1
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Han S, Narsing Rao MP, Yang S, Xie CJ, Liu GH, Zhou SG. Lederbergia citrea sp. nov., isolated from citrus rhizosphere. Int J Syst Evol Microbiol 2023; 73. [PMID: 37129938 DOI: 10.1099/ijsem.0.005833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
Three Gram-positive-staining strains FJAT-49754T, FJAT-49682 and FJAT-49731 were isolated from the citrus rhizosphere soil sample. These strains showed the highest 16S rRNA gene sequence similarity with the type strain of Lederbergia panacisoli (97.8-97.9 %). The 16S rRNA gene sequence similarities between strains FJAT-49754T, FJAT-49682, and FJAT-49731 were 99.9 %. The average nucleotide identity (ANI) values between strains FJAT-49754T, FJAT-49682 and FJAT-49731 were above 96 %, while the ANI values with the members of the genus Lederbergia were below 95 %, which were below the cut-off level for prokaryotic species delineation. The above results suggest that strains FJAT-49754T, FJAT-49682 and FJAT-49731 belong to a novel species of the genus Lederbergia. Growth of strain FJAT-49754T was observed at 10-40 °C (optimum at 30 °C, pH 6.0-10.0 (optimum at pH 8.0), and NaCl tolerance up to 7 % (w/v) (optimum at 1 %). MK-7 was the only menaquinone detected in strain FJAT-49754T, and the main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids of strain FJAT-49754T were anteiso-C15 : 0, iso-C15 : 0, and C16 : 0. The genomic DNA G+C content of strain FJAT-49754T was 38.7 %. Based on the above results, strain FJAT-49754T represents a novel species of the genus Lederbergia, for which the name Lederbergia citrea sp. nov., is proposed. The type strain is FJAT-49754T (=CCTCC AB 2019211T=LMG 31589T).
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Affiliation(s)
- Shuang Han
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, 350002, PR China
| | - Manik Prabhu Narsing Rao
- Programa de Doctorado en Ciencias Aplicadas, Universidad Autónoma de Chile, Talca, 3460000, Chile
| | - Shang Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, 350002, PR China
| | - Cheng-Jie Xie
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, 350002, PR China
| | - Guo-Hong Liu
- Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou City, Fujian Province, 350003, PR China
| | - Shun-Gui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, 350002, PR China
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2
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Liu GH, Narsing Rao MP, Chen QQ, Che JM, Shi H, Liu B, Li WJ. Lederbergia citri sp. nov., and Lederbergia citrisecundus sp. nov., isolated from citrus rhizosphere. Curr Microbiol 2022; 79:43. [PMID: 34982261 DOI: 10.1007/s00284-021-02741-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 12/06/2021] [Indexed: 11/28/2022]
Abstract
Two Gram-positive, rod-shaped, motile, endospore-forming strains, FJAT-49780T and FJAT-49732T were isolated from a citrus rhizosphere soil sample. The optimal growth temperatures for strains FJAT-49780T and FJAT-49732T were 45 and 35-40 °C, respectively. The optimal growth pH for strains FJAT-49732T and FJAT-49780T were pH 8.0 and pH 6.0, respectively. The 16S rRNA gene sequence similarity between FJAT-49780T and FJAT-49732T was 98.6%. Strains FJAT-49780T and FJAT-49732T shared 97.9-98.4% 16S rRNA gene sequence similarities to the type strain of Lederbergia wuyishanensis. In phylogenetic trees (based on 16S rRNA gene sequence), strains FJAT-49732T and FJAT-49780T clade with Lederbergia members. Both strains contained meso-diaminopimelic acid in their cell-wall peptidoglycan and MK-7 was the only isoprenoid quinone detected. The major fatty acids of strains FJAT-49732T and FJAT-49780T were anteiso-C15:0 and iso-C15:0. The polar lipids of strain FJAT-49780T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, unidentified phospholipid and unidentified lipids while strain FJAT-49732T contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified glycolipid, unidentified aminolipid and unidentified phospholipid. The genomic DNA G+C content of strains FJAT-49780T and FJAT-49732T were 37.0 and 36.7%, respectively. The digital DNA-DNA hybridization and average nucleotide identity values between strains FJAT-49780T and FJAT-49732T and with other members of the genus Lederbergia were below the cut-off level for species delineation. Thus, based on the above results, strains FJAT-49780T and FJAT-49732T represent two novel species of the genus Lederbergia, for which the names Lederbergia citri sp. nov., and Lederbergia citrisecundus sp. nov., are proposed. The type strains are FJAT-49780T (= CCTCC AB 2019242T = LMG 31583T) and FJAT-49732T (= CCTCC AB 2019246T = LMG 31584T).
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Affiliation(s)
- Guo-Hong Liu
- Agricultural Bio-Resources Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, People's Republic of China
| | - Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Qian-Qian Chen
- Agricultural Bio-Resources Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, People's Republic of China
| | - Jian-Mei Che
- Agricultural Bio-Resources Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, People's Republic of China
| | - Huai Shi
- Agricultural Bio-Resources Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, People's Republic of China
| | - Bo Liu
- Agricultural Bio-Resources Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, People's Republic of China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
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3
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Gupta RS, Patel S, Saini N, Chen S. Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species. Int J Syst Evol Microbiol 2020; 70:5753-5798. [PMID: 33112222 DOI: 10.1099/ijsem.0.004475] [Citation(s) in RCA: 191] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To clarify the evolutionary relationships and classification of Bacillus species, comprehensive phylogenomic and comparative analyses were performed on >300 Bacillus/Bacillaceae genomes. Multiple genomic-scale phylogenetic trees were initially reconstructed to identify different monophyletic clades of Bacillus species. In parallel, detailed analyses were performed on protein sequences of genomes to identify conserved signature indels (CSIs) that are specific for each of the identified clades. We show that in different reconstructed trees, most of the Bacillus species, in addition to the Subtilis and Cereus clades, consistently formed 17 novel distinct clades. Additionally, some Bacillus species reliably grouped with the genera Alkalicoccus, Caldalkalibacillus, Caldibacillus, Salibacterium and Salisediminibacterium. The distinctness of identified Bacillus species clades is independently strongly supported by 128 identified CSIs which are unique characteristics of these clades, providing reliable means for their demarcation. Based on the strong phylogenetic and molecular evidence, we are proposing that these 17 Bacillus species clades should be recognized as novel genera, with the names Alteribacter gen. nov., Ectobacillus gen. nov., Evansella gen. nov., Ferdinandcohnia gen. nov., Gottfriedia gen. nov., Heyndrickxia gen. nov., Lederbergia gen. nov., Litchfieldia gen. nov., Margalitia gen. nov., Niallia gen. nov., Priestia gen. nov., Robertmurraya gen. nov., Rossellomorea gen. nov., Schinkia gen. nov., Siminovitchia gen. nov., Sutcliffiella gen. nov. and Weizmannia gen. nov. We also propose to transfer 'Bacillus kyonggiensis' to Robertmurraya kyonggiensis sp. nov. (type strain: NB22=JCM 17569T=DSM 26768). Additionally, we report 31 CSIs that are unique characteristics of either the members of the Subtilis clade (containing the type species B. subtilis) or the Cereus clade (containing B. anthracis and B. cereus). As most Bacillus species which are not part of these two clades can now be assigned to other genera, we are proposing an emended description of the genus Bacillus to restrict it to only the members of the Subtilis and Cereus clades.
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Key Words
- classification of Bacillus species
- conserved signature indels
- emendation of genus Bacillus
- genus Bacillus and the family Bacillaceae
- novel Bacillaceae genera Alteribacter, Ectobacillus, Evansella, Ferdinandcohnia, Gottfriedia, Heyndrickxia, Lederbergia, Litchfieldia, Margalitia, Niallia, Priestia, Robertmurraya, Rossellomorea, Schinkia, Siminovitchia, Sutcliffiella and Weizmannia
- phylogenomic and comparative genomic analyses
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
| | - Sudip Patel
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
| | - Navneet Saini
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
| | - Shu Chen
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
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Yang B, Li X, Lin Z, Hu D, Liu Y, Pan X. Evolution of enzyme activity, heavy metals bioavailability and microbial community in different temperature stages of the co-bioevaporation process. WASTE MANAGEMENT (NEW YORK, N.Y.) 2020; 102:751-762. [PMID: 31805448 DOI: 10.1016/j.wasman.2019.11.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
Laboratory investigations documented enzyme activity, heavy metals' bioavailability and the bacterial community during co-bioevaporation treatment of food waste and landfill leachate. The activities of dehydrogenase, protease, urease and phosphatase were sensitive to the changes in operating temperature inherent in co-bioevaporation. The maximum dehydrogenase activity was appeared at warming 30 °C. The maximum hydrolytic activity of the microorganisms on protein, urea and phosphorus-containing organic compounds appeared at warming 50 °C. The bacteria mainly gathered on the surface and in the pores of the sludge particles used as a bulking agent. Bacterial abundance reached its maximum at warming 50 °C. Firmicutes, Actinobacterica and Proteobacterica were the dominant bacterial phyla involved. Even though co-bioevaporation concentrated the heavy metals in the leachate, their bioavailability was substantially reduced during the process.
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Affiliation(s)
- Benqin Yang
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China
| | - Xukun Li
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China
| | - Zhiqiang Lin
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China
| | - Die Hu
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China
| | - Yanmei Liu
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China
| | - Xuejun Pan
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China.
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5
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Wang HF, Li QL, Zhang YG, Xiao M, Zhou XK, Guo JW, Duan YQ, Li WJ. Bacillus capparidis sp. nov., an endophytic bacterium isolated from roots of Capparis spinosa L. Int J Syst Evol Microbiol 2017; 67:282-287. [DOI: 10.1099/ijsem.0.001616] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Hong-Fei Wang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China
- College of Life Science, Liaoning Normal University, Dalian 116029, PR China
| | - Qiu-Li Li
- College of Life Science, Liaoning Normal University, Dalian 116029, PR China
| | - Yong-Guang Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Xing-Kui Zhou
- China Tobacco Yunnan Industrial Co., Ltd, Kunming 650231, PR China
| | - Jian-Wei Guo
- Key Laboratory of Crops with High Quality and Efficient Cultivation and Security Control, Yunnan Higher Education Institutions, Honghe University, Mengzi 661100, PR China
| | - Yan-Qing Duan
- China Tobacco Yunnan Industrial Co., Ltd, Kunming 650231, PR China
| | - Wen-Jun Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
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6
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Zhang XX, Gao JS, Zhang L, Zhang CW, Ma XT, Zhang J. Bacillus oryzisoli sp. nov., isolated from rice rhizosphere. Int J Syst Evol Microbiol 2016; 66:3432-3436. [DOI: 10.1099/ijsem.0.001215] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Xiao-Xia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Ju-Sheng Gao
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
- Qiyang Agro-ecosystem of National Field Experimental Station, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Qiyang 426182, PR China
| | - Lei Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
- Institute of Genetics and Physiology, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050051, PR China
| | - Cai-Wen Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xiao-Tong Ma
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Jun Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
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7
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Chung EJ, Hossain MT, Khan A, Kim KH, Jeon CO, Chung YR. Bacillus oryzicola sp. nov., an Endophytic Bacterium Isolated from the Roots of Rice with Antimicrobial, Plant Growth Promoting, and Systemic Resistance Inducing Activities in Rice. THE PLANT PATHOLOGY JOURNAL 2015; 31:152-64. [PMID: 26060434 PMCID: PMC4453996 DOI: 10.5423/ppj.oa.12.2014.0136] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 04/06/2015] [Accepted: 04/07/2015] [Indexed: 05/07/2023]
Abstract
Biological control of major rice diseases has been attempted in several rice-growing countries in Asia during the last few decades and its application using antagonistic bacteria has proved to be somewhat successful for controlling various fungal diseases in field trials. Two novel endophytic Bacillus species, designated strains YC7007 and YC7010(T), with anti-microbial, plant growth-promoting, and systemic resistance-inducing activities were isolated from the roots of rice in paddy fields at Jinju, Korea, and their multifunctional activities were analyzed. Strain YC7007 inhibited mycelial growth of major rice fungal pathogens strongly in vitro. Bacterial blight and panicle blight caused by Xanthomonas oryzae pv. oryzae (KACC 10208) and Burkholderia glumae (KACC 44022), respectively, were also suppressed effectively by drenching a bacterial suspension (10(7) cfu/ml) of strain YC7007 on the rhizosphere of rice. Additionally, strain YC7007 promoted the growth of rice seedlings with higher germination rates and more tillers than the untreated control. The taxonomic position of the strains was also investigated. Phylogenetic analyses based on 16S rRNA gene sequences indicated that both strains belong to the genus Bacillus, with high similarity to the closely related strains, Bacillus siamensis KACC 15859(T) (99.67%), Bacillus methylotrophicus KACC 13105(T) (99.65%), Bacillus amyloliquefaciens subsp. plantarum KACC 17177(T) (99.60%), and Bacillus tequilensis KACC 15944(T) (99.45%). The DNA-DNA relatedness value between strain YC7010(T) and the most closely related strain, B. siamensis KACC 15859(T) was 50.4±3.5%, but it was 91.5±11.0% between two strains YC7007 and YC7010(T), indicating the same species. The major fatty acids of two strains were anteiso-C15:0 and iso C15:0. Both strains contained MK-7 as a major respiratory quinone system. The G+C contents of the genomic DNA of two strains were 50.5 mol% and 51.2 mol%, respectively. Based on these polyphasic studies, the two strains YC7007 and YC7010(T) represent novel species of the genus Bacillus, for which the name Bacillus oryzicola sp. nov. is proposed. The type strain is YC7010(T) (= KACC 18228(T)). Taken together, our findings suggest that novel endophytic Bacillus strains can be used for the biological control of rice diseases.
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Affiliation(s)
- Eu Jin Chung
- Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
| | - Mohammad Tofajjal Hossain
- Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
| | - Ajmal Khan
- Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
| | - Kyung Hyun Kim
- Department of Life Science, Chung-Ang University, Seoul 156-756,
Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 156-756,
Korea
| | - Young Ryun Chung
- Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
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8
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Liu B, Liu GH, Hu GH, Chen MC. Bacillus mesonae sp. nov., isolated from the root of Mesona chinensis. Int J Syst Evol Microbiol 2014; 64:3346-3352. [DOI: 10.1099/ijs.0.059485-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, short rod-shaped and motile, mildly halotolerant, endospore-forming bacterium, FJAT-13985T, was isolated from the internal tissues of Mesona chinensis root. Strain FJAT-13985T grew at 20–45 °C (optimum 30 °C) and pH 5.7–9.0 (optimum pH 7.0) and in the presence of 0–2 % (w/v) NaCl [optimum 1 % (w/v)]. The strain was catalase-positive and oxidase-negative. The cell wall of strain FJAT-13985T contained meso-diaminopimelic acid and the predominant isoprenoid quinone was MK-7 (97.4 %). The major fatty acids of the strain were anteiso-C15 : 0 (23.3 %) and iso-C15 : 0 (40.8 %). The DNA G+C content was 41.64 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain FJAT-13985T is a member of the genus
Bacillus
and is most closely related to
Bacillus drentensis
DSM 15600T (98.4 %),
Bacillus vireti
DSM 15602T (98.2 %) and
Bacillus novalis
DSM 15603T (98.3 %). DNA–DNA hybridization indicated that relatedness between strain FJAT-13985T and its closest relative,
B. drentensis
DSM 15600T, was 36.63 %. The phenotypic, chemotaxonomic and genotypic properties clearly indicate that strain FJAT-13985T represents a novel species of the genus
Bacillus
, for which the name
Bacillus
mesonae sp. nov. is proposed. The type strain is FJAT-13985T ( = DSM 25968T = CGMCC1.12238T).
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Affiliation(s)
- Bo Liu
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Guo-Hong Liu
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Gui-Hing Hu
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Mei-Chun Chen
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
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Abstract
ABSTRACT
The family
Bacillaceae
constitutes a phenotypically diverse and globally ubiquitous assemblage of bacteria. Investigation into how evolution has shaped, and continues to shape, this family has relied on several widely ranging approaches from classical taxonomy, ecological field studies, and evolution in soil microcosms to genomic-scale phylogenetics, laboratory, and directed evolution experiments. One unifying characteristic of the
Bacillaceae
, the endospore, poses unique challenges to answering questions regarding both the calculation of evolutionary rates and claims of extreme longevity in ancient environmental samples.
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10
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Zhao F, Feng YZ, Chen RR, Zhang HY, Wang JH, Lin XG. Bacillus fengqiuensis sp. nov., isolated from a typical sandy loam soil under long-term fertilization. Int J Syst Evol Microbiol 2014; 64:2849-2856. [PMID: 24871777 DOI: 10.1099/ijs.0.063081-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-positive, endospore-forming, moderately alkaliphilic bacterium, strain NPK15(T), was isolated from a typical sandy loam soil under long-term NPK fertilization in northern China and was subjected to a polyphasic taxonomic study. The diamino acid of the cell-wall peptidoglycan of strain NPK15(T) was found to be meso-diaminopimelic acid and the cell-wall sugars were xylose, glucose and traces of mannose. The only respiratory quinone found in strain NPK15(T) was menaquinone 7 (MK-7). The major cellular fatty acids were iso-C(15 : 0), anteiso-C(15 : 0), C(16 : 0) and C(16 : 1)ω6c/C(16 : 1)ω7c. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Phylogenetic analysis of the strain based on its 16S rRNA gene sequence showed that it was related most closely to 'Bacillus thaonhiensis' KACC 17216 (99.59%), B. songklensis KCTC 13881(T) (99.52%) and B. abyssalis CCTCC AB 2012074(T) (99.00%). DNA-DNA hybridization results indicated that the strain was distinct from other species of the genus Bacillus, the degree of relatedness being 35.4% with B. abyssalis CCTCC AB 2012074(T), 39.7% with B. songklensis KCTC 13881(T) and 51.2% with 'B. thaonhiensis' KACC 17216. The DNA G+C content of strain NPK15(T) was 45.5 mol%. Phenotypic, chemotaxonomic and molecular analyses identified strain NPK15(T) as a member of a novel species of the genus Bacillus, for which the name Bacillus fengqiuensis sp. nov. is proposed. The type strain is NPK15(T) ( = DSM 26745(T) = CCTCC AB 2013156(T)).
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Affiliation(s)
- Fei Zhao
- Joint Open Laboratory of Soil and the Environment, Hong Kong Baptist University & Institute of Soil Science, Chinese Academy of Sciences, Nanjing, PR China.,State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - You-Zhi Feng
- Joint Open Laboratory of Soil and the Environment, Hong Kong Baptist University & Institute of Soil Science, Chinese Academy of Sciences, Nanjing, PR China.,State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Rui-Rui Chen
- Joint Open Laboratory of Soil and the Environment, Hong Kong Baptist University & Institute of Soil Science, Chinese Academy of Sciences, Nanjing, PR China.,State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Hua-Yong Zhang
- Joint Open Laboratory of Soil and the Environment, Hong Kong Baptist University & Institute of Soil Science, Chinese Academy of Sciences, Nanjing, PR China.,State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Jun-Hua Wang
- Joint Open Laboratory of Soil and the Environment, Hong Kong Baptist University & Institute of Soil Science, Chinese Academy of Sciences, Nanjing, PR China.,State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Xian-Gui Lin
- Joint Open Laboratory of Soil and the Environment, Hong Kong Baptist University & Institute of Soil Science, Chinese Academy of Sciences, Nanjing, PR China.,State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
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11
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Choi JH, Cha CJ. Bacillus panacisoli sp. nov., isolated from ginseng soil. Int J Syst Evol Microbiol 2013; 64:901-906. [PMID: 24277860 DOI: 10.1099/ijs.0.054320-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-positive, motile, facultatively anaerobic, endospore-forming and rod-shaped bacterium, designated strain CJ32(T), was isolated from ginseng soil at Geumsan in Korea. The isolate grew optimally at 30 °C, 2% (w/v) NaCl and pH 7.0. Colonies of strain CJ32(T) were beige and circular with an entire margin on LB agar plates. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CJ32(T) was associated with the genus Bacillus and was most closely related to Bacillus graminis YC6957(T) (97.3% similarity) and Bacillus lentus IAM 12466(T) (97.1%). DNA-DNA hybridization with closely related strains was below 31.3%. The major respiratory isoprenoid quinone was MK-7. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The polar lipid profile of strain CJ32(T) consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several unidentified lipids, including phospholipids, aminolipids and aminophospholipids. The predominant fatty acids of strain CJ32(T) were iso-C15:0 and anteiso-C15:0. The G+C content of the genomic DNA was 35.1 mol%. Based on phenotypic, genotypic and phylogenetic data, strain CJ32(T) should be classified within a novel species of the genus Bacillus, for which the name Bacillus panacisoli sp. nov. is proposed. The type strain is strain CJ32(T) ( = KACC 17503(T) = JCM 19226(T)).
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Affiliation(s)
- Jung-Hye Choi
- Department of Systems Biotechnology, Chung-Ang University, Anseong 456-756, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong 456-756, Republic of Korea
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