51
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Gao JL, Sun P, Wang XM, Lv FY, Mao XJ, Sun JG. Rhizobium wenxiniae sp. nov., an endophytic bacterium isolated from maize root. Int J Syst Evol Microbiol 2017; 67:2798-2803. [PMID: 28820092 DOI: 10.1099/ijsem.0.002025] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, aerobic, rod-shaped strain designated 166T was isolated from surface-sterilized root tissue of maize planted in the Fangshan District of Beijing, PR China. The 16S rRNA gene sequence analysis indicated that strain 166T belongs to the genus Rhizobium and is closely related to Rhizobium cellulosilyticum ALA10B2T and Rhizobium yantingense H66T with sequence similarities of 98.8 and 98.3 %, respectively. According to atpD and recA sequence analysis, the highest sequence similarity between strain 166T and R. cellulosilyticum ALA10B2T is 93.8 and 84.7 %, respectively. However, the new isolate exhibited relatively low levels of DNA-DNA relatedness with respect to R. cellulosilyticum DSM 18291T (20.8±2.3 %) and Rhizobium yantingense CCTCC AB 2014007T (47.2±1.4 %). The DNA G+C content of strain 166T was 59.8 mol%. The main polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, an unidentified aminophospholipid and an unidentified aminolipid. The major fatty acids of strain 166T were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The results of the physiological and biochemical tests and minor differences in the fatty acid profiles allowed a clear phenotypic differentiation of strain 166T from the type strains of closely related species, R. cellulosilyticum DSM 18291T and R. yantingense CCTCC AB 2014007T. Strain 166T represents a novel species within the genus Rhizobium, for which the name Rhizobium wenxiniae sp. nov. is proposed, with the type strain 166T (=CGMCC 1.15279T=DSM 100734T).
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Affiliation(s)
- Jun-Lian Gao
- Beijing Agro- Biotechnology Research Center, Beijing Academy of Agriculture and Forestry/Beijing Municipal Key Laboratory of Agricultural Gene Resources and Biotechnology, Beijing 100097, PR China
| | - Pengbo Sun
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Xu-Ming Wang
- Beijing Agro- Biotechnology Research Center, Beijing Academy of Agriculture and Forestry/Beijing Municipal Key Laboratory of Agricultural Gene Resources and Biotechnology, Beijing 100097, PR China
| | - Fan-Yang Lv
- Key Laboratory of Microbial Resources, Ministry of Agriculture/ Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xiao-Jie Mao
- Key Laboratory of Microbial Resources, Ministry of Agriculture/ Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Jian-Guang Sun
- Key Laboratory of Microbial Resources, Ministry of Agriculture/ Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
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Marcos-García M, García-Fraile P, Filipová A, Menéndez E, Mateos PF, Velázquez E, Cajthaml T, Rivas R. Mesorhizobium bacterial strains isolated from the legume Lotus corniculatus are an alternative source for the production of polyhydroxyalkanoates (PHAs) to obtain bioplastics. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:17436-17445. [PMID: 28593540 DOI: 10.1007/s11356-017-9319-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 05/19/2017] [Indexed: 06/07/2023]
Abstract
Polyhydroxyalkanoic acids (PHAs) are natural polyesters that can be used to produce bioplastics which are biodegradable. Numerous microorganisms accumulate PHAs as energy reserves. Combinations of different PHAs monomers lead to the production of bioplastics with very different properties. In the present work, we show the capability of strains belonging to various phylogenetic lineages within the genus Mesorhizobium, isolated from Lotus corniculatus nodules, to produce different PHA monomers. Among our strains, we found the production of 3-hydroxybutyrate, 3-hydroxyvalerate, 3-hydroxydodecanoate, and 3-hydroxyhexadecanoate. Most of the PHA-positive strains were phylogenetically related to the species M. jarvisii. However, our findings suggest that the ability to produce different monomers forming PHAs is strain-dependent.
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Affiliation(s)
- Marta Marcos-García
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Salamanca, Spain
| | - Paula García-Fraile
- Mikrobiologický ústav, Akademie věd České republiky, Prague, Czech Republic.
| | - Alena Filipová
- Mikrobiologický ústav, Akademie věd České republiky, Prague, Czech Republic
- Přírodovědecká fakulta, Univerzita Karlova, Prague, Czech Republic
| | - Esther Menéndez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- ICAAM - Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Universidade de Évora, Évora, Portugal
| | - Pedro F Mateos
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Salamanca, Spain
- Unidad Asociada Universidad de Salamanca-CSIC (IRNASA), Salamanca, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Salamanca, Spain
- Unidad Asociada Universidad de Salamanca-CSIC (IRNASA), Salamanca, Spain
| | - Tomáš Cajthaml
- Mikrobiologický ústav, Akademie věd České republiky, Prague, Czech Republic
- Přírodovědecká fakulta, Univerzita Karlova, Prague, Czech Republic
| | - Raúl Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Salamanca, Spain
- Unidad Asociada Universidad de Salamanca-CSIC (IRNASA), Salamanca, Spain
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Devosia nitraria sp. nov., a novel species isolated from the roots of Nitraria sibirica in China. Antonie van Leeuwenhoek 2017. [PMID: 28647822 PMCID: PMC5644702 DOI: 10.1007/s10482-017-0901-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
An aerobic, Gram-stain negative, short rod-shaped and motile strain, 36-5-1T, was isolated from the roots of Nitraria sibirica in Zhangye city, Gansu province, north-west of China. Phylogenetic analysis based on the 16S rRNA gene sequence and two housekeeping genes (glnA and atpD) indicated that the strain represents a novel species closely related to the Devosia, Rhizobium and Devosia genera with 98.3, 96.2 and 91.1% similarities, respectively. The strain 36-5-1T contained Q-10 as the predominant ubiquinone and 16:0 (36.8%) as the major fatty acid; a large amount of unidentified glycolipid, diphosphatidylglycerol, phosphatidylglycerol and a small amount of unidentified polar lipids were present as polar lipids. In addition, the G+C content of the genomic DNA was 61.7 mol% and the DNA-DNA hybridization with type strains Devosia geojensis BD-c194T and Devosia pacifica NH131T 44.1 ± 1.1 and 40.2 ± 1.7, respectively. Based on chemotaxonomic data and molecular properties, strain 36-5-1T represents a novel species within the genus Devosia, for which the name Devosia nitraria sp. nov. is proposed. The type strain is 36-5-1T (=CGMCC1.15704T=NBRC112416T).
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Naqvi SUEK, Qin Y, Tahir A, Stougaard P. Pararhizobium antarcticum sp. nov., isolated from Antarctic water samples. Int J Syst Evol Microbiol 2017; 67:1650-1655. [PMID: 28141485 DOI: 10.1099/ijsem.0.001828] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two bacterial strains were isolated from sediments and microbial mats of Kingfisher Pond, Antarctica and characterized in a taxonomic study using a polyphasic approach. Cells were strictly aerobic, Gram-stain-negative, rod-shaped, motile (+50 flagellum-specific genes present in the genome sequence; motility observed under microscope) and formed creamy white, half-transparent colonies. Growth occurred at 4 to 28 °C with an optimum at 20 °C, with 0-5.0 % (w/v) NaCl (optimum at 0-1.0 %) and at pH 4.0-11.0 (optimum pH 7.0-9.0). The major fatty acid was C18 : 1ω7c. The respiratory quinone was ubiquinone 10 (Q-10). The DNA G+C content was 60.7 mol %. The polar lipids were phosphatidylglycerol, phosphatidylethanolamine and phosphatidylmethanolamine in addition to three unidentified lipids, one unknown glycolipid and five unidentified phospholipids. Comparative analysis of 16S rRNA gene sequences showed highest sequence similarity (98.1 %) to Pararhizobium giardinii H152T, Pararhizobium herbae CCBAU 83011T, and 'Pararhizobium polonicum' F5.1. In silico average nucleotide identity (ANI) and genome-to-genome distance calculator (GGDC) showed 81.1 % identity (ANI) and 22.6 % identity (GGDC) to the closest relative, 'P. polonicum' F5.1. On the basis of phenotypic, phylogenetic, genomic and chemotaxonomic data, the two strains represent a novel species of the genus Pararhizobium, for which the name Pararhizobium antarcticum sp. nov. is proposed. The type strain is NAQVI 59T(=DSM 103442T=LMG 29675T).
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Affiliation(s)
- Syeda Um-E-Kalsoom Naqvi
- Department of Environmental Science, Lahore College for Women University, Lahore, Pakistan.,Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Yanan Qin
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Arifa Tahir
- Department of Environmental Science, Lahore College for Women University, Lahore, Pakistan
| | - Peter Stougaard
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
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Helene LCF, Delamuta JRM, Ribeiro RA, Hungria M. Bradyrhizobium mercantei sp. nov., a nitrogen-fixing symbiont isolated from nodules of Deguelia costata (syn. Lonchocarpus costatus). Int J Syst Evol Microbiol 2017. [DOI: 10.1099/ijsem.0.001870] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Luisa Caroline Ferraz Helene
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020 Brasília, Distrito Federal, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970 Londrina, Paraná, Brazil
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
| | - Jakeline Renata Marçon Delamuta
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020 Brasília, Distrito Federal, Brazil
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
| | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, Distrito Federal, Brazil
| | - Mariangela Hungria
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, Distrito Federal, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970 Londrina, Paraná, Brazil
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Yan J, Li Y, Yan H, Chen WF, Zhang X, Wang ET, Han XZ, Xie ZH. Agrobacterium salinitolerans sp. nov., a saline–alkaline-tolerant bacterium isolated from root nodule of Sesbania cannabina. Int J Syst Evol Microbiol 2017. [DOI: 10.1099/ijsem.0.001885] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jun Yan
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, PR China
| | - Yan Li
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China
| | - Hui Yan
- Rhizobium Research Center and College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
- State Key Laboratory for Agro-Biotechnology, Beijing 100193, PR China
| | - Wen Feng Chen
- Rhizobium Research Center and College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
- State Key Laboratory for Agro-Biotechnology, Beijing 100193, PR China
| | - Xiaoxia 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
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, México DF, México
| | - Xiao Zeng Han
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, PR China
| | - Zhi Hong Xie
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China
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57
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Bradyrhizobium brasilense sp. nov., a symbiotic nitrogen-fixing bacterium isolated from Brazilian tropical soils. Arch Microbiol 2017; 199:1211-1221. [DOI: 10.1007/s00203-017-1390-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/17/2017] [Accepted: 05/18/2017] [Indexed: 12/22/2022]
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58
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Zhao JJ, Zhang J, Sun L, Zhang RJ, Zhang CW, Yin HQ, Zhang XX. Rhizobium oryziradicis sp. nov., isolated from rice roots. Int J Syst Evol Microbiol 2017; 67:963-968. [PMID: 27959784 DOI: 10.1099/ijsem.0.001724] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-negative, aerobic, rod-shaped endophytic bacterial strains, N19T and N11-2, were isolated from fresh rice (Oryza sativa) roots during investigation of the rice endophytic bacterial diversity. The 16S rRNA gene sequence results indicated that the similarity between strains N19T and N11-2 was 100 %. Both of them belong to the genus Rhizobium, with close similarity to Rhizobium taibaishanense CCNWSX 0483T (97.7 %), followed by Rhizobium vitis NCPPB 3554T (97.5 %). The sequence similarities of the housekeeping genes recA, gyrB and glnA between the novel isolates and members of the established species of the genus Rhizobium were less than 87 %. The DNA-DNA hybridization rates between strains N19T and N11-2 were 87.9 % using the initial renaturation rate method. Based on draft genome sequences, strain N19T showed 18.2 % and 19.6 % DNA-DNA hybridization values to R. taibaishanense CCNWSX 0483T and R. vitis S4, which demonstrated that these new isolates represent a novel species in the genus Rhizobium. The main cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The DNA G+C content of strain N19T was 58.7 mol% (Tm). The polar lipid profile of N19T consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unknown lipid, two unknown aminolipids and an unidentified aminophospholipid. According to physiological and biochemical characteristics and genotypic data, strains N19T and N11-2 are considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium oryziradicis sp. nov. is proposed, with N19T (=ACCC 19962T=KCTC 52413T) as the type strain.
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Affiliation(s)
- Juan-Juan Zhao
- 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
| | - Lei Sun
- College of Life Sciences, Hebei University, Baoding 071002, PR China
| | - Rui-Jie 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
| | - 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
| | - Hua-Qun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, PR China
| | - 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
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Yan J, Li Y, Han XZ, Chen WF, Zou WX, Xie Z, Li M. Agrobacterium deltaense sp. nov., an endophytic bacteria isolated from nodule of Sesbania cannabina. Arch Microbiol 2017; 199:1003-1009. [DOI: 10.1007/s00203-017-1367-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/05/2017] [Accepted: 03/15/2017] [Indexed: 10/19/2022]
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Chen WH, Yang SH, Li ZH, Zhang XX, Sui XH, Wang ET, Chen WX, Chen WF. Ensifer shofinae sp. nov., a novel rhizobial species isolated from root nodules of soybean (Glycine max). Syst Appl Microbiol 2017; 40:144-149. [PMID: 28209394 DOI: 10.1016/j.syapm.2017.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 11/09/2016] [Accepted: 01/04/2017] [Indexed: 10/20/2022]
Abstract
Two bacterial strains isolated from root nodules of soybean were characterized phylogenetically as members of a distinct group in the genus Ensifer based on 16S rRNA gene comparisons. They were also verified as a separated group by the concatenated sequence analyses of recA, atpD and glnII (with similarities ≤93.9% to the type strains for defined species), and by the average nucleotide identities (ANI) between the whole genome sequence of the representative strain CCBAU 251167T and those of the closely related strains in Ensifer glycinis and Ensifer fredii (90.5% and 90.3%, respectively). Phylogeny of symbiotic genes (nodC and nifH) grouped these two strains together with some soybean-nodulating strains of E. fredii, E. glycinis and Ensifer sojae. Nodulation tests indicated that the representative strain CCBAU 251167T could form root nodules with capability of nitrogen fixing on its host plant and Glycine soja, Cajanus cajan, Vigna unguiculata, Phaseolus vulgaris and Astragalus membranaceus, and it formed ineffective nodules on Leucaena leucocephala. Strain CCBAU 251167T contained fatty acids 18:1 ω9c, 18:0 iso and 20:0, differing from other related strains. Utilization of l-threonine and d-serine as carbon source, growth at pH 6.0 and intolerance of 1% (w/v) NaCl distinguished strain CCBAU 251167T from other type strains of the related species. The genome size of CCBAU 251167T was 6.2Mbp, comprising 7,581 predicted genes with DNA G+C content of 59.9mol% and 970 unique genes. Therefore, a novel species, Ensifer shofinae sp. nov., is proposed, with CCBAU 251167T (=ACCC 19939T=LMG 29645T) as type strain.
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Affiliation(s)
- Wen Hao Chen
- State Key Laboratory of Agro-Biotechnology; College of Biological Sciences and Rhizobium Research Center, China Agricultural University; MOA Key Laboratory of Soil Microbiology; Beijing 100193, PR China; Engineering Research Centre of Plant Growth Regulators, Ministry of Education; College of Agronomy and Biotechnology, China Agricultural University; Beijing 100193, PR China; College of Life Science & Food Engineering, Yibin University, Yibin 644000, Sichuan Province, PR China
| | - Sheng Hui Yang
- State Key Laboratory of Agro-Biotechnology; College of Biological Sciences and Rhizobium Research Center, China Agricultural University; MOA Key Laboratory of Soil Microbiology; Beijing 100193, PR China; Shandong Shofine Seed Technology Co. Ltd., Jiaxiang 272400, PR China
| | - Zhao Hu Li
- Engineering Research Centre of Plant Growth Regulators, Ministry of Education; College of Agronomy and Biotechnology, China Agricultural University; Beijing 100193, PR China
| | - 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
| | - Xin Hua Sui
- State Key Laboratory of Agro-Biotechnology; College of Biological Sciences and Rhizobium Research Center, China Agricultural University; MOA Key Laboratory of Soil Microbiology; Beijing 100193, PR China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D. F. 11340, Mexico.
| | - Wen Xin Chen
- State Key Laboratory of Agro-Biotechnology; College of Biological Sciences and Rhizobium Research Center, China Agricultural University; MOA Key Laboratory of Soil Microbiology; Beijing 100193, PR China
| | - Wen Feng Chen
- State Key Laboratory of Agro-Biotechnology; College of Biological Sciences and Rhizobium Research Center, China Agricultural University; MOA Key Laboratory of Soil Microbiology; Beijing 100193, PR China.
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Leite J, Passos SR, Simões-Araújo JL, Rumjanek NG, Xavier GR, Zilli JÉ. Genomic identification and characterization of the elite strains Bradyrhizobium yuanmingense BR 3267 and Bradyrhizobium pachyrhizi BR 3262 recommended for cowpea inoculation in Brazil. Braz J Microbiol 2017; 49:703-713. [PMID: 28410799 PMCID: PMC6175698 DOI: 10.1016/j.bjm.2017.01.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 01/03/2017] [Accepted: 01/12/2017] [Indexed: 11/21/2022] Open
Abstract
The leguminous inoculation with nodule-inducing bacteria that perform biological nitrogen fixation is a good example of an “eco-friendly agricultural practice”. Bradyrhizobium strains BR 3267 and BR 3262 are recommended for cowpea (Vigna unguiculata) inoculation in Brazil and showed remarkable responses; nevertheless neither strain was characterized at species level, which is our goal in the present work using a polyphasic approach. The strains presented the typical phenotype of Bradyrhizobium with a slow growth and a white colony on yeast extract-mannitol medium. Strain BR 3267 was more versatile in its use of carbon sources compared to BR 3262. The fatty acid composition of BR 3267 was similar to the type strain of Bradyrhizobium yuanmingense; while BR 3262 was similar to Bradyrhizobium elkanii and Bradyrhizobium pachyrhizi. Phylogenetic analyses based on 16S rRNA and three housekeeping genes placed both strains within the genus Bradyrhizobium: strain BR 3267 was closest to B. yuanmingense and BR 3262 to B. pachyrhizi. Genome average nucleotide identity and DNA–DNA reassociation confirmed the genomic identification of B. yuanmingense BR 3267 and B. pachyrhizi BR 3262. The nodC and nifH gene analyses showed that strains BR 3267 and BR 3262 hold divergent symbiotic genes. In summary, the results indicate that cowpea can establish effective symbiosis with divergent bradyrhizobia isolated from Brazilian soils.
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Affiliation(s)
- Jakson Leite
- Departamento de Solos, Universidade Federal Rural do Rio de Janeiro, 23851-970 Seropédica, RJ, Brazil
| | - Samuel Ribeiro Passos
- Departamento de Ciências Ambientais, Universidade Federal Rural do Rio de Janeiro, 23851-970 Seropédica, RJ, Brazil
| | - Jean Luiz Simões-Araújo
- Laboratório de Genética e Bioquímica, Embrapa Agrobiologia, 23851-970 Seropédica, RJ, Brazil
| | - Norma Gouvêa Rumjanek
- Laboratório de Ecologia Microbiana, Embrapa Agrobiologia, 23851-970 Seropédica, RJ, Brazil
| | - Gustavo Ribeiro Xavier
- Laboratório de Ecologia Microbiana, Embrapa Agrobiologia, 23851-970 Seropédica, RJ, Brazil
| | - Jerri Édson Zilli
- Laboratório de Ecologia Microbiana, Embrapa Agrobiologia, 23851-970 Seropédica, RJ, Brazil.
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Bradyrhizobium centrolobii and Bradyrhizobium macuxiense sp. nov. isolated from Centrolobium paraense grown in soil of Amazonia, Brazil. Arch Microbiol 2017; 199:657-664. [DOI: 10.1007/s00203-017-1340-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/06/2017] [Accepted: 01/09/2017] [Indexed: 10/20/2022]
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63
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Zhao JJ, Zhang J, Zhang RJ, Zhang CW, Yin HQ, Zhang XX. Rhizobium rhizosphaerae sp. nov., a novel species isolated from rice rhizosphere. Antonie van Leeuwenhoek 2017; 110:651-656. [PMID: 28154946 DOI: 10.1007/s10482-017-0831-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/16/2017] [Indexed: 11/25/2022]
Abstract
Two novel, Gram-negative, motile, rod-shaped, aerobic bacterial strains, MH17T and RD15, were isolated from the sterilized root and rhizosphere soil of rice, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that the similarity between strains MH17T and RD15 was 100%. The isolates exhibit high sequence similarities to Rhizobium oryzae CGMCC 1.7048T (98.7%) and Rhizobium petrolearium SL-1T (97.0% and 97.1%), which supports that they belong to a novel species in the genus Rhizobium. Strains MH17T and RD15 exhibited growth at 15-45 °C, pH 5.0-11.0, 0-2.0% sodium chloride (w/v). Sequence analysis of housekeeping genes gyrB, recA, atpD, ropB, gltA showed that these two novel strains had less than 94% similarity with the known species, indicating the distinct position of MH17T and RD15 in the genus Rhizobium. The major cellular fatty acids were identified as summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). Type strain MH17T had 87.5% DNA-DNA relatedness with RD15 by using the initial renaturation rate method. Based on draft genome sequences, strain MH17T showed 30.1% DNA-DNA hybridization values to R. oryzae CGMCC 1.7048T, the closely related strain, which supported that MH17T represents a novel species in the genus Rhizobium. Average nucleotide identity (ANI) between strains MH17T and RD15 were 97.8%, and strain MH17T showed 82.2% ANI value with R. oryzae CGMCC 1.7048T. The DNA G+C content was 60.4 mol% (Tm). Based on physiological, biochemical characteristic, genotypic data, strains MH17T and RD15 are concluded to represent a new species within the genus Rhizobium, for which the name Rhizobium rhizosphaerae sp. nov. is proposed. The type strain is MH17T (=ACCC 19963T = KCTC 52414T).
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Affiliation(s)
- Juan-Juan Zhao
- 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, People's Republic of 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, People's Republic of China
| | - Rui-Jie 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, People's Republic of 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, People's Republic of China
| | - Hua-Qun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, People's Republic of China
| | - 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, People's Republic of China.
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Xu L, Shi J, Li C, Zhu S, Li B. Rhizobium hedysari sp. nov., a novel species isolated from a root nodule of Hedysarum multijugum in China. Antonie van Leeuwenhoek 2017; 110:479-488. [DOI: 10.1007/s10482-016-0817-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 12/08/2016] [Indexed: 11/28/2022]
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65
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Li Y, Yan J, Yu B, Wang ET, Li X, Yan H, Liu W, Xie Z. Ensifer alkalisoli sp. nov. isolated from root nodules of Sesbania cannabina grown in saline–alkaline soils. Int J Syst Evol Microbiol 2016; 66:5294-5300. [DOI: 10.1099/ijsem.0.001510] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yan Li
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, PR China
| | - Jun Yan
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, PR China
| | - Bing Yu
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, PR China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 Mexico City, D.F., México
| | - Xiangyue Li
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, PR China
| | - Hui Yan
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, PR China
| | - Wei Liu
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, PR China
| | - Zhihong Xie
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, PR China
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Shamseldin A, Abdelkhalek A, Sadowsky MJ. Recent changes to the classification of symbiotic, nitrogen-fixing, legume-associating bacteria: a review. Symbiosis 2016. [DOI: 10.1007/s13199-016-0462-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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67
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Torres Tejerizo G, Rogel MA, Ormeño-Orrillo E, Althabegoiti MJ, Nilsson JF, Niehaus K, Schlüter A, Pühler A, Del Papa MF, Lagares A, Martínez-Romero E, Pistorio M. Rhizobium favelukesii sp. nov., isolated from the root nodules of alfalfa (Medicago sativa L). Int J Syst Evol Microbiol 2016; 66:4451-4457. [DOI: 10.1099/ijsem.0.001373] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Gonzalo Torres Tejerizo
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
- CeBiTec, Bielefeld Universität, Bielefeld, Germany
| | - Marco Antonio Rogel
- Centro de Ciencias Genómicas Av. Universidad 1001, Col. Chamilpa. 62210 Cuernavaca, Universidad Nacional Autónoma de México, Morelos, Mexico
| | - Ernesto Ormeño-Orrillo
- Centro de Ciencias Genómicas Av. Universidad 1001, Col. Chamilpa. 62210 Cuernavaca, Universidad Nacional Autónoma de México, Morelos, Mexico
| | - María Julia Althabegoiti
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - Juliet Fernanda Nilsson
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | | | | | | | - María Florencia Del Papa
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - Antonio Lagares
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - Esperanza Martínez-Romero
- Centro de Ciencias Genómicas Av. Universidad 1001, Col. Chamilpa. 62210 Cuernavaca, Universidad Nacional Autónoma de México, Morelos, Mexico
| | - Mariano Pistorio
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
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An arsenate-reducing and alkane-metabolizing novel bacterium, Rhizobium arsenicireducens sp. nov., isolated from arsenic-rich groundwater. Arch Microbiol 2016; 199:191-201. [PMID: 27663709 DOI: 10.1007/s00203-016-1286-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/31/2016] [Accepted: 09/01/2016] [Indexed: 01/09/2023]
Abstract
A novel arsenic (As)-resistant, arsenate-respiring, alkane-metabolizing bacterium KAs 5-22T, isolated from As-rich groundwater of West Bengal was characterized by physiological and genomic properties. Cells of strain KAs 5-22T were Gram-stain-negative, rod-shaped, motile, and facultative anaerobic. Growth occurred at optimum of pH 6.0-7.0, temperature 30 °C. 16S rRNA gene affiliated the strain KAs 5-22T to the genus Rhizobium showing maximum similarity (98.4 %) with the type strain of Rhizobium naphthalenivorans TSY03bT followed by (98.0 % similarity) Rhizobium selenitireducens B1T. The genomic G + C content was 59.4 mol%, and DNA-DNA relatedness with its closest phylogenetic neighbors was 50.2 %. Chemotaxonomy indicated UQ-10 as the major quinone; phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol as major polar lipids; C16:0, C17:0, 2-OH C10:0, 3-OH C16:0, and unresolved C18:1 ɷ7C/ɷ9C as predominant fatty acids. The cells were found to reduce O2, As5+, NO3-, SO42- and Fe3+ as alternate electron acceptors. The strain's ability to metabolize dodecane or other alkanes as sole carbon source using As5+ as terminal electron acceptor was supported by the presence of genes encoding benzyl succinate synthase (bssA like) and molybdopterin-binding site (mopB) of As5+ respiratory reductase (arrA). Differential phenotypic, chemotaxonomic, genotypic as well as physiological properties revealed that the strain KAs 5-22T is separated from its nearest recognized Rhizobium species. On the basis of the data presented, strain KAs 5-22T is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium arsenicireducens sp. nov. is proposed as type strain (=LMG 28795T=MTCC 12115T).
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69
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Yan H, Yan J, Sui XH, Wang ET, Chen WX, Zhang XX, Chen WF. Ensifer glycinis sp. nov., a rhizobial species associated with species of the genus Glycine. Int J Syst Evol Microbiol 2016; 66:2910-2916. [PMID: 27125987 DOI: 10.1099/ijsem.0.001120] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
Rhizobial strains from root nodules of Astragalus mongholicus and soybean (Glycine max) were characterized phylogenetically as members of the genus Ensifer (formerly named Sinorhizobium), based on 16S rRNA gene sequence comparisons. Results based upon concatenated sequence analysis of three housekeeping genes (recA, atpD and glnII, ≤ 93.8 % similarities to known species) and average nucleotide identity (ANI) values of whole genome sequence comparisons (ranging from 89.6 % to 83.4 % to Ensifer fredii and Ensifer saheli, respectively) indicated the distinct positions of these novel strains within the genus Ensifer. Phylogeny of symbiotic genes (nodC and nifH) of three novel strains clustered them with rhizobial species Ensifer fredii and Ensifer sojae, both isolated from nodules of Glycine max. Cross-nodulation tests showed that the representative strain CCBAU 23380T could form root nodules with nitrogen fixation capability on Glycine soja, Albizia julibrissin, Vigna unguiculata and Cajanus cajan, but failed to nodulate Astragalus mongholicus, its original host legume. Strain CCBAU 23380T formed inefficient nodules on G. max, and it did not contain 18 : 0, 18 : 1ω7c 11-methyl or summed feature 1 fatty acids, which differed from other related strains. Failure to utilize malonic acid as a carbon source distinguished strain CCBAU 23380T from the type strains of related species. The genome size of CCBAU 23380T was 6.0 Mbp, comprising 5624 predicted genes with DNA G+C content of 62.4 mol%. Based on the results above, a novel species, Ensifer glycinis sp. nov., is proposed, with CCBAU 23380T (=LMG 29231T =HAMBI 3645T) as the type strain.
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Affiliation(s)
- Hui Yan
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University; MOA Key Laboratory of Soil Microbiology, Beijing 100193, PR China
| | - Jun Yan
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, PR China
| | - Xin Hua Sui
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University; MOA Key Laboratory of Soil Microbiology, Beijing 100193, PR China
| | - En Tao Wang
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University; MOA Key Laboratory of Soil Microbiology, Beijing 100193, PR China
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D. F. 11340, Mexico
| | - Wen Xin Chen
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University; MOA Key Laboratory of Soil Microbiology, Beijing 100193, PR China
| | - 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
| | - Wen Feng Chen
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University; MOA Key Laboratory of Soil Microbiology, Beijing 100193, PR China
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Yan J, Yan H, Liu LX, Chen WF, Zhang XX, Verástegui-Valdés MM, Wang ET, Han XZ. Rhizobium hidalgonense sp. nov., a nodule endophytic bacterium of Phaseolus vulgaris in acid soil. Arch Microbiol 2016; 199:97-104. [DOI: 10.1007/s00203-016-1281-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 07/27/2016] [Accepted: 08/16/2016] [Indexed: 01/20/2023]
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71
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Yuan CG, Jiang Z, Xiao M, Zhou EM, Kim CJ, Hozzein WN, Park DJ, Zhi XY, Li WJ. Mesorhizobium sediminum sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2016; 66:4797-4802. [PMID: 27535803 DOI: 10.1099/ijsem.0.001432] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-staining-negative, short rod, non-motile, non-spore-forming, aerobic bacterium, designated strain YIM M12096T, was isolated from deep-sea sediment collected from the Indian Ocean. Optimal growth conditions of the strain were observed at 25-30 °C, pH 6.0 and in the presence of 3-5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM M12096T was closely related to Nitratireductor indicus C115T (97.4 % 16S rRNA gene sequence similarity) and Mesorhizobium thiogangeticum SJTT (97.3 %). The strain, however, formed a robust clade with members of the genus Mesorhizobium in phylogenetic dendrograms generated with neighbour-joining, maximum-likelihood and maximum-parsimony trees. Analysis based on the sequence of housekeeping gene recA also gave a similar phylogenetic relationship, indicating that strain YIM M12096T is a member of the genus Mesorhizobium. DNA-DNA relatedness values between strain YIM M12096T and related type strains N. indicus CCTCC AB209298T and M. thiogangeticum DSM 17097T were 40.5 % and 36.7 %, respectively. Chemotaxonomic features of the isolate included phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified aminophospholipid and an unidentified phospholipid as its characteristic polar lipids and Q-10 as respiratory ubiquinone. Major fatty acids (>10 %) detected were C18 : 1ω7c and/or C18 : 1ω6c, 11-methyl-C18 : 1ω7c and cyclo-C19 : 0ω8c. Based on the chemotaxonomic properties and phylogenetic analyses, strain YIM M12096T is determined to be a member of the genus Mesorhizobium. The strain could be differentiated from the closely related species by the differences in physiological and biochemical properties supported by low DNA-DNA relatedness values. It is therefore concluded that strain YIM M12096T represents a novel species of the genus Mesorhizobium, for which the name Mesorhizobiumsediminum sp. nov. is proposed. The type strain is YIM M12096T (=CCTCC AB 2014219T=KCTC 42205T).
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Affiliation(s)
- Chang-Guo Yuan
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Zhao Jiang
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - En-Min Zhou
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Chang-Jin Kim
- Microbial Resource Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon 305-806, Republic of Korea
| | - Wael N Hozzein
- Bioproducts Research Chair, Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Dong-Jin Park
- Microbial Resource Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon 305-806, Republic of Korea
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
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72
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Delamuta JRM, Ribeiro RA, Araújo JLS, Rouws LFM, Zilli JÉ, Parma MM, Melo IS, Hungria M. Bradyrhizobium stylosanthis sp. nov., comprising nitrogen-fixing symbionts isolated from nodules of the tropical forage legume Stylosanthes spp. Int J Syst Evol Microbiol 2016; 66:3078-3087. [DOI: 10.1099/ijsem.0.001148] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jakeline Renata Marçon Delamuta
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, BlocoL, Lote 06, Edifício Capes, 70.040-020 Brasília, Distrito Federal, Brazil
| | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, Distrito Federal, Brazil
| | | | | | - Jerri Édson Zilli
- Embrapa Agrobiologia, C.P. 74.505, 23891-000 Seropédica, Rio de Janeiro, Brazil
| | | | | | - Mariangela Hungria
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, Distrito Federal, Brazil
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73
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Baraúna AC, Rouws LFM, Simoes-Araujo JL, Dos Reis Junior FB, Iannetta PPM, Maluk M, Goi SR, Reis VM, James EK, Zilli JE. Rhizobium altiplani sp. nov., isolated from effective nodules on Mimosa pudica growing in untypically alkaline soil in central Brazil. Int J Syst Evol Microbiol 2016; 66:4118-4124. [PMID: 27453319 DOI: 10.1099/ijsem.0.001322] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Root nodule bacteria were isolated from nodules on Mimosa pudica L. growing in neutral-alkaline soils from the Distrito Federal in central Brazil. The 16S rRNA gene sequence analysis of 10 strains placed them into the genus Rhizobium with the closest neighbouring species (each with 99 % similarity) being Rhizobium grahamii, Rhizobium cauense, Rhizobium mesoamericanum and Rhizobium tibeticum. This high similarity, however, was not confirmed by multi-locus sequence analysis (MLSA) using three housekeeping genes (recA, glnII and rpoB), which revealed R. mesoamericanum CCGE 501T to be the closest type strain (92 % sequence similarity or less). Chemotaxonomic data, including fatty acid profiles [with majority being C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1ω7c/C18 : 1ω6c)], DNA G+C content (57.6 mol%), and carbon compound utilization patterns supported the placement of the novel strains in the genus Rhizobium. Results of average nucleotide identity (ANI) differentiated the novel strains from the closest species of the genus Rhizobium, R. mesoamericanum, R. grahamii and R. tibeticum with 89.0, 88.1 and 87.8 % similarity, respectively. The symbiotic genes essential for nodulation (nodC) and nitrogen fixation (nifH) were most similar (99-100 %) to those of R. mesoamericanum, another Mimosa-nodulating species. Based on the current data, these 10 strains represent a novel species of the genus Rhizobium for which the name Rhizobium altiplani sp. nov. is proposed. The type strain is BR 10423T (=HAMBI 3664T).
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Affiliation(s)
- Alexandre C Baraúna
- Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23890-000, Brazil
| | - Luc F M Rouws
- Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23891-000, Brazil
| | - Jean L Simoes-Araujo
- Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23891-000, Brazil
| | | | | | - Marta Maluk
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Silvia R Goi
- Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23890-000, Brazil
| | - Veronica M Reis
- Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23891-000, Brazil
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Jerri E Zilli
- Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23891-000, Brazil
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74
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Coutinho DJG, Barbosa MO, Silva RM, da Silva SI, de Oliveira AFM. Fatty-Acid Composition of Seeds and Chemotaxonomic Evaluation of Sixteen Sapindaceae Species. Chem Biodivers 2016; 12:1271-80. [PMID: 26265579 DOI: 10.1002/cbdv.201400325] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Indexed: 11/07/2022]
Abstract
Circumscriptions for the Sapindaceae family and its infrafamilial relationships have been widely discussed. Certain groups are highly morphologically similar; thus, it is difficult to identify certain taxa. DNA Analyses have also indicated complex phylogenetic relationships, and it is difficult to relate such analyses to morphological data. Given the above concerns, this study aimed to investigate the fatty-acid profiles of the seed oils of 16 Sapindaceae species belonging to five tribes and to evaluate their potential chemotaxonomic significance. In total, eleven fatty acids were identified, and eicosenoic acid predominated in nine species. Multivariate analyses (principal component and cluster analyses) of the fatty-acid profiles of the seed oils allowed to separate them in two major clusters. The first cluster, characterized by oils with high eicosenoic acid levels, included all species belonging to the Paullinieae tribe (Cardiospermum, Paullinia, and Serjania species). In the second main cluster, the chemical similarity of the oils was lower, and the species belonged to different tribes. Nevertheless, the tree investigated Allophylus species (Thouinieae tribe) constituted a separate subcluster. Thus, the results showed that the fatty-acid composition of the seed oils of Sapindaceae species provide chemotaxonomic support for the separation of the Paullinieae tribe from the other tribes studied.
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Affiliation(s)
- Diogenes J Gusmão Coutinho
- Department of Botany, Federal University of Pernambuco, Av. Prof. Moraes Rego, s/n, Cidade Universitária, 50670-901 Recife, PE, Brazil, (phone: +55-81-21267813; fax: +55-81-21267803)
| | - Mariana O Barbosa
- Department of Botany, Federal University of Pernambuco, Av. Prof. Moraes Rego, s/n, Cidade Universitária, 50670-901 Recife, PE, Brazil, (phone: +55-81-21267813; fax: +55-81-21267803)
| | - Rejane M Silva
- Department of Biology, Federal Rural University of Pernambuco, 52171-900 Recife, PE, Brazil
| | - Suzene I da Silva
- Department of Biology, Federal Rural University of Pernambuco, 52171-900 Recife, PE, Brazil
| | - Antonio Fernando M de Oliveira
- Department of Botany, Federal University of Pernambuco, Av. Prof. Moraes Rego, s/n, Cidade Universitária, 50670-901 Recife, PE, Brazil, (phone: +55-81-21267813; fax: +55-81-21267803).
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75
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Zhu YJ, Lu JK, Chen YL, Wang SK, Sui XH, Kang LH. Mesorhizobium acaciae sp. nov., isolated from root nodules of Acacia melanoxylon R. Br. Int J Syst Evol Microbiol 2016; 65:3558-3563. [PMID: 26296667 DOI: 10.1099/ijsem.0.000455] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three novel strains, RITF741T, RITF1220 and RITF909, isolated from root nodules of Acacia melanoxylon in Guangdong Province of China, have been previously identified as members of the genus Mesorhizobium, displaying the same 16S rRNA gene RFLP pattern. Phylogenetic analysis of 16S rRNA gene sequences indicated that the three strains belong to the genus Mesorhizobium and had highest similarity (100.0 %) to Mesorhizobium plurifarium LMG 11892T. Phylogenetic analyses of housekeeping genes recA, atpD and glnII revealed that these strains represented a distinct evolutionary lineage within the genus Mesorhizobium. Strain RITF741T showed >73 % DNA–DNA relatedness with strains RITF1220 and RITF909, but < 60 % DNA–DNA relatedness with the closest type strains of recognized species of the genus Mesorhizobium. They differed from each other and from their closest phylogenetic neighbours by presence/absence of several fatty acids, or by large differences in the relative amounts of particular fatty acids. While showing distinctive features, they were generally able to utilize a wide range of substrates as sole carbon sources based on API 50CH and API 20NE tests. The three strains were able to form nodules with the original host Acacia melanoxylon and other woody legumes such as Acacia aneura, Albizia falcataria and Leucaena leucocephala. In conclusion, these strains represent a novel species belonging to the genus Mesorhizobium based on the data obtained in the present and previous studies, for which the name Mesorhizobium acaciae sp. nov. is proposed. The type strain is RITF741T ( = CCBAU 101090T = JCM 30534T), the DNA G+C content of which is 64.1 mol% (T m).
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Affiliation(s)
- Ya Jie Zhu
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, PR China
| | - Jun Kun Lu
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, PR China
| | - Ying Long Chen
- Institute of Soil and Water Conservation, Chinese Academy of Sciences, and Northwest A&F University, Yangling 712100, PR China
- School of Earth and Environment, and UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
| | - Sheng Kun Wang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, PR China
| | - Xin Hua Sui
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
| | - Li Hua Kang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, PR China
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76
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Behrendt U, Kämpfer P, Glaeser SP, Augustin J, Ulrich A. Characterization of the N2O-producing soil bacterium Rhizobium azooxidifex sp. nov. Int J Syst Evol Microbiol 2016; 66:2354-2361. [PMID: 27030972 DOI: 10.1099/ijsem.0.001036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the context of studying the bacterial community involved in nitrogen transformation processes in arable soils exposed to different extents of erosion and sedimentation in a long-term experiment (CarboZALF), a strain was isolated that reduced nitrate to nitrous oxide without formation of molecular nitrogen. The presence of the functional gene nirK, encoding the respiratory copper-containing nitrite reductase, and the absence of the nitrous oxide reductase gene nosZ indicated a truncated denitrification pathway and that this bacterium may contribute significantly to the formation of the important greenhouse gas N2O. Phylogenetic analysis based on the 16S rRNA gene sequence and the housekeeping genes recA and atpD demonstrated that the investigated soil isolate belongs to the genus Rhizobium. The closest phylogenetic neighbours were the type strains of Rhizobium. subbaraonis and Rhizobium. halophytocola. The close relationship with R. subbaraonis was reflected by similarity analysis of the recA and atpD genes and their amino acid positions. DNA-DNA hybridization studies revealed genetic differences at the species level, which were substantiated by analysis of the whole-cell fatty acid profile and several distinct physiological characteristics. Based on these results, it was concluded that the soil isolate represents a novel species of the genus Rhizobium, for which the name Rhizobium azooxidifex sp. nov. (type strain Po 20/26T=DSM 100211T=LMG 28788T) is proposed.
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Affiliation(s)
- Undine Behrendt
- Leibniz Centre for Agricultural Landscape Research (ZALF), Institute for Landscape Biogeochemistry, Eberswalder Str. 84, D-15374 Müncheberg, Germany
| | - Peter Kämpfer
- Department of Applied Microbiology, Justus-Liebig University Giessen, IFZ-Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Stefanie P Glaeser
- Department of Applied Microbiology, Justus-Liebig University Giessen, IFZ-Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Jürgen Augustin
- Leibniz Centre for Agricultural Landscape Research (ZALF), Institute for Landscape Biogeochemistry, Eberswalder Str. 84, D-15374 Müncheberg, Germany
| | - Andreas Ulrich
- Leibniz Centre for Agricultural Landscape Research (ZALF), Institute for Landscape Biogeochemistry, Eberswalder Str. 84, D-15374 Müncheberg, Germany
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77
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Yao Z, Guo J, Tang W, Sun Z, Hou Y, Li X. Production of a single cyclic type of fructooligosaccharide structure by inulin-degrading Paenibacillus sp. LX16 newly isolated from Jerusalem artichoke root. Microb Biotechnol 2016; 9:419-29. [PMID: 26996537 PMCID: PMC4835578 DOI: 10.1111/1751-7915.12358] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 01/21/2016] [Accepted: 01/29/2016] [Indexed: 11/28/2022] Open
Abstract
A novel inulin‐degrading bacterium was isolated from a soil sample collected on Jerusalem artichoke roots. It is a Gram‐positive, aerobic, motile and central endospore‐forming straight rod, and exhibits phenotypic properties being consistent with its classification in the genus Paenibacillus. The predominant cellular fatty acids were anteiso‐C15:0, C16:0 and anteiso‐C17:0. This strain represents a novel species of the genus Paenibacillus on the basis of phenotypic data together with phylogenetic analysis, and it is here designated as LX16 and deposited in China centre for type collection, China (= CCTCC 2015256). Strain LX16 could produce a cyclofructooligosaccharide fructanotransferase catalysing the formation of one type of fructooligosaccharide (FOS) from inulin. The FOS was identified as a cyclofructooligosaccharide with a degree of polymerization of 6. Such homology in inulin degradation products may be beneficial for the functional FOS production.
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Affiliation(s)
- Zhihua Yao
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Jiqiang Guo
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Wenzhu Tang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Zhen Sun
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Yingmin Hou
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Xianzhen Li
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
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78
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Woolfolk S, Stokes CE, Watson C, Brown R, Baird R. Bacteria Associated with Red Imported Fire Ants (Solenopsis invicta) from Mounds in Mississippi. SOUTHEAST NAT 2016. [DOI: 10.1656/058.015.0107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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79
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Rhizobium puerariae sp. nov., an endophytic bacterium from the root nodules of the medicinal plant Pueraria candollei var. candollei. Int J Syst Evol Microbiol 2016; 66:1236-1241. [DOI: 10.1099/ijsem.0.000863] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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80
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Wdowiak-Wróbel S, Małek W, Palusińska-Szysz M. Low temperature adaptation and the effects of cryoprotectants on mesorhizobia strains. J Basic Microbiol 2016; 56:379-91. [PMID: 26879468 DOI: 10.1002/jobm.201500615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 01/05/2016] [Indexed: 11/07/2022]
Abstract
In this study, the tolerance of Mesorhizobium sp. ACMP18, Mesorhizobium sp. USDA3350, and Mesorhizobium temperatum LMG23931 strains, to cold and freezing were investigated. The ability to withstand freezing at -20 °C and -70 °C for 24 months was different among the studied strains and depended on the cryoprotectant used. The survivability of mesorhizobial strains at -20 °C and -70 °C was significantly improved by some cryoprotectans (glycerol and sucrose/peptone). It is worth noting that the greatest resistance to freezing was detected when stress treatments were performed in glycerol as a cryoprotectant. Using PCR analysis, cspA genes were identified in the studied strains. Their nucleotide sequences were most similar to the sequences of the corresponding genes of the Mesorhizobium species. The expression of the cspA gene in the studied bacteria was analyzed using the RT-PCR technique. The fatty acid composition of the mesorhizobia was determined at 5, 10, 15, and 28 °C. It was noticed that growth temperature significantly affected the fatty acid composition and the amounts of unsaturated fatty acids, especially that of cis-vaccenic acid (18:1ɷ(11)), increased markedly in bacterial cells cultivated at 5, 10, and 15 °C.
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Affiliation(s)
- Sylwia Wdowiak-Wróbel
- Department of Genetics and Microbiology, Maria Curie Sklodowska University, Lublin, Poland
| | - Wanda Małek
- Department of Genetics and Microbiology, Maria Curie Sklodowska University, Lublin, Poland
| | - Marta Palusińska-Szysz
- Department of Genetics and Microbiology, Maria Curie Sklodowska University, Lublin, Poland
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81
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Mesorhizobium calcicola sp. nov., Mesorhizobium waitakense sp. nov., Mesorhizobium sophorae sp. nov., Mesorhizobium newzealandense sp. nov. and Mesorhizobium kowhaii sp. nov. isolated from Sophora root nodules. Int J Syst Evol Microbiol 2016; 66:786-795. [DOI: 10.1099/ijsem.0.000796] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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82
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Kocuria arsenatis sp. nov., an arsenic-resistant endophytic actinobacterium associated with Prosopis laegivata grown on high-arsenic-polluted mine tailing. Int J Syst Evol Microbiol 2016; 66:1027-1033. [DOI: 10.1099/ijsem.0.000830] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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83
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Sheu SY, Chen ZH, Young CC, Chen WM. Rhizobium ipomoeae sp. nov., isolated from a water convolvulus field. Int J Syst Evol Microbiol 2016; 66:1633-1640. [PMID: 26739022 DOI: 10.1099/ijsem.0.000875] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated shin9-1T, was isolated from a water sample taken from a water convolvulus field in Taiwan and characterized using a polyphasic taxonomical approach. Cells of strain shin9-1T were aerobic, Gram-stain-negative, rod-shaped and surrounded by a thick capsule and formed cream-coloured colonies. Growth occurred at 10-45 °C (optimum, 30 °C), with 0-3.0% NaCl (optimum, 0.5%) and at pH 7.0-9.0 (optimum, pH 7.0). Strain shin9-1T did not form nodules on a legume plant, Macroptilium atropurpureum, and the nodulation genes nodA, nodC and the nitrogenase reductase gene nifH were not detected by PCR. Phylogenetic analyses based on 16S rRNA and three housekeeping gene sequences (recA, atpD and rpoB) showed that strain shin9-1T belonged to the genus Rhizobium. Strain shin9-1T had the highest level of 16S rRNA gene sequence similarity with respect to Rhizobium daejeonense L61T (97.6 %). The major fatty acid of strain shin9-1T was C18:1ω7c. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, phosphatidylmonomethylethanolamine and several uncharacterized lipids. The DNA G+C content was 58.3 mol%. The DNA-DNA relatedness of strain shin9-1T with respect to recognized species of the genus Rhizobium was less than 70%. Phenotypic characteristics of the novel strain also differed from those of the most closely related species of the genus Rhizobium. On the basis of the phylogenetic inference and phenotypic data, strain shin9-1T should be classified as a representative of a novel species, for which the name Rhizobium ipomoeae sp. nov. is proposed. The type strain is shin9-1T (=LMG 27163T=KCTC 32148T).
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Affiliation(s)
- Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142 Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Zih-Han Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142 Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Chiu-Chung Young
- College of Agriculture and Natural Resources, Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142 Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
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84
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Román-Ponce B, Jing Zhang Y, Soledad Vásquez-Murrieta M, Hua Sui X, Feng Chen W, Carlos Alberto Padilla J, Wu Guo X, Lian Gao J, Yan J, Hong Wei G, Tao Wang E. Rhizobium acidisoli sp. nov., isolated from root nodules of Phaseolus vulgaris in acid soils. Int J Syst Evol Microbiol 2016; 66:398-406. [DOI: 10.1099/ijsem.0.000732] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Brenda Román-Ponce
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D. F. 11340, México
| | - Yu Jing Zhang
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - María Soledad Vásquez-Murrieta
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D. F. 11340, México
| | - Xin Hua Sui
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Wen Feng Chen
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | | | - Xian Wu Guo
- Centro de Biotecnología Genómica, IPN, Cd. Reynosa, Tamaulipas, C.P. 88710, México
| | - Jun Lian Gao
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry/Beijing Municipal Key Laboratory of Agricultural Gene Resources and Biotechnology, Beijing 100097, PR China
| | - Jun Yan
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, PR China
| | - Ge Hong Wei
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling Shaanxi 712100, PR China
| | - En Tao Wang
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D. F. 11340, México
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85
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Ferraz Helene LC, Marçon Delamuta JR, Augusto Ribeiro R, Ormeño-Orrillo E, Antonio Rogel M, Martínez-Romero E, Hungria M. Bradyrhizobium viridifuturi sp. nov., encompassing nitrogen-fixing symbionts of legumes used for green manure and environmental services. Int J Syst Evol Microbiol 2015; 65:4441-4448. [DOI: 10.1099/ijsem.0.000591] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Symbiotic nitrogen-fixing bacteria, commonly called rhizobia, are agronomically important because they can provide significant amounts of nitrogen to plants and help in recovery of impoverished soils and improvement of degraded environments. In recent years, with advances in molecular techniques, several studies have shown that these bacteria have high levels of genetic diversity, resulting in taxonomic reclassifications and descriptions of new species. However, despite the advances achieved, highly conserved 16S ribosomal genes (16S rRNA) do not elucidate differences between species of several genera, including the genus Bradyrhizobium. Other methodologies, such as multilocus sequence analysis (MLSA), have been used in such cases, with good results. In this study, three strains (SEMIAs 690T, 6387 and 6428) of the genus Bradyrhizobium, isolated from nitrogen-fixing nodules of Centrosema and Acacia species, without clear taxonomic positions, were studied. These strains differed from genetically closely related species according to the results of MLSA of four housekeeping genes (dnaK, glnII, gyrB and recA) and nucleotide identities of the concatenated genes with those of related species ranged from 87.8 % to 95.7 %, being highest with Bradyrhizobium elkanii. DNA–DNA hybridization (less than 32 % DNA relatedness) and average nucleotide identity values of the whole genomes (less than 90.5 %) indicated that these strains represented a novel species, and phenotypic traits were determined. Our data supported the description of the SEMIA strains as Bradyrhizobium viridifuturi sp. nov., and SEMIA 690T ( = CNPSo 991T = C 100aT = BR 1804T = LMG 28866T), isolated from Centrosema pubescens, was chosen as type strain.
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Affiliation(s)
- Luisa Caroline Ferraz Helene
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- Universidade Estadual de Londrina, Dept. of Microbiology, C.P. 10.011, 86057-970, Londrina, Paraná, Brazil
| | - Jakeline Renata Marçon Delamuta
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- Universidade Estadual de Londrina, Dept. of Microbiology, C.P. 10.011, 86057-970, Londrina, Paraná, Brazil
| | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B – Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, Distrito Federal, Brazil
| | | | - Marco Antonio Rogel
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | | | - Mariangela Hungria
- Universidade Estadual de Londrina, Dept. of Microbiology, C.P. 10.011, 86057-970, Londrina, Paraná, Brazil
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B – Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, Distrito Federal, Brazil
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86
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Li YH, Wang R, Zhang XX, Young JPW, Wang ET, Sui XH, Chen WX. Bradyrhizobium guangdongense sp. nov. and Bradyrhizobium guangxiense sp. nov., isolated from effective nodules of peanut. Int J Syst Evol Microbiol 2015; 65:4655-4661. [DOI: 10.1099/ijsem.0.000629] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seven slow-growing rhizobia isolated from effective nodules of Arachis hypogaea were assigned to the genus Bradyrhizobium based on sharing 96.3–99.9 % 16S rRNA gene sequence similarity with the type strains of recognized Bradyrhizobium species. Multilocus sequence analysis of glnII, recA, gyrB and dnaK genes indicated that the seven strains belonged to two novel species represented by CCBAU 51649T and CCBAU 53363T. Strain CCBAU 51649T shared 94, 93.4, 92.3 and 94.9 % and CCBAU 53363T shared 91.4, 94.5, 94.6 and 97.7 % sequence similarity for the glnII, recA, gyrB and dnaK genes, respectively, with respect to the closest related species Bradyrhizobium manausense BR 3351T and Bradyrhizobium yuanmingense CCBAU 10071T. Summed feature 8 and C16 : 0 were the predominant fatty acid components for strains CCBAU 51649T and CCBAU 53363T. DNA–DNA hybridization and analysis of phenotypic characteristics also distinguished these strains from the closest related Bradyrhizobium species. The strains formed effective nodules on Arachis hypogaea, Lablab purpureus and Aeschynomene indica, and they had identical nodA genes to Bradyrhizobium sp. PI237 but were phylogenetically divergent from other available nodA genes at less than 66 % similarity. Based in these results, strains CCBAU 51649T ( = CGMCC 1.15034T = LMG 28620T) and CCBAU 53363T ( = CGMCC 1.15035T = LMG 28621T) are designated the type strains of two novel species, for which the names Bradyrhizobium guangdongense sp. nov. and Bradyrhizobium guangxiense sp. nov. are proposed, respectively.
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Affiliation(s)
- Yong Hua Li
- State Key Lab for Agro-Biotechnology, Ministry of Agriculture Key Lab of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
| | - Rui Wang
- State Key Lab for Agro-Biotechnology, Ministry of Agriculture Key Lab of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
| | - Xiao Xia Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | | | - En Tao Wang
- State Key Lab for Agro-Biotechnology, Ministry of Agriculture Key Lab of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México D. F., Mexico
| | - Xin Hua Sui
- State Key Lab for Agro-Biotechnology, Ministry of Agriculture Key Lab of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
| | - Wen Xin Chen
- State Key Lab for Agro-Biotechnology, Ministry of Agriculture Key Lab of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
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87
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Delamuta JRM, Ribeiro RA, Ormeño-Orrillo E, Parma MM, Melo IS, Martínez-Romero E, Hungria M. Bradyrhizobium tropiciagri sp. nov. and Bradyrhizobium embrapense sp. nov., nitrogen-fixing symbionts of tropical forage legumes. Int J Syst Evol Microbiol 2015; 65:4424-4433. [PMID: 26362866 DOI: 10.1099/ijsem.0.000592] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
Biological nitrogen fixation is a key process for agricultural production and environmental sustainability, but there are comparatively few studies of symbionts of tropical pasture legumes, as well as few described species of the genus Bradyrhizobium, although it is the predominant rhizobial genus in the tropics. A detailed polyphasic study was conducted with two strains of the genus Bradyrhizobium used in commercial inoculants for tropical pastures in Brazil, CNPSo 1112T, isolated from perennial soybean (Neonotonia wightii), and CNPSo 2833T, from desmodium (Desmodium heterocarpon). Based on 16S-rRNA gene phylogeny, both strains were grouped in the Bradyrhizobium elkanii superclade, but were not clearly clustered with any known species. Multilocus sequence analysis of three (glnII, gyrB and recA) and five (plus atpD and dnaK) housekeeping genes confirmed that the strains are positioned in two distinct clades. Comparison with intergenic transcribed spacer sequences of type strains of described species of the genus Bradyrhizobium showed similarity lower than 93.1 %, and differences were confirmed by BOX-PCR analysis. Nucleotide identity of three housekeeping genes with type strains of described species ranged from 88.1 to 96.2 %. Average nucleotide identity of genome sequences showed values below the threshold for distinct species of the genus Bradyrhizobium ( < 90.6 %), and the value between the two strains was also below this threshold (91.2 %). Analysis of nifH and nodC gene sequences positioned the two strains in a clade distinct from other species of the genus Bradyrhizobium. Morphophysiological, genotypic and genomic data supported the description of two novel species in the genus Bradyrhizobium, Bradyrhizobium tropiciagri sp. nov. (type strain CNPSo 1112T = SMS 303T = BR 1009T = SEMIA 6148T = LMG 28867T) and Bradyrhizobium embrapense sp. nov. (type strain CNPSo 2833T = CIAT 2372T = BR 2212T = SEMIA 6208T = U674T = LMG 2987).
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Affiliation(s)
- Jakeline Renata Marçon Delamuta
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
- Universidade Estadual de Londrina, Department of Microbiology, C.P. 10.011, 86057-970 Londrina, Paraná, Brazil
| | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, Distrito Federal, Brazil
| | | | | | | | | | - Mariangela Hungria
- Universidade Estadual de Londrina, Department of Microbiology, C.P. 10.011, 86057-970 Londrina, Paraná, Brazil
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, Distrito Federal, Brazil
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88
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Román-Ponce B, Li YH, Vásquez-Murrieta MS, Sui XH, Chen WF, Estrada-de los Santos P, Wang ET. Brevibacterium metallicus sp. nov., an endophytic bacterium isolated from roots of Prosopis laegivata grown at the edge of a mine tailing in Mexico. Arch Microbiol 2015; 197:1151-8. [DOI: 10.1007/s00203-015-1156-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 09/09/2015] [Accepted: 09/24/2015] [Indexed: 10/23/2022]
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89
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De Meyer SE, Wee Tan H, Heenan PB, Andrews M, Willems A. Mesorhizobium waimense sp. nov. isolated from Sophora longicarinata root nodules and Mesorhizobium cantuariense sp. nov. isolated from Sophora microphylla root nodules. Int J Syst Evol Microbiol 2015; 65:3419-3426. [DOI: 10.1099/ijsem.0.000430] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In total 14 strains of Gram-stain-negative, rod-shaped bacteria were isolated from Sophora longicarinata and Sophora microphylla root nodules and authenticated as rhizobia on these hosts. Based on the 16S rRNA gene phylogeny, they were shown to belong to the genus Mesorhizobium, and the strains from S. longicarinata were most closely related to Mesorhizobium amorphae ACCC 19665T (99.8–99.9 %), Mesorhizobium huakuii IAM 14158T (99.8–99.9 %), Mesorhizobium loti USDA 3471T (99.5–99.9 %) and Mesorhizobium septentrionale SDW 014T (99.6–99.8 %), whilst the strains from S. microphylla were most closely related to Mesorhizobium ciceri UPM-Ca7T (99.8–99.9 %), Mesorhizobium qingshengii CCBAU 33460T (99.7 %) and Mesorhizobium shangrilense CCBAU 65327T (99.6 %). Additionally, these strains formed two distinct groups in phylogenetic trees of the housekeeping genes glnII, recA and rpoB. Chemotaxonomic data, including fatty acid profiles, supported the assignment of the strains to the genus Mesorhizobium and allowed differentiation from the closest neighbours. Results of DNA–DNA hybridizations, MALDI-TOF MS analysis, ERIC-PCR, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of our strains from their closest neighbouring species. Therefore, the strains isolated from S. longicarinata and S. microphylla represent two novel species for which the names Mesorhizobium waimense sp. nov. (ICMP 19557T = LMG 28228T = HAMBI 3608T) and Mesorhizobium cantuariense sp. nov. (ICMP 19515T = LMG 28225T = HAMBI 3604T), are proposed respectively.
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Affiliation(s)
- Sofie E. De Meyer
- Centre for Rhizobium Studies, Murdoch University, Western Australia 6150, Australia
- Laboratory of Microbiology, Dept. Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Heng Wee Tan
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Peter B. Heenan
- Allan Herbarium, Landcare Research, Lincoln 7640, New Zealand
| | - Mitchell Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Anne Willems
- Allan Herbarium, Landcare Research, Lincoln 7640, New Zealand
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90
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Wei X, Yan S, Li D, Pang H, Li Y, Zhang J. Rhizobium helianthi sp. nov., isolated from the rhizosphere of sunflower. Int J Syst Evol Microbiol 2015; 65:4455-4460. [PMID: 26364048 DOI: 10.1099/ijsem.0.000594] [Citation(s) in RCA: 9] [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-stain-negative, non-spore-forming, rod-shaped and aerobic bacterium, designated Xi19T, was isolated from a soil sample collected from the rhizosphere of sunflower (Helianthus annuus) in Wuyuan county of Inner Mongolia, China and was characterized taxonomically by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel isolate was related to species of the genus Rhizobium, sharing the greatest 16S rRNA gene sequence similarity with Rhizobium rhizoryzae J3-AN59T (98.4 %), followed by Rhizobium pseudoryzae J3-A127T (97.4 %). There were low similarities ( < 91 %) between the atpD, recA and glnII gene sequences of the novel strain and those of members of the genus Rhizobium. DNA-DNA hybridization values between strain Xi19T and the most related strain Rhizobium rhizoryzae J3-AN59T were low. The major cellular fatty acids of strain Xi19T were C16 : 0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C19 : 0 cyclo ω8c. Q-10 was identified as the predominant ubiquinone and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The DNA G+C content of strain Xi19T was 60.2 mol%. On the basis of physiological and biochemical characteristics, coupled with genotypic data obtained in this work, strain Xi19T represents a novel species of the genus Rhizobium, for which the name Rhizobium helianthi is proposed. The type strain is Xi19T ( = CGMCC 1.12192T = KCTC 23879T).
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Affiliation(s)
- Xuexin Wei
- School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Shouwei Yan
- School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Dai Li
- School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Huancheng Pang
- Institute of Agri-resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Yuyi Li
- Institute of Agri-resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Jianli Zhang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
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91
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Zhang YJ, Zheng WT, Everall I, Young JPW, Zhang XX, Tian CF, Sui XH, Wang ET, Chen WX. Rhizobium anhuiense sp. nov., isolated from effective nodules of Vicia faba and Pisum sativum. Int J Syst Evol Microbiol 2015; 65:2960-2967. [PMID: 26025940 DOI: 10.1099/ijs.0.000365] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four rhizobia-like strains, isolated from root nodules of Pisum sativum and Vicia faba grown in Anhui and Jiangxi Provinces of China, were grouped into the genus Rhizobium but were distinct from all recognized species of the genus Rhizobium by phylogenetic analysis of 16S rRNA and housekeeping genes. The combined sequences of the housekeeping genes atpD, recA and glnII for strain CCBAU 23252(T) showed 86.9 to 95% similarity to those of known species of the genus Rhizobium. All four strains had nodC and nifH genes and could form effective nodules with Pisum sativum and Vicia faba, and ineffective nodules with Phaseolus vulgaris, but did not nodulate Glycine max, Arachis hypogaea, Medicago sativa, Trifolium repens or Lablab purpureus in cross-nodulation tests. Fatty acid composition, DNA-DNA relatedness and a series of phenotypic tests also separated these strains from members of closely related species. Based on all the evidence, we propose a novel species, Rhizobium anhuiense sp. nov., and designate CCBAU 23252(T) ( = CGMCC 1.12621(T) = LMG 27729(T)) as the type strain. This strain was isolated from a root nodule of Vicia faba and has a DNA G+C content of 61.1 mol% (Tm).
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Affiliation(s)
- Yu Jing Zhang
- State Key Lab for Agro-Biotechnology, Ministry of Agriculture Key Lab of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Wen Tao Zheng
- State Key Lab for Agro-Biotechnology, Ministry of Agriculture Key Lab of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Isobel Everall
- Department of Biology, University of York, York YO10 5DD, UK
| | - J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK
| | - Xiao Xia Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Chang Fu Tian
- State Key Lab for Agro-Biotechnology, Ministry of Agriculture Key Lab of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Xin Hua Sui
- State Key Lab for Agro-Biotechnology, Ministry of Agriculture Key Lab of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - En Tao Wang
- State Key Lab for Agro-Biotechnology, Ministry of Agriculture Key Lab of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México D. F., Mexico
| | - Wen Xin Chen
- State Key Lab for Agro-Biotechnology, Ministry of Agriculture Key Lab of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
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92
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Ribeiro RA, Martins TB, Ormeño-Orrillo E, Marçon Delamuta JR, Rogel MA, Martínez-Romero E, Hungria M. Rhizobium ecuadorense sp. nov., an indigenous N2-fixing symbiont of the Ecuadorian common bean (Phaseolus vulgaris L.) genetic pool. Int J Syst Evol Microbiol 2015; 65:3162-3169. [DOI: 10.1099/ijsem.0.000392] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
There are two major centres of genetic diversification of common bean (Phaseolus vilgaris L.), the Mesoamerican and the Andean, and the legume is capable of establishing nitrogen-fixing symbioses with several rhizobia; Rhizobium etli seems to be the dominant species in both centres. Another genetic pool of common bean, in Peru and Ecuador, is receiving increasing attention, and studies of microsymbionts from the region can help to increase our knowledge about coevolution of this symbiosis. We have previously reported several putative new lineages from this region and here present data indicating that strains belonging to one of them, PEL4, represent a novel species. Based on 16S rRNA gene sequence phylogeny, PEL4 strains are positioned in the Rhizobium phaseoli/R. etli/Rhizobium leguminosarum clade, but show unique properties in several morphological, physiological and biochemical analyses, as well as in BOX-PCR profiles ( < 75 % similarity with related species). PEL4 strains also differed from related species based on multilocus sequence analysis of three housekeeping genes (glnII, gyrB and recA). Nucleotide identities of the three concatenated genes between PEL4 strains and related species ranged from 91.8 to 94.2 %, being highest with Rhizobium fabae. DNA–DNA hybridization ( < 47 % DNA relatedness) and average nucleotide identity values of the whole genomes ( < 90.2 %) also supported the novel species status. The PEL4 strains were effective in nodulating and fixing N2 with common beans. The data supported the view that PEL4 strains represent a novel species, Rhizobium ecuadorense sp. nov. The type strain is CNPSo 671T ( = UMR 1450T = PIMAMPIRS I 5T = LMG 27578T).
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Affiliation(s)
- Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, Distrito Federal, Brazil
| | - Talita Busulini Martins
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- Universidade Estadual de Londrina, Department of Biochemistry and Biotechnology, C.P. 10.011, 86057-970, Londrina, Paraná, Brazil
| | - Ernesto Ormeño-Orrillo
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Jakeline Renata Marçon Delamuta
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- Universidade Estadual de Londrina, Department of Microbiology, C.P. 10.011, 86057-9970, Londrina, Paraná, Brazil
| | - Marco Antonio Rogel
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | | | - Mariangela Hungria
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- Universidade Estadual de Londrina, Department of Biochemistry and Biotechnology, C.P. 10.011, 86057-970, Londrina, Paraná, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, Distrito Federal, Brazil
- Universidade Estadual de Londrina, Department of Microbiology, C.P. 10.011, 86057-9970, Londrina, Paraná, Brazil
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93
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Kuzmanović N, Puławska J, Prokić A, Ivanović M, Zlatković N, Jones JB, Obradović A. Agrobacterium arsenijevicii sp. nov., isolated from crown gall tumors on raspberry and cherry plum. Syst Appl Microbiol 2015; 38:373-8. [DOI: 10.1016/j.syapm.2015.06.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 05/27/2015] [Accepted: 06/04/2015] [Indexed: 11/28/2022]
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94
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Reeve W, Sullivan J, Ronson C, Tian R, Munk C, Han C, Reddy T, Seshadri R, Woyke T, Pati A, Markowitz V, Ivanova N, Kyrpides N. High-Quality draft genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain CJ3Sym. Stand Genomic Sci 2015; 10:54. [PMID: 26380641 PMCID: PMC4572658 DOI: 10.1186/s40793-015-0049-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 07/23/2015] [Indexed: 11/23/2022] Open
Abstract
Mesorhizobium loti strain CJ3Sym was isolated in 1998 following transfer of the integrative and conjugative element ICEMlSym(R7A), also known as the R7A symbiosis island, in a laboratory mating from the donor M. loti strain R7A to a nonsymbiotic recipient Mesorhizobium strain CJ3. Strain CJ3 was originally isolated from a field site in the Rocklands range in New Zealand in 1994. CJ3Sym is an aerobic, Gram-negative, non-spore-forming rod. This report reveals the genome of M. loti strain CJ3Sym currently comprises 70 scaffolds totaling 7,563,725 bp. The high-quality draft genome is arranged in 70 scaffolds of 71 contigs, contains 7,331 protein-coding genes and 70 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.
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Affiliation(s)
- Wayne Reeve
- />Centre for Rhizobium Studies, Murdoch University, Perth, WA Australia
| | - John Sullivan
- />Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Clive Ronson
- />Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Rui Tian
- />Centre for Rhizobium Studies, Murdoch University, Perth, WA Australia
| | - Christine Munk
- />Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM USA
| | - Cliff Han
- />Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM USA
| | - T.B.K. Reddy
- />DOE Joint Genome Institute, Walnut Creek, CA USA
| | | | - Tanja Woyke
- />DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Amrita Pati
- />DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Victor Markowitz
- />Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | | | - Nikos Kyrpides
- />DOE Joint Genome Institute, Walnut Creek, CA USA
- />Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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95
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Karaś MA, Turska-Szewczuk A, Trapska D, Urbanik-Sypniewska T. Growth and Survival of Mesorhizobium loti Inside Acanthamoeba Enhanced Its Ability to Develop More Nodules on Lotus corniculatus. MICROBIAL ECOLOGY 2015; 70:566-75. [PMID: 25779926 PMCID: PMC4494150 DOI: 10.1007/s00248-015-0587-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 02/16/2015] [Indexed: 05/12/2023]
Abstract
The importance of protozoa as environmental reservoirs of pathogens is well recognized, while their impact on survival and symbiotic properties of rhizobia has not been explored. The possible survival of free-living rhizobia inside amoebae could influence bacterial abundance in the rhizosphere of legume plants and the nodulation competitiveness of microsymbionts. Two well-characterized strains of Mesorhizobium: Mesorhizobium loti NZP2213 and Mesorhizobium huakuii symbiovar loti MAFF303099 were assayed for their growth ability within the Neff strain of Acanthamoeba castellanii. Although the association ability and the initial uptake rate of both strains were similar, recovery of viable M. huakuii MAFF303099 after 4 h postinfection decreased markedly and that of M. loti NZP2213 increased. The latter strain was also able to survive prolonged co-incubation within amoebae and to self-release from the amoeba cell. The temperature 28 °C and PBS were established as optimal for the uptake of Mesorhizobium by amoebae. The internalization of mesorhizobia was mediated by the mannose-dependent receptor. M. loti NZP2213 bacteria released from amoebae developed 1.5 times more nodules on Lotus corniculatus than bacteria cultivated in an amoebae-free medium.
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Affiliation(s)
- Magdalena A Karaś
- Department of Genetics and Microbiology, Maria Curie-Sklodowska University, Akademicka 19, 20-033, Lublin, Poland,
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96
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Kimes NE, López-Pérez M, Flores-Félix JD, Ramírez-Bahena MH, Igual JM, Peix A, Rodriguez-Valera F, Velázquez E. Pseudorhizobium pelagicum gen. nov., sp. nov. isolated from a pelagic Mediterranean zone. Syst Appl Microbiol 2015; 38:293-9. [DOI: 10.1016/j.syapm.2015.05.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 05/15/2015] [Accepted: 05/19/2015] [Indexed: 10/23/2022]
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97
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Tang Q, Luo Y, Zheng C, Yin K, Ali MK, Li X, He J. Functional Analysis of a c-di-AMP-specific Phosphodiesterase MsPDE from Mycobacterium smegmatis. Int J Biol Sci 2015; 11:813-24. [PMID: 26078723 PMCID: PMC4466462 DOI: 10.7150/ijbs.11797] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/04/2015] [Indexed: 12/21/2022] Open
Abstract
Cyclic di‑AMP (c-di-AMP) is a second signaling molecule involved in the regulation of bacterial physiological processes and interaction between pathogen and host. However, the regulatory network mediated by c-di-AMP in Mycobacterium remains obscure. In M. smegmatis, a diadenylate cyclase (DAC) was reported recently, but there is still no investigation on c-di-AMP phosphodiesterase (PDE). Here, we provide a systematic study on signaling mechanism of c-di-AMP PDE in M. smegmatis. Based on our enzymatic analysis, MsPDE (MSMEG_2630), which contained a DHH-DHHA1 domain, displayed a 200-fold higher hydrolytic efficiency (kcat/Km) to c-di-AMP than to c-di-GMP. MsPDE was capable of converting c-di-AMP to pApA and AMP, and hydrolyzing pApA to AMP. Site-directed mutations in DHH and DHHA1 revealed that DHH domain was critical for the phosphodiesterase activity. To explore the regulatory role of c-di-AMP in vivo, we constructed the mspde mutant (Δmspde) and found that deficiency of MsPDE significantly enhanced intracellular C12-C20 fatty acid accumulation. Deficiency of DAC in many bacteria results in cell death. However, we acquired the M. smegmatis strain with DAC gene disrupted (ΔmsdisA) by homologous recombination approach. Deletion of msdisA reduced bacterial C12-C20 fatty acids production but scarcely affected bacterial survival. We also provided evidences that superfluous c-di-AMP in M. smegmatis could lead to abnormal colonial morphology. Collectively, our results indicate that MsPDE is a functional c-di-AMP-specific phosphodiesterase both in vitro and in vivo. Our study also expands the regulatory network mediated by c-di-AMP in M. smegmatis.
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Affiliation(s)
- Qing Tang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Yunchao Luo
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Cao Zheng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Kang Yin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Maria Kanwal Ali
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xinfeng Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Jin He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
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98
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Zhang XX, Gao JS, Cao YH, Sheirdil RA, Wang XC, Zhang L. Rhizobium oryzicola sp. nov., potential plant-growth-promoting endophytic bacteria isolated from rice roots. Int J Syst Evol Microbiol 2015; 65:2931-2936. [PMID: 26016492 DOI: 10.1099/ijs.0.000358] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial strains ZYY136(T) and ZYY9 were isolated from surface-sterilized rice roots from a long-term experiment of rice-rice--Astragalus sinicus rotation. The 16S rRNA gene sequences of strains ZYY136(T) and ZYY9 showed the highest similarity, of 97.0%, to Rhizobium tarimense PL-41(T). Sequence analysis of the housekeeping genes recA, thrC and atpD clearly differentiated the isolates from currently described species of the genus Rhizobium. The DNA-DNA relatedness value between ZYY136(T) and ZYY9 was 82.3%, and ZYY136(T) showed 34.0% DNA-DNA relatedness with the most closely related type strain, R. tarimense PL-41(T). The DNA G+C content of strain ZYY136(T) was 58.1 mol%. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and C16 : 0 3-OH. Strains ZYY136(T) and ZYY9 could be differentiated from the previously defined species of the genus Rhizobium by several phenotypic characteristics. Therefore, we conclude that strains ZYY136(T) and ZYY9 represent a novel species of the genus Rhizobium, for which the name Rhizobium oryzicola sp. nov. is proposed (type strain ZYY136(T) = ACCC 05753(T) = KCTC 32088(T)).
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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
| | - Yan-Hua Cao
- 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
| | - Rizwan Ali Sheirdil
- 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.,Department of Soil Science and Soil Water Conservation, PMAS Arid Agriculture University, Rawalpindi, Pakistan
| | - Xiu-Cheng Wang
- 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
| | - 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
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99
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Mesorhizobium soli sp. nov., a novel species isolated from the rhizosphere of Robinia pseudoacacia L. in South Korea by using a modified culture method. Antonie van Leeuwenhoek 2015; 108:301-10. [DOI: 10.1007/s10482-015-0481-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 05/13/2015] [Indexed: 10/23/2022]
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100
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Grison CM, Jackson S, Merlot S, Dobson A, Grison C. Rhizobium metallidurans sp. nov., a symbiotic heavy metal resistant bacterium isolated from the Anthyllis vulneraria Zn-hyperaccumulator. Int J Syst Evol Microbiol 2015; 65:1525-1530. [DOI: 10.1099/ijs.0.000130] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, rod-shaped, non-spore-forming bacterium (ChimEc512T) was isolated from 56 host seedlings of the hyperaccumulating Anthyllis vulneraria legume, which was on an old zinc mining site at Les Avinières, Saint-Laurent-Le-Minier, Gard, South of France. On the basis of 16S rRNA gene sequence similarities, strain ChimEc512T was shown to belong to the genus
Rhizobium
and to be most closely related to
Rhizobium endophyticum
CCGE 2052T (98.4 %),
Rhizobium tibeticum
CCBAU 85039T (98.1 %),
Rhizobium grahamii
CCGE 502T (98.0 %) and
Rhizobium mesoamericanum
CCGE 501T (98.0 %). The phylogenetic relationships of ChimEc512T were confirmed by sequencing and analyses of recA and atpD genes. DNA–DNA relatedness values of strain ChimEc512T with
R. endophyticum
CCGE 2052T,
R. tibeticum
CCBAU 85039T,
R. mesoamericanum
CCGE 52T,
Rhizobium grahamii
CCGE 502T,
Rhizobium etli
CCBAU 85039T and
Rhizobium radiobacter
KL09-16-8-2T were 27, 22, 16, 18, 19 and 11 %, respectively. The DNA G+C content of strain ChimEc512T was 58.9 mol%. The major cellular fatty acid was C18 : 1ω7c, characteristic of the genus
Rhizobium
. The polar lipid profile included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol and phosphatidylcholine and moderate amounts of aminolipids, phospholipid and sulfoquinovosyl diacylglycerol. Although ChimEc512T was able to nodulate A. vulneraria, the nodC and nifH genes were not detected by PCR. The rhizobial strain was tolerant to high concentrations of heavy metals: up to 35 mM Zn and up to 0.5 mM Cd and its growth kinetics was not impacted by Zn. The results of DNA–DNA hybridizations and physiological tests allowed genotypic and phenotypic differentiation of strain ChimEc512T from species of the genus
Rhizobium
with validly published names. Strain ChimEc512T, therefore, represents a novel species, for which the name Rhizobium metallidurans sp. nov. is proposed, with the type strain ChimEc512T ( = DSM 26575 = CIP 110550T).
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Affiliation(s)
- Claire M. Grison
- Environmental Research Institute, Lee road, University College Cork, Cork, Ireland
| | - Stephen Jackson
- Environmental Research Institute, Lee road, University College Cork, Cork, Ireland
| | - Sylvain Merlot
- Institut des Sciences du Végétal, CNRS, UPR 2355, Bât. 22, 1 avenue de la terrasse, 91198 Gif-sur-Yvette cedex, France
| | - Alan Dobson
- Environmental Research Institute, Lee road, University College Cork, Cork, Ireland
| | - Claude Grison
- FRE 3673 – Bioinspired chemistry and ecological innovation – CNRS, University of Montpellier 2, Stratoz – Cap Alpha, Avenue de l’Europe 34830 Clapiers, France
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