- Culture Collection University Göteborg, Dept. of Clinical Bacteriology, S-41346 Göteborg, Sweden
| | - Hans-Jürgen Busse
- Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität, A-1210 Wien, Austria
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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Paenibacillus frigoriresistens sp. nov., a novel psychrotroph isolated from a peat bog in Heilongjiang, Northern China. Antonie van Leeuwenhoek 2012; 102:297-305. [DOI: 10.1007/s10482-012-9738-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 04/12/2012] [Indexed: 10/28/2022]
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Identification and characterization of psychrotolerant sporeformers associated with fluid milk production and processing. Appl Environ Microbiol 2012; 78:1853-64. [PMID: 22247129 DOI: 10.1128/aem.06536-11] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Psychrotolerant spore-forming bacteria represent a major challenge to the goal of extending the shelf life of pasteurized dairy products. The objective of this study was to identify prominent phylogenetic groups of dairy-associated aerobic sporeformers and to characterize representative isolates for phenotypes relevant to growth in milk. Analysis of sequence data for a 632-nucleotide fragment of rpoB showed that 1,288 dairy-associated isolates (obtained from raw and pasteurized milk and from dairy farm environments) clustered into two major divisions representing (i) the genus Paenibacillus (737 isolates, including the species Paenibacillus odorifer, Paenibacillus graminis, and Paenibacillus amylolyticus sensu lato) and (ii) Bacillus (n = 467) (e.g., Bacillus licheniformis sensu lato, Bacillus pumilus, Bacillus weihenstephanensis) and genera formerly classified as Bacillus (n = 84) (e.g., Viridibacillus spp.). When isolates representing the most common rpoB allelic types (ATs) were tested for growth in skim milk broth at 6°C, 6/9 Paenibacillus isolates, but only 2/8 isolates representing Bacillus subtypes, grew >5 log CFU/ml over 21 days. In addition, 38/40 Paenibacillus isolates but only 3/47 Bacillus isolates tested were positive for β-galactosidase activity (including some isolates representing Bacillus licheniformis sensu lato, a common dairy-associated clade). Our study confirms that Paenibacillus spp. are the predominant psychrotolerant sporeformers in fluid milk and provides 16S rRNA gene and rpoB subtype data and phenotypic characteristics facilitating the identification of aerobic spore-forming spoilage organisms of concern. These data will be critical for the development of detection methods and control strategies that will reduce the introduction of psychrotolerant sporeformers and extend the shelf life of dairy products.
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Paenibacillus sacheonensis sp. nov., a xylanolytic and cellulolytic bacterium isolated from tidal flat sediment. Int J Syst Evol Microbiol 2011; 61:2753-2757. [DOI: 10.1099/ijs.0.029066-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative-staining, rod-shaped bacterium, designated strain SY01T, was isolated from tidal flat sediment from Sacheon Bay, South Korea. Strain SY01T was characterized with respect to its phenotypic and phylogenetic characteristics. The novel strain was spore-forming, motile, catalase-negative and oxidase-positive. Optimal growth of the strain occurred at 30 °C and pH 7.0. The DNA G+C content was 56.1 mol%. The predominant menaquinone was MK-7. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and several unknown lipids were detected in the polar lipid profile. Anteiso-C15 : 0 (47.2 %), iso-C15 : 0 (18.9 %) and iso-C16 : 0 (10.5 %) were the major cellular fatty acids of strain SY01T. The highest 16S rRNA gene sequence similarities were found with Paenibacillus phyllosphaerae PALXIL04T (95.9 %), Paenibacillus tarimensis SA-7-6T (94.6 %) and Paenibacillus mendelii C/2T (94.4 %). Based on the phylogenetic, chemotaxonomic and physiological characteristics presented in this study, strain SY01T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus sacheonensis sp. nov. is proposed. The type strain is SY01T ( = DSM 23054T = KACC 14895T).
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Khianngam S, Tanasupawat S, Akaracharanya A, Kim KK, Lee KC, Lee JS. Paenibacillus xylanisolvens sp. nov., a xylan-degrading bacterium from soil. Int J Syst Evol Microbiol 2011; 61:160-164. [DOI: 10.1099/ijs.0.022269-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A xylan-degrading bacterium, strain X11-1T, was isolated from soil collected in Nan province, Thailand. The strain was characterized based on its phenotypic and genotypic characteristics. Strain X11-1T was a Gram-stain-positive, facultatively anaerobic, spore-forming, rod-shaped bacterium. It contained meso-diaminopimelic acid in the cell-wall peptidoglycan. The major menaquinone was MK-7, anteiso-C15 : 0 (56.6 %) and C16 : 0 (14.0 %) were the predominant cellular fatty acids and diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine and phosphatidylglycerol were the major phospholipids. The DNA G+C content was 51.6 mol%. Phylogenetic analysis using 16S rRNA gene sequences showed that strain X11-1T was affiliated to the genus Paenibacillus and was closely related to Paenibacillus naphthalenovorans KACC 11505T and Paenibacillus validus CCM 3894T, with 96.5 % sequence similarity. Therefore, the strain represents a novel species of the genus Paenibacillus, for which the name Paenibacillus xylanisolvens sp. nov. is proposed. The type strain is X11-1T (=KCTC 13042T =PCU 311T =TISTR 1829T).
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Affiliation(s)
- Saowapar Khianngam
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Ancharida Akaracharanya
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kwang Kyu Kim
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong, Daejeon 305-806, Republic of Korea
| | - Keun Chul Lee
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong, Daejeon 305-806, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong, Daejeon 305-806, Republic of Korea
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Baik KS, Lim CH, Choe HN, Kim EM, Seong CN. Paenibacillus rigui sp. nov., isolated from a freshwater wetland. Int J Syst Evol Microbiol 2010; 61:529-534. [PMID: 20382792 DOI: 10.1099/ijs.0.021485-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A rod-shaped, endospore-forming, Gram-reaction-variable bacterial strain, designated WPCB173(T), was isolated from freshwater collected from the Woopo wetland, Republic of Korea. Based on its phenotypic characteristics and phylogenetic position inferred from 16S rRNA gene sequence analysis, the isolate was identified as being a member of the genus Paenibacillus. Major polar lipids present in strain WPCB173(T) included phosphatidylethanolamine and several unidentified phospholipids. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The predominant menaquinone was MK-7. The major cellular fatty acid was anteiso-C₁₅:₀ (65.2 %). The DNA G+C content was 48.3 %. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain WPCB173(T) clustered with species of the genus Paenibacillus, its closest neighbours being Paenibacillus chinjuensis WN9(T) (96.7 %) and Paenibacillus soli DCY03(T) (96.4 %). DNA-DNA hybridization of strain WPCB173(T) with P. soli DCY03(T) and P. chinjuensis WN9(T) showed relatedness values of only 10 and 19 %, respectively. On the basis of the phenotypic and phylogenetic evidence, strain WPCB173(T) represents a novel species of the genus Paenibacillus, for which the name Paenibacillus rigui sp. nov. is proposed. The type strain of the novel species is WPCB173(T) (=KCTC 13282(T) =JCM 16352(T)).
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Affiliation(s)
- Keun Sik Baik
- Department of Biological Science, Sunchon National University, Suncheon 540-742, Republic of Korea
| | - Chae Hong Lim
- Department of Biological Science, Sunchon National University, Suncheon 540-742, Republic of Korea
| | - Han Na Choe
- Department of Biological Science, Sunchon National University, Suncheon 540-742, Republic of Korea
| | - Eun Mi Kim
- Department of Dental Hygiene, Gwangju Health College University, Gwangju 506-701, Republic of Korea
- Department of Biological Science, Sunchon National University, Suncheon 540-742, Republic of Korea
| | - Chi Nam Seong
- Department of Biological Science, Sunchon National University, Suncheon 540-742, Republic of Korea
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Paenibacillus filicis sp. nov., isolated from the rhizosphere of the fern. J Microbiol 2009; 47:524-9. [PMID: 19851723 DOI: 10.1007/s12275-009-0266-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Accepted: 10/06/2009] [Indexed: 10/20/2022]
Abstract
A Gram-positive and endospore-forming bacterial strain, designated S4(T), was isolated from the rhizosphere of ferns in Daejeon, Republic of Korea. This isolate is strictly aerobic, motile, and rod-like in shape, and it is positive for catalase, oxidase, esterase lipase, and beta-galactosidase activities. In addition, this strain grows when cultured at temperatures between 15 and 37 degrees C and at pH values ranging from 5.5 to 9.0. The DNA G+C content was determined to be 53.2 mol%. Strain S4(T) has meso-diaminopimelic acid in the cell-wall peptidoglycan; it also contains menaquinone 7 (MK-7) as the predominant isoprenoid quinone and anteiso-C(15:0) (57.5%), iso-C(16:0) (11.3%), and C(16:0) (9.4%) as the major cellular fatty acids. Phylogenetic analysis based on alignments of the 16S rRNA gene sequence showed that S4(T) is affiliated with a cluster of strains within the genus Paenibacillaceae and is most closely related to Paenibacillus chinjuensis WN9(T), with 96.8% similarity. Based on the phylogenetic and phenotypic characteristics of strain S4(T), we believe that this isolate should be distinguished from all type species of the genus Paenibacillus and should thus represent a novel taxon within the genus Paenibacillus. We propose naming this type species Paenibacillus filicis sp. nov. for the rhizosphere isolate; the type strain will be known as S4(T) (=KCTC 13693(T) =KACC 14197(T) =JCM 16417(T)).
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Scherling C, Ulrich K, Ewald D, Weckwerth W. A metabolic signature of the beneficial interaction of the endophyte paenibacillus sp. isolate and in vitro-grown poplar plants revealed by metabolomics. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2009; 22:1032-7. [PMID: 19589078 DOI: 10.1094/mpmi-22-8-1032] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Metabolic profiling via gas chromatography coupled to mass spectrometry was used to investigate the influence of endophytic bacteria on shoots of in vitro-grown poplar plants free from culturable endophytic bacteria. The results demonstrate that the occurrence of an endophytic Paenibacillus strain strongly affects the composition of the plant metabolites of in vitro-grown poplars. Eleven metabolites were significantly changed between inoculated and non-inoculated poplar plants as determined by two independent experiments. Detected shifts in the primary metabolism of the poplar plants pointed to a mutualistic interaction between bacteria able to fix nitrogen and the host plant with altered nitrogen assimilation patterns. The corresponding metabolic signature comprises increased asparagine and urea levels as well as depleted sugars and organic acids of the tricarboxylic acid cycle. These observations coincide with the fact that the Paenibacillus sp. strain P22 is able to grow without nitrogen in the medium, indicating nitrogen fixation from the air also known from other Paenibacillus spp. In combination with the detected plant-growth-promoting effects of the endophyte Paenibacillus P22, a novel mutualistic interaction is observed.
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Nelson DM, Glawe AJ, Labeda DP, Cann IKO, Mackie RI. Paenibacillus tundrae sp. nov. and Paenibacillus xylanexedens sp. nov., psychrotolerant, xylan-degrading bacteria from Alaskan tundra. Int J Syst Evol Microbiol 2009; 59:1708-14. [DOI: 10.1099/ijs.0.004572-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Khianngam S, Tanasupawat S, Lee JS, Lee KC, Akaracharanya A. Paenibacillus siamensis sp. nov., Paenibacillus septentrionalis sp. nov. and Paenibacillus montaniterrae sp. nov., xylanase-producing bacteria from Thai soils. Int J Syst Evol Microbiol 2009; 59:130-4. [DOI: 10.1099/ijs.0.65851-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Jeon CO, Lim JM, Lee SS, Chung BS, Park DJ, Xu LH, Jiang CL, Kim CJ. Paenibacillus harenae sp. nov., isolated from desert sand in China. Int J Syst Evol Microbiol 2009; 59:13-7. [DOI: 10.1099/ijs.0.65664-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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