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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: 0.8] [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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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: 9] [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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Genetic diversity and distribution of bradyrhizobia nodulating peanut in acid-neutral soils in Guangdong Province. Syst Appl Microbiol 2016; 39:418-27. [PMID: 27499533 DOI: 10.1016/j.syapm.2016.06.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/02/2016] [Accepted: 06/06/2016] [Indexed: 11/20/2022]
Abstract
To reveal the genetic diversity and geographic distribution of peanut (Arachis hypogaea L.) rhizobia in Guangdong Province, one of the main peanut producing regions in China, 216 bradyrhizobial isolates were trapped by peanut plants inoculated with soil samples (pH 4.7-7.4) collected from ten sites in Guangdong. Based on BOX-PCR fingerprinting analysis, 71 representative isolates were selected for sequence analyses of ribosomal IGS, recA, atpD and symbiotic gene nodA. As a result, 22 genospecies were detected in the peanut rhizobia, including eight minor groups or single strains corresponding to Bradyrhizobium diazoefficiens, B. japonicum, B. yuanmingense, B. arachidis, B. guangdongense, B. guangxiense, B. iriomotense and B. liaoningense, as well as 14 novel Bradyrhizobium genospecies covering the majority of isolates. Five symbiotic clusters were obtained based on the phylogenetic relationships of nodA genes, related to the soybean-nodulating or peanut-nodulating reference strains. Biogeographic patterns, which were mainly correlated with potassium content and pH, were detected in the peanut bradyrhizobial community in Guangdong Province. These findings enriched the diversity of peanut rhizobia, and added the K content as a special determinant for peanut rhizobial distribution in acid soils.
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Rhizobium straminoryzae sp. nov., isolated from the surface of rice straw. Int J Syst Evol Microbiol 2014; 64:2962-2968. [DOI: 10.1099/ijs.0.062117-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, Gram-stain-negative, rod-shaped bacterium, designated strain CC-LY845T, was isolated from the surface of rice straw in Taiwan. Cells were non-motile, and no flagellum was detected. Comparison of 16S rRNA gene sequences indicated that the strain was phylogenetically related to species of the genus
Rhizobium
, with closest similarity to
Rhizobium pseudoryzae
KCTC 23294T (97.6 %),
R. rhizoryzae
KCTC 23652T (97.0 %) and
R. oryzae
LMG 24253T (96.7 %); other species showed lower levels of similarity (<96.6 %). The DNA–DNA relatedness of strain CC-LY845T and
R. pseudoryzae
KCTC 23294T was 34.8±3.1 % (reciprocal value 39.2±2.2 %). Phylogenetic analysis based on the housekeeping atpD and recA genes showed that the novel strain could be distinguished from
R. pseudoryzae
KCTC 23294T (92.7 and 91.5 %, respectively) and other species of the genus
Rhizobium
. The temperature range for growth was 25–42 °C, the pH range was 5.0–9.0 and NaCl concentrations up to 4.0 % (w/v) were tolerated. Strain CC-LY845T did not form nodules on four different legumes, and the nodD and nifH genes were not detected by PCR. The major fatty acids were C16 : 0 and summed feature 8 (C18 : 1ω7c/C18 : 1ω6c). The polyamine pattern of strain CC-LY845T showed spermidine and putrescine as major polyamines. The predominant quinone system was ubiquinone 10 (Q-10). The DNA G+C content was 68.3±2.4 mol%. Base on its phylogenetic, phenotypic and chemotaxonomic features, strain CC-LY845T is proposed to represent a novel species within the genus
Rhizobium
, for which the name Rhizobium straminoryzae sp. nov. is proposed. The type strain is strain CC-LY845T ( = BCRC 80698T = JCM 19536T).
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Chen JY, Gu J, Wang ET, Ma XX, Kang ST, Huang LZ, Cao XP, Li LB, Wu YL. Wild peanut Arachis duranensis are nodulated by diverse and novel Bradyrhizobium species in acid soils. Syst Appl Microbiol 2014; 37:525-32. [PMID: 24985193 DOI: 10.1016/j.syapm.2014.05.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/09/2014] [Accepted: 05/12/2014] [Indexed: 11/17/2022]
Abstract
Aiming at learning the microsymbionts of Arachis duranensis, a diploid ancestor of cultivated peanut, genetic and symbiotic characterization of 32 isolates from root nodules of this plant grown in its new habitat Guangzhou was performed. Based upon the phylogeny of 16S rRNA, atpD and recA genes, diverse bacteria belonging to Bradyrhizobium yuanmingense, Bradyrhizobium elkanii, Bradyrhizobium iriomotense and four new lineages of Bradyrhizobium (19 isolates), Rhizobium/Agrobacterium (9 isolates), Herbaspirillum (2 isolates) and Burkholderia (2 isolates) were defined. In the nodulation test on peanut, only the bradyrhizobial strains were able to induce effective nodules. Phylogeny of nodC divided the Bradyrhizobium isolates into four lineages corresponding to the grouping results in phylogenetic analysis of housekeeping genes, suggesting that this symbiosis gene was mainly maintained by vertical gene transfer. These results demonstrate that A. duranensis is a promiscuous host preferred the Bradyrhizobium species with different symbiotic gene background as microsymbionts, and that it might have selected some native rhizobia, especially the novel lineages Bradyrhizobium sp. I and sp. II, in its new habitat Guangzhou. These findings formed a basis for further study on adaptation and evolution of symbiosis between the introduced legumes and the indigenous rhizobia.
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Affiliation(s)
- Jing Yu Chen
- School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Jun Gu
- School of Life Science, South China Normal University, Guangzhou 510631, China.
| | - En Tao Wang
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 Mexico, DF, Mexico
| | - Xing Xian Ma
- School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Shi Tong Kang
- School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Ling Zi Huang
- School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Xue Ping Cao
- School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Liang Bing Li
- School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Yan Ling Wu
- School of Life Science, South China Normal University, Guangzhou 510631, China
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Wang YC, Wang F, Hou BC, Wang ET, Chen WF, Sui XH, Chen WX, Li Y, Zhang YB. Proposal of Ensifer psoraleae sp. nov., Ensifer sesbaniae sp. nov., Ensifer morelense comb. nov. and Ensifer americanum comb. nov. Syst Appl Microbiol 2013; 36:467-73. [DOI: 10.1016/j.syapm.2013.05.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Wang YC, Wang F, Hou BC, Wang ET, Chen WF, Sui XH, Chen WX, Li Y, Zhang YB. WITHDRAWN: Ensifer psoraleae sp. nov. and Ensifer sesbaniae sp. nov., isolated from the root nodules of Psoralea corylifolia, Sesbania cannabina and other legumes. Syst Appl Microbiol 2013:S0723-2020(13)00011-8. [PMID: 23453021 DOI: 10.1016/j.syapm.2013.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Revised: 01/07/2013] [Accepted: 01/08/2013] [Indexed: 11/21/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
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Affiliation(s)
- Yuan Chun Wang
- State Key Lab for Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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Wang JY, Wang R, Zhang YM, Liu HC, Chen WF, Wang ET, Sui XH, Chen WX. Bradyrhizobium daqingense sp. nov., isolated from soybean nodules. Int J Syst Evol Microbiol 2013; 63:616-624. [PMID: 22544787 DOI: 10.1099/ijs.0.034280-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thirteen slow-growing rhizobial strains isolated from root nodules of soybean (Glycine max L.) grown in Daqing city in China were classified in the genus Bradyrhizobium based on 16S rRNA gene sequence analysis. Multilocus sequence analysis of IGS, atpD, glnII and recA genes revealed that the isolates represented a novel clade in this genus. DNA-DNA relatedness lower than 42.5 % between the representative strain CCBAU 15774(T) and the type strains of the closely related species Bradyrhizobium liaoningense USDA 3622(T), Bradyrhizobium yuanmingense CCBAU 10071(T) and Bradyrhizobium betae LMG 21987(T), further confirmed that this group represented a novel species. CCBAU 15774(T) shared seven cellular fatty acids with the three above-mentioned species, but the fatty acids 15 : 0 iso and summed feature 5 (18 : 2ω6,9c and/or 18 : 0 anteiso) were unique for this strain. The respiratory quinone in CCBAU 15774(T) was ubiquinone-10 and the cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, cardiolipin and unknown aminolipid, polar lipid and phospholipid. In addition, some phenotypic features could be used to differentiate the novel group from the related species. On basis of these results, we propose the name Bradyrhizobium daqingense sp. nov., with CCBAU 15774(T) ( = LMG 26137(T) = HAMBI 3184(T) = CGMCC 1.10947(T)) as the type strain. The DNA G+C content of the type strain is 61.2 mol% (T(m)).
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Affiliation(s)
- Jing Yu Wang
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Rui Wang
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Yan Ming Zhang
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Hong Can Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Wen Feng Chen
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México DF, Mexico
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Xin Hua Sui
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Wen Xin Chen
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
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Li QQ, Wang ET, Chang YL, Zhang YZ, Zhang YM, Sui XH, Chen WF, Chen WX. Ensifer sojae sp. nov., isolated from root nodules of Glycine max grown in saline-alkaline soils. Int J Syst Evol Microbiol 2011; 61:1981-1988. [PMID: 20851917 DOI: 10.1099/ijs.0.025049-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
Thirteen bacterial isolates from root nodules of soybean grown in saline-alkaline soils in the Chinese province of Hebei were identified as a unique group in the genus Ensifer based upon BOX-PCR patterns, sequencing analyses of 16S rRNA and housekeeping genes and DNA-DNA hybridization. Phenotypically, positive tests for acid production and negative results for reduction in litmus milk and sensitivity to 50 µg ampicillin ml(-1), as well as some other features, could differentiate the novel group from defined species of the Ensifer-Sinorhizobium group. The novel group had symbiotic gene sequences (nodC and nifH) that were identical or very similar to those of Ensifer (Sinorhizobium) fredii, and formed effective nodules with Glycine max (soybean), Vigna unguiculata and Glycine soja. Based upon the consensus of these analyses, a novel species, Ensifer sojae sp. nov., is proposed, with CCBAU 05684(T) ( = LMG 25493(T) = HAMBI 3098(T)) as the type strain. The DNA G+C content of strain CCBAU 05684(T) was 60.9 mol% (T(m)).
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Affiliation(s)
- Qin Qin Li
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México DF, Mexico
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Yue Li Chang
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Yun Zeng Zhang
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Yan Ming Zhang
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Xin Hua Sui
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Wen Feng Chen
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Wen Xin Chen
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
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Wang F, Wang ET, Wu LJ, Sui XH, Li Y, Chen WX. Rhizobium vallis sp. nov., isolated from nodules of three leguminous species. Int J Syst Evol Microbiol 2010; 61:2582-2588. [PMID: 21131504 DOI: 10.1099/ijs.0.026484-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four bacterial strains isolated from root nodules of Phaseolus vulgaris, Mimosa pudica and Indigofera spicata plants grown in the Yunnan province of China were identified as a lineage within the genus Rhizobium according to the analysis of 16S rRNA gene sequences, sharing most similarity with Rhizobium lusitanum P1-7(T) (99.1 % sequence similarity) and Rhizobium rhizogenes IAM 13570(T) (99.0 %). These strains also formed a distinctive group from the reference strains for defined species of the genus Rhizobium in a polyphasic approach, including the phylogenetic analyses of the 16S rRNA gene and housekeeping genes (recA, atpD, glnII), DNA-DNA hybridization, BOX-PCR fingerprinting, phenotypic characterization, SDS-PAGE of whole-cell proteins, and cellular fatty acid profiles. All the data obtained in this study suggested that these strains represent a novel species of the genus Rhizobium, for which the name Rhizobium vallis sp. nov. is proposed. The DNA G+C content (mol%) of this species varied between 60.9 and 61.2 (T(m)). The type strain of R. vallis sp. nov. is CCBAU 65647(T) ( = LMG 25295(T) =HAMBI 3073(T)), which has a DNA G+C content of 60.9 mol% and forms effective nodules on Phaseolus vulgaris.
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Affiliation(s)
- Fang Wang
- State Key Lab for Agrobiotechnology, College of Biological Sciences and Center for Biomass Engineering, China Agricultural University, Beijing 100193, PR China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México D. F., Mexico.,State Key Lab for Agrobiotechnology, College of Biological Sciences and Center for Biomass Engineering, China Agricultural University, Beijing 100193, PR China
| | - Li Juan Wu
- State Key Lab for Agrobiotechnology, College of Biological Sciences and Center for Biomass Engineering, China Agricultural University, Beijing 100193, PR China
| | - Xin Hua Sui
- State Key Lab for Agrobiotechnology, College of Biological Sciences and Center for Biomass Engineering, China Agricultural University, Beijing 100193, PR China
| | - Ying Li
- State Key Lab for Agrobiotechnology, College of Biological Sciences and Center for Biomass Engineering, China Agricultural University, Beijing 100193, PR China
| | - Wen Xin Chen
- State Key Lab for Agrobiotechnology, College of Biological Sciences and Center for Biomass Engineering, China Agricultural University, Beijing 100193, PR China
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Chang YL, Wang JY, Wang ET, Liu HC, Sui XH, Chen WX. Bradyrhizobium lablabi sp. nov., isolated from effective nodules of Lablab purpureus and Arachis hypogaea. Int J Syst Evol Microbiol 2010; 61:2496-2502. [PMID: 21112989 DOI: 10.1099/ijs.0.027110-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Five strains isolated from root nodules of Lablab purpureus and Arachis hypogaea grown in the Anhui and Sichuan provinces of China were classified as members of the genus Bradyrhizobium. These strains had identical 16S rRNA gene sequences which shared 99.48 %, 99.48 % and 99.22 % similarity with the most closely related strains of Bradyrhizobium jicamae PAC68(T), Bradyrhizobium pachyrhizi PAC48(T) and Bradyrhizobium elkanii USDA 76(T), respectively. A study using a polyphasic approach, including 16S rRNA gene RFLP, IGS-RFLP, BOX-PCR, comparative sequence analysis of the 16S-23S rRNA intergenic spacer (IGS) and the recA, atpD and glnII genes, DNA-DNA hybridization and phenotypic tests, showed that the five strains clustered into a coherent group that differentiated them from all recognized species of the genus Bradyrhizobium. Sequencing of nifH and nodC genes and cross-nodulation tests showed that the representative strains CCBAU 23086(T), CCBAU 23160 and CCBAU 61434, isolated from different plants, had identical nifH and nodC gene sequences and were all able to nodulate Lablab purpureus, Arachis hypogaea and Vigna unguiculata. Based upon these results, the name Bradyrhizobium lablabi sp. nov. is proposed for this novel species and strain CCBAU 23086(T) ( = LMG 25572(T) = HAMBI 3052(T)) is designated as the type strain. The DNA G+C mol% is 60.14 (T(m)).
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Affiliation(s)
- Yue Li Chang
- State Key Laboratory for Agro-Biotechnology, Key Laboratory of Agro-Microbial Resource and Application, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
| | - Jing Yu Wang
- State Key Laboratory for Agro-Biotechnology, Key Laboratory of Agro-Microbial Resource and Application, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México D. F., Mexico
| | - Hong Can Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Xin Hua Sui
- State Key Laboratory for Agro-Biotechnology, Key Laboratory of Agro-Microbial Resource and Application, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
| | - Wen Xin Chen
- State Key Laboratory for Agro-Biotechnology, Key Laboratory of Agro-Microbial Resource and Application, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
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Han TX, Han LL, Wu LJ, Chen WF, Sui XH, Gu JG, Wang ET, Chen WX. Mesorhizobium gobiense sp. nov. and Mesorhizobium tarimense sp. nov., isolated from wild legumes growing in desert soils of Xinjiang, China. Int J Syst Evol Microbiol 2008; 58:2610-8. [DOI: 10.1099/ijs.0.2008/000125-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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13
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Han TX, Wang ET, Wu LJ, Chen WF, Gu JG, Gu CT, Tian CF, Chen WX. Rhizobium multihospitium sp. nov., isolated from multiple legume species native of Xinjiang, China. Int J Syst Evol Microbiol 2008; 58:1693-9. [DOI: 10.1099/ijs.0.65568-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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14
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Wang FQ, Wang ET, Zhang YF, Chen WX. Characterization of rhizobia isolated from Albizia spp. in comparison with microsymbionts of Acacia spp. and Leucaena leucocephala grown in China. Syst Appl Microbiol 2006; 29:502-17. [PMID: 16406708 DOI: 10.1016/j.syapm.2005.12.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2005] [Indexed: 10/25/2022]
Abstract
This is the first systematic study of rhizobia associated with Albizia trees. The analyses of PCR-RFLP and sequencing of 16S rRNA genes, SDS-PAGE of whole-cell proteins and clustering of phenotypic characters grouped the 31 rhizobial strains isolated from Albizia into eight putative species within the genera Bradyrhizobium, Mesorhizobium and Rhizobium. Among these eight rhizobial species, five were unique to Albizia and the remaining three were shared with Acacia and Leucaena, two legume trees coexisting with Albizia in China. These results indicated that Albizia species nodulate with a wide range of rhizobial species and had preference of microsymbionts different from Acacia and Leucaena. The definition of four novel groups, Mesorhizobium sp., Rhizobium sp. I, Rhizobium sp. II and "R. giardinii", indicates that further studies with enlarged rhizobial population are necessary to better understand the diversity and to clarify the taxonomic relationships of Albizia-associated rhizobia.
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MESH Headings
- Acacia/microbiology
- Albizzia/microbiology
- Bacterial Proteins/analysis
- Bacterial Proteins/isolation & purification
- Biodiversity
- China
- Cluster Analysis
- DNA Fingerprinting
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Electrophoresis, Polyacrylamide Gel
- Genes, rRNA
- Molecular Sequence Data
- Phylogeny
- Polymorphism, Restriction Fragment Length
- Proteome/analysis
- Proteome/isolation & purification
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Rhizobiaceae/chemistry
- Rhizobiaceae/classification
- Rhizobiaceae/genetics
- Rhizobiaceae/isolation & purification
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Feng Qin Wang
- Key Laboratory of Agro-Microbial Resource and Application, Ministry of Agriculture/College of Biological Sciences, China Agricultural University, Beijing 100094, China
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15
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Zakhia F, de Lajudie P. [Modern bacterial taxonomy: techniques review--application to bacteria that nodulate leguminous plants (BNL)]. Can J Microbiol 2006; 52:169-81. [PMID: 16604113 DOI: 10.1139/w05-092] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Taxonomy is the science that studies the relationships between organisms. It comprises classification, nomenclature, and identification. Modern bacterial taxonomy is polyphasic. This means that it is based on several molecular techniques, each one retrieving the information at different cellular levels (proteins, fatty acids, DNA...). The obtained results are combined and analysed to reach a "consensus taxonomy" of a microorganism. Until 1970, a small number of classification techniques were available for microbiologists (mainly phenotypic characterization was performed: a legume species nodulation ability for a Rhizobium, for example). With the development of techniques based on polymerase chain reaction for characterization, the bacterial taxonomy has undergone great changes. In particular, the classification of the legume nodulating bacteria has been repeatedly modified over the last 20 years. We present here a review of the currently used molecular techniques in bacterial characterization, with examples of application of these techniques for the study of the legume nodulating bacteria.
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Affiliation(s)
- Frédéric Zakhia
- Laboratoire des symbioses tropicales et Méditerranéennes, Unité mixte de recherche (UMR) 113, Institut de recherche pour le développement, Université Montpellier II (UM-II), CEDEX, France
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16
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Bhattacharya D, Sarma PM, Krishnan S, Mishra S, Lal B. Evaluation of genetic diversity among Pseudomonas citronellolis strains isolated from oily sludge-contaminated sites. Appl Environ Microbiol 2003; 69:1435-41. [PMID: 12620826 PMCID: PMC150093 DOI: 10.1128/aem.69.3.1435-1441.2003] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The diversity among a set of bacterial strains that have the capacity to degrade total petroleum hydrocarbons (TPH) in soil contaminated with oily sludge (hazardous hydrocarbon waste from oil refineries) was determined. TPH is composed of alkane, aromatics, nitrogen-, sulfur-, and oxygen-containing compound, and asphaltene fractions of crude oil. The 150 bacterial isolates which could degrade TPH were isolated from soil samples obtained from diverse geoclimatic regions of India. All the isolates were biochemically characterized and identified with a Biolog microbial identification system and by 16S rDNA sequencing. Pseudomonas citronellolis predominated among the 150 isolates obtained from six different geographically diverse samplings. Of the isolates, 29 strains of P. citronellolis were selected for evaluating their genetic diversity. This was performed by molecular typing with repetitive sequence (Rep)-based PCR with primer sets ERIC (enterobacterial repetitive intergenic consensus), REP (repetitive extragenic palindromes), and BOXAIR and PCR-based ribotyping. Strain-specific and unique genotypic fingerprints were distinguished by these molecular typing strategies. The 29 strains of P. citronellolis were separated into 12 distinguishable genotypic groups by Rep-PCR and into seven genomic patterns by PCR-based ribotyping. The genetic diversity of the strains was related to the different geoclimatic isolation sites, type of oily sludge, and age of contamination of the sites. These results indicate that a combination of Rep-PCR fingerprinting and PCR-based ribotyping can be used as a high-resolution genomic fingerprinting method for elucidating intraspecies diversity among strains of P. citronellolis.
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Affiliation(s)
- Dhruva Bhattacharya
- Centre of Bioresources and Biotechnology, TERI School of Advanced Studies, Habitat Place, Lodhi Road, New Delhi 110003, India
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17
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Andronov EE, Terefework Z, Roumiantseva ML, Dzyubenko NI, Onichtchouk OP, Kurchak ON, Dresler-Nurmi A, Young JPW, Simarov BV, Lindström K. Symbiotic and genetic diversity of Rhizobium galegae isolates collected from the Galega orientalis gene center in the Caucasus. Appl Environ Microbiol 2003; 69:1067-74. [PMID: 12571030 PMCID: PMC143604 DOI: 10.1128/aem.69.2.1067-1074.2003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2002] [Accepted: 11/13/2002] [Indexed: 11/20/2022] Open
Abstract
This paper explores the relationship between the genetic diversity of rhizobia and the morphological diversity of their plant hosts. Rhizobium galegae strains were isolated from nodules of wild Galega orientalis and Galega officinalis in the Caucasus, the center of origin for G. orientalis. All 101 isolates were characterized by genomic amplified fragment length polymorphism fingerprinting and by PCR-restriction fragment length polymorphism (RFLP) of the rRNA intergenic spacer and of five parts of the symbiotic region adjacent to nod box sequences. By all criteria, the R. galegae bv. officinalis and R. galegae bv. orientalis strains form distinct clusters. The nod box regions are highly conserved among strains belonging to each of the two biovars but differ structurally to various degrees between the biovars. The findings suggest varying evolutionary pressures in different parts of the symbiotic genome of closely related R. galegae biovars. Sixteen R. galegae bv. orientalis strains harbored copies of the same insertion sequence element; all were isolated from a particular site and belonged to a limited range of chromosomal genotypes. In all analyses, the Caucasian R. galegae bv. orientalis strains were more diverse than R. galegae bv. officinalis strains, in accordance with the gene center theory.
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Affiliation(s)
- E E Andronov
- Research Institute of Agricultural Microbiology, St. Petersburg, Pushkin 196608, Russia.
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18
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Zhang X, Nick G, Kaijalainen S, Terefework Z, Paulin L, Tighe SW, Graham PH, Lindström K. Phylogeny and diversity of Bradyrhizobium strains isolated from the root nodules of peanut (Arachis hypogaea) in Sichuan, China. Syst Appl Microbiol 1999; 22:378-86. [PMID: 10553290 DOI: 10.1016/s0723-2020(99)80046-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Twenty-two rhizobial strains isolated from the root nodules of two Chinese peanut cultivars (Arachis hypogaea L. Tianfu no. 3 and a local cultivar) growing at four different sites in the Sichuan province, Southwest China, were characterized by growth rate, rep-PCR, PCR-RFLP of 16S rDNA, partial sequencing of ribosomal genes, and fatty acid-methyl ester analysis (FAME), and compared with strains representing Bradyrhizobium japanicum, B. elkanii and other unclassified Bradyrhizobium sp. All peanut isolates from Sichuan were bradyrhizobia. Dendrograms constructed using the rep-PCR fingerprints grouped the strains mainly according to their geographic and cultivar origin. Based on PCR-RFLP and partial sequence analysis of 16S rDNA it appears that peanut bradyrhizobial strains from Sichuan are similar to peanut strains from Africa and Israel, and closely related to B. japonicum. In contrast, analysis of FAME data using two-dimensional principal component analysis indicated that Bradyrhizobium sp. (Arachis) were similar to, but slightly different from other bradyrhizobia. The presence and level of fatty acid 16:1 w5c was the distinguishing feature. The results of PCR-RFLP of the 16S rRNA gene, the partial sequence analysis of 16S rDNA, and FAME were in good agreement.
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Affiliation(s)
- X Zhang
- Department of Applied Chemistry and Microbiology, University of Helsinki, Finland
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19
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Nick G, Jussila M, Hoste B, Niemi RM, Kaijalainen S, de Lajudie P, Gillis M, de Bruijn FJ, Lindström K. Rhizobia Isolated from Root Nodules of Tropical Leguminous Trees Characterized Using DNA-DNA dot-blot Hybridisation and rep-PCR Genomic Fingerprinting. Syst Appl Microbiol 1999. [DOI: 10.1016/s0723-2020(99)80076-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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SantamarıÌa M, Agius F, Monza J, Gutiérrez-Navarro A, Corzo J. Comparative performance of enterobacterial repetitive intragenic consensus-polymerase chain reaction and lipopolysaccharide electrophoresis for the identification of Bradyrhizobium sp. (Lotus) strains. FEMS Microbiol Ecol 1999. [DOI: 10.1111/j.1574-6941.1999.tb00571.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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21
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Rasmussen U, Svenning MM. Fingerprinting of cyanobacteria based on PCR with primers derived from short and long tandemly repeated repetitive sequences. Appl Environ Microbiol 1998; 64:265-72. [PMID: 16349487 PMCID: PMC124704 DOI: 10.1128/aem.64.1.265-272.1998] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/1997] [Accepted: 10/29/1997] [Indexed: 11/20/2022] Open
Abstract
The presence of repeated DNA (short tandemly repeated repetitive [STRR] and long tandemly repeated repetitive [LTRR]) sequences in the genome of cyanobacteria was used to generate a fingerprint method for symbiotic and free-living isolates. Primers corresponding to the STRR and LTRR sequences were used in the PCR, resulting in a method which generate specific fingerprints for individual isolates. The method was useful both with purified DNA and with intact cyanobacterial filaments or cells as templates for the PCR. Twenty-three Nostoc isolates from a total of 35 were symbiotic isolates from the angiosperm Gunnera species, including isolates from the same Gunnera species as well as from different species. The results show a genetic similarity among isolates from different Gunnera species as well as a genetic heterogeneity among isolates from the same Gunnera species. Isolates which have been postulated to be closely related or identical revealed similar results by the PCR method, indicating that the technique is useful for clustering of even closely related strains. The method was applied to nonheterocystus cyanobacteria from which a fingerprint pattern was obtained.
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Affiliation(s)
- U Rasmussen
- Department of Plant Physiology and Microbiology, IBG, University of Tromsö, 9037 Tromsö, Norway
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22
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Schneider M, de Bruijn FJ. Rep-PCR mediated genomic fingerprinting of rhizobia and computer-assisted phylogenetic pattern analysis. World J Microbiol Biotechnol 1996; 12:163-74. [DOI: 10.1007/bf00364681] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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23
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Smith JJ, Offord LC, Holderness M, Saddler GS. Genetic diversity of Burkholderia solanacearum (synonym Pseudomonas solanacearum) race 3 in Kenya. Appl Environ Microbiol 1995; 61:4263-8. [PMID: 8534093 PMCID: PMC167737 DOI: 10.1128/aem.61.12.4263-4268.1995] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Genetic diversity among isolates of the bacterial plant pathogen Burkholderia solanacearum (synonym Pseudomonas solanacearum) race 3 biovar II of Kenya was determined by PCR with repetitive sequences (ERIC and BOX repetitive primer sets) and pulsed-field gel electrophoresis of genomic DNA digested by rare-cutting restriction endonucleases (RC-PFGE). The study comprised 46 isolates collected during 1992 from the major potato-growing regions of Kenya (45 were identified as race 3 biovar II, and 1 belonged to race 3 biovar N2) and 39 reference isolates from 19 other countries. RC-PFGE identified 10 distinct profile types among the Kenyan race 3 biovar II isolates (29 of the isolates exhibited identical profiles) and a further 27 distinct profile types among the reference isolates. ERIC and BOX primer sets were unable to differentiate race 3 biovar II isolates within the Kenyan population but differentiated a further two distinct profile types among the reference isolates. The race 3 biovar N2 isolate had a highly distinct RC-PFGE and repetitive sequence PCR profile. Statistical analysis of the data identified biogeographic trends consistent with conclusions drawn from previous studies on the origin and worldwide dissemination of race 3 biovar II isolates; however, genomic fingerprinting by RC-PFGE revealed a level of genetic diversity previously unrealized.
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Affiliation(s)
- J J Smith
- International Mycological Institute, Egham, Surrey, United Kingdom
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24
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Selenska-Pobell S, Gigova L, Petrova N. Strain-specific fingerprints of Rhizobium galegae generated by PCR with arbitrary and repetitive primers. THE JOURNAL OF APPLIED BACTERIOLOGY 1995; 79:425-31. [PMID: 7592135 DOI: 10.1111/j.1365-2672.1995.tb03157.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Strain-specific genomic patterns of Rhizobium galegae were generated by PCR using both arbitrary and repetitive (BOX, ERIC and REP) primers. The identification of the strains was achieved also by RFLP analysis. However, the PCR genomic fingerprinting has significant advantages: it is not only simpler and faster, but it is also much more discriminative because it deals with the full bacterial genome and not only with parts of it as is the case with RFLP. In addition, both kinds of PCR fingerprinting (using arbitrary or repetitive primers) generated highly specific and reproducible patterns when parallel reactions with total bacterial DNA, extracted from independent liquid cultures were performed. The latter shows that AP- and rep-PCR are convenient for controlling the production and application of Rhizobium inoculants.
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25
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Selenska-Pobell S, Evguenieva-Hackenberg E, Schwickerath O. Random and Repetitive Primer Amplified Polymorphic DNA Analysis of Five Soil and Two Clinical Isolates of Rahnella aquatilis. Syst Appl Microbiol 1995. [DOI: 10.1016/s0723-2020(11)80435-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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