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Sun H, Miao Z, Liu S, Liu X, Chen B, Liao B, Xiao B. Neorhizobium turbinariae sp. nov., a coral-beneficial bacterium isolated from Turbinaria peltata. Int J Syst Evol Microbiol 2023; 73. [PMID: 37750757 DOI: 10.1099/ijsem.0.006057] [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] [Indexed: 09/27/2023] Open
Abstract
Coral reef ecosystems are facing decline due to climate change, overfishing, habitat destruction and pollution. Bacteria play an essential role in maintaining the stability of coral reef ecosystems, influencing the well-being and fitness of coral hosts. The exploitation of coral probiotics has become an urgent issue. A short-rod shaped aerobic bacterium, designated NTR19T, was isolated in a healthy coral Turbinaria peltata from Daya Bay, Shenzhen, PR China. Its cells were Gram-negative, motile with a polar flagellum. The activities of catalase and oxidase were positive. Strain NTR19T grew at 10-41 °C (optimum, 28 °C), with NaCl concentrations of 0-4 % (w/v; optimum, 0.5 %) and at pH 5.0-9.5 (optimum, pH 7.0-7.5). The predominant fatty acids (>10 %) were summed feature 8 (57.6 %), C19 : 0 cyclo ω8c (12.6 %) and C16 : 0 (12.0 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phospholipid and phosphatidylcholine. The major respiratory quinone was Q-10. The draft genome was 4.68 Mbp with 61.2 mol% DNA G+C content. In total, 4477 coding sequences were annotated and there were 64 RNA genes. The average nucleotide identity (ANI) and average amino acid identity (AAI) values between strain NTR19T and the related Neorhizobium species were 78.23-79.70% and 80.26-80.50 %, respectively. This strain encoded many proteins for the activities of catalase and oxidase in the genome. Strain NTR19T was clearly distinct from its closest neighbours Rhizobium oryzicola ACCC 05753T and Neorhizobium petrolearium ACCC 11238T with the 16S rRNA gene sequence similarity values of 96.86 and 96.36 %, respectively. The results of phylogenetic analysis, as well as ANI and AAI values, revealed that strain NTR19T belongs to Neorhizobium and was distinct from other species of this genus. The physiological, biochemical and chemotaxonomic characteristics also supported the species novelty of strain NTR19T. Thus, strain NTR19T is considered to be classified as a novel species in the genus Neorhizobium, for which the name Neorhizobium turbinariae sp. nov. is proposed. The type strain is NTR19T (=JCM 35342T=MCCC 1K07226T).
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Affiliation(s)
- Hao Sun
- School of Ocean, Yantai University, Yantai, 264005, PR China
| | - Zhiyuan Miao
- Shenzhen Institute of Guangdong Ocean University, Binhai 2 Road, Shenzhen, 518120, PR China
| | - Shuai Liu
- School of Ocean, Yantai University, Yantai, 264005, PR China
| | - Xuerui Liu
- School of Ocean, Yantai University, Yantai, 264005, PR China
| | - Bogui Chen
- Shenzhen Institute of Guangdong Ocean University, Binhai 2 Road, Shenzhen, 518120, PR China
| | - Baolin Liao
- Shenzhen Institute of Guangdong Ocean University, Binhai 2 Road, Shenzhen, 518120, PR China
| | - Baohua Xiao
- Shenzhen Institute of Guangdong Ocean University, Binhai 2 Road, Shenzhen, 518120, PR China
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, PR China
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Volpiano CG, Sant'Anna FH, Ambrosini A, de São José JFB, Beneduzi A, Whitman WB, de Souza EM, Lisboa BB, Vargas LK, Passaglia LMP. Genomic Metrics Applied to Rhizobiales ( Hyphomicrobiales): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains. Front Microbiol 2021; 12:614957. [PMID: 33841347 PMCID: PMC8026895 DOI: 10.3389/fmicb.2021.614957] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/04/2021] [Indexed: 12/13/2022] Open
Abstract
Taxonomic decisions within the order Rhizobiales have relied heavily on the interpretations of highly conserved 16S rRNA sequences and DNA–DNA hybridizations (DDH). Currently, bacterial species are defined as including strains that present 95–96% of average nucleotide identity (ANI) and 70% of digital DDH (dDDH). Thus, ANI values from 520 genome sequences of type strains from species of Rhizobiales order were computed. From the resulting 270,400 comparisons, a ≥95% cut-off was used to extract high identity genome clusters through enumerating maximal cliques. Coupling this graph-based approach with dDDH from clusters of interest, it was found that: (i) there are synonymy between Aminobacter lissarensis and Aminobacter carboxidus, Aurantimonas manganoxydans and Aurantimonas coralicida, “Bartonella mastomydis,” and Bartonella elizabethae, Chelativorans oligotrophicus, and Chelativorans multitrophicus, Rhizobium azibense, and Rhizobium gallicum, Rhizobium fabae, and Rhizobium pisi, and Rhodoplanes piscinae and Rhodoplanes serenus; (ii) Chelatobacter heintzii is not a synonym of Aminobacter aminovorans; (iii) “Bartonella vinsonii” subsp. arupensis and “B. vinsonii” subsp. berkhoffii represent members of different species; (iv) the genome accessions GCF_003024615.1 (“Mesorhizobium loti LMG 6125T”), GCF_003024595.1 (“Mesorhizobium plurifarium LMG 11892T”), GCF_003096615.1 (“Methylobacterium organophilum DSM 760T”), and GCF_000373025.1 (“R. gallicum R-602 spT”) are not from the genuine type strains used for the respective species descriptions; and v) “Xanthobacter autotrophicus” Py2 and “Aminobacter aminovorans” KCTC 2477T represent cases of misuse of the term “type strain”. Aminobacter heintzii comb. nov. and the reclassification of Aminobacter ciceronei as A. heintzii is also proposed. To facilitate the downstream analysis of large ANI matrices, we introduce here ProKlust (“Prokaryotic Clusters”), an R package that uses a graph-based approach to obtain, filter, and visualize clusters on identity/similarity matrices, with settable cut-off points and the possibility of multiple matrices entries.
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Affiliation(s)
- Camila Gazolla Volpiano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Fernando Hayashi Sant'Anna
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Adriana Ambrosini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Anelise Beneduzi
- Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria Estadual da Agricultura, Pecuária e Desenvolvimento Rural, Porto Alegre, Brazil
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA, United States
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Centro Politécnico, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Bruno Brito Lisboa
- Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria Estadual da Agricultura, Pecuária e Desenvolvimento Rural, Porto Alegre, Brazil
| | - Luciano Kayser Vargas
- Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria Estadual da Agricultura, Pecuária e Desenvolvimento Rural, Porto Alegre, Brazil
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Neorhizobium lilium sp. nov., an endophytic bacterium isolated from Lilium pumilum bulbs in Hebei province. Arch Microbiol 2019; 202:609-616. [PMID: 31768560 DOI: 10.1007/s00203-019-01774-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/13/2019] [Accepted: 11/13/2019] [Indexed: 10/25/2022]
Abstract
A novel gram-negative, aerobic, non-spore-forming, rod-shaped and non-nitrogen fixing bacterium named strain 24NRT was isolated from wild Lilium pumilum bulbs in Fuping, Baoding City, Hebei province, PR China. The 16S rRNA gene sequences of strains 24NRT showed the highest similarity to Neorhizobium alkalisoli DSM 21826T (98.5%) and N. galegae HAMBI 540T (98.1%). Phylogenetic analysis based on 16S rRNA genes and multilocus sequence analysis (MLSA) based on the partial sequences of atpD-glnII-glnA-recA-ropD-thrC housekeeping genes both indicated that strain 24NRT is a member of the genus Neorhizobium. The average nucleotide identity between the genome sequence of strain 24NRT and that of the isolate N. alkalisoli DSM 21826T was 83.1%, and the digital DNA-DNA hybridization was 20.1%. The G+C content of strain 24NRT was 60.3 mol %. The major cellular fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C19:0 cyclo ω8c. Based on phenotypic, phylogenetic, and genotypic data, strain 24NRT is considered to represent a novel species of the genus Neorhizobium, for which the name Neorhizobium lilium sp. nov. is proposed. The type strain is 24NRT (= ACCC 61588T = JCM 33731T).
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Krishnan HB, Oehrle NW, Alaswad AA, Stevens WG, Maria John KM, Luthria DL, Natarajan SS. Biochemical and Anatomical Investigation of Sesbania herbacea (Mill.) McVaugh Nodules Grown under Flooded and Non-Flooded Conditions. Int J Mol Sci 2019; 20:E1824. [PMID: 31013805 PMCID: PMC6514687 DOI: 10.3390/ijms20081824] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 01/26/2023] Open
Abstract
Sesbania herbacea, a native North American fast-growing legume, thrives in wet and waterlogged conditions. This legume enters into symbiotic association with rhizobia, resulting in the formation of nitrogen-fixing nodules on the roots. A flooding-induced anaerobic environment imposes a challenge for the survival of rhizobia and negatively impacts nodulation. Very little information is available on how S. herbacea is able to thrive and efficiently fix N2 in flooded conditions. In this study, we found that Sesbania plants grown under flooded conditions were significantly taller, produced more biomass, and formed more nodules when compared to plants grown on dry land. Transmission electron microscopy of Sesbania nodules revealed bacteroids from flooded nodules contained prominent polyhydroxybutyrate crystals, which were absent in non-flooded nodules. Gas and ion chromatography mass spectrometry analysis of nodule metabolites revealed a marked decrease in asparagine and an increase in the levels of gamma aminobutyric acid in flooded nodules. 2-D gel electrophoresis of nodule bacteroid proteins revealed flooding-induced changes in their protein profiles. Several of the bacteroid proteins that were prominent in flooded nodules were identified by mass spectrometry to be members of the ABC transporter family. The activities of several key enzymes involved in nitrogen metabolism was altered in Sesbania flooded nodules. Aspartate aminotransferase (AspAT), an enzyme with a vital role in the assimilation of reduced nitrogen, was dramatically elevated in flooded nodules. The results of our study highlight the potential of S. herbacea as a green manure and sheds light on the morphological, structural, and biochemical adaptations that enable S. herbacea to thrive and efficiently fix N2 in flooded conditions.
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Affiliation(s)
- Hari B Krishnan
- Plant Genetics Research Unit, USDA-ARS, Columbia, MO 65211, USA.
- Plant Science Division, University of Missouri, Columbia, MO 65211, USA.
| | - Nathan W Oehrle
- Plant Genetics Research Unit, USDA-ARS, Columbia, MO 65211, USA.
| | - Alaa A Alaswad
- Plant Science Division, University of Missouri, Columbia, MO 65211, USA.
| | - William Gene Stevens
- Plant Science Division, University of Missouri, Delta Center, Portageville, MO 63873, USA.
| | - K M Maria John
- Food Composition and Methods Development Laboratory, BHNRC, USDA-ARS, Beltsville, MD 20705, USA.
| | - Devanand L Luthria
- Food Composition and Methods Development Laboratory, BHNRC, USDA-ARS, Beltsville, MD 20705, USA.
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Haryono M, Tsai YM, Lin CT, Huang FC, Ye YC, Deng WL, Hwang HH, Kuo CH. Presence of an Agrobacterium-Type Tumor-Inducing Plasmid in Neorhizobium sp. NCHU2750 and the Link to Phytopathogenicity. Genome Biol Evol 2018; 10:3188-3195. [PMID: 30398651 PMCID: PMC6286910 DOI: 10.1093/gbe/evy249] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2018] [Indexed: 12/02/2022] Open
Abstract
The genus Agrobacterium contains a group of plant-pathogenic bacteria that have been developed into an important tool for genetic transformation of eukaryotes. To further improve this biotechnology application, a better understanding of the natural genetic variation is critical. During the process of isolation and characterization of wild-type strains, we found a novel strain (i.e., NCHU2750) that resembles Agrobacterium phenotypically but exhibits high sequence divergence in several marker genes. For more comprehensive characterization of this strain, we determined its complete genome sequence for comparative analysis and performed pathogenicity assays on plants. The results demonstrated that this strain is closely related to Neorhizobium in chromosomal organization, gene content, and molecular phylogeny. However, unlike the characterized species within Neorhizobium, which all form root nodules with legume hosts and are potentially nitrogen-fixing mutualists, NCHU2750 is a gall-forming pathogen capable of infecting plant hosts across multiple families. Intriguingly, this pathogenicity phenotype could be attributed to the presence of an Agrobacterium-type tumor-inducing plasmid in the genome of NCHU2750. These findings suggest that these different lineages within the family Rhizobiaceae are capable of transitioning between ecological niches by having novel combinations of replicons. In summary, this work expanded the genomic resources available within Rhizobiaceae and provided a strong foundation for future studies of this novel lineage. With an infectivity profile that is different from several representative Agrobacterium strains, this strain may be useful for comparative analysis to better investigate the genetic determinants of host range among these bacteria.
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Affiliation(s)
- Mindia Haryono
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Ming Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chien-Ting Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Fan-Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, Taiwan
| | - Yan-Chen Ye
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Wen-Ling Deng
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| | - Hau-Hsuan Hwang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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Suleiman MK, Dixon K, Commander L, Nevill P, Quoreshi AM, Bhat NR, Manuvel AJ, Sivadasan MT. Evaluating the diversity and composition of bacterial communities associated with Vachellia pachyceras - the only existing native tree species in the Kuwait desert. Can J Microbiol 2018; 65:235-251. [PMID: 30495976 DOI: 10.1139/cjm-2018-0421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We investigated the diversity and composition of bacterial communities in rhizospheric and non-rhizospheric bulk soils as well as root nodule bacterial communities of Vachellia pachyceras - the only native tree species existing in the Kuwait desert. Community fingerprinting comparisons and 16S rDNA sequence identifications were used for characterization of the bacterial population using specific primers. The bacterial characterization of soil samples revealed four major phyla: Acidobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. In situ (desert) samples of both rhizospheric and non-rhizospheric bulk soil were dominated by the bacterial phyla Firmicutes and Bacteroidetes, whereas the phylum Betaproteobacteria was present only in non-rhizospheric bulk soil. Ex situ (nursery growing condition) V. pachyceras resulted in restricted bacterial communities dominated by members of a single phylum, Bacteroidetes. Results indicated that the soil organic matter and rhizospheric environments might drive the bacterial community. Despite harsh climatic conditions, data demonstrated that V. pachyceras roots harbor endophytic bacterial populations. Our findings on bacterial community composition and structure have major significance for evaluating how Kuwait's extreme climatic conditions affect bacterial communities. The baseline data obtained in this study will be useful and assist in formulating strategies in ecological restoration programs, including the application of inoculation technologies.
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Affiliation(s)
- Majda K Suleiman
- a Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait
| | - Kingsley Dixon
- b Department of Environment and Agriculture, ARC Centre for Mine Site Restoration Curtin University, Bentley, WA 6102, Australia
| | - Lucy Commander
- c School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Paul Nevill
- d Department of Environment and Agriculture, Curtin University, Bentley, WA 6102, Australia
| | - Ali M Quoreshi
- a Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait
| | - Narayana R Bhat
- a Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait
| | - Anitha J Manuvel
- a Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait
| | - Mini T Sivadasan
- a Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait
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Soenens A, Gomila M, Imperial J. Neorhizobium tomejilense sp. nov., first non-symbiotic Neorhizobium species isolated from a dryland agricultural soil in southern Spain. Syst Appl Microbiol 2018; 42:128-134. [PMID: 30268635 DOI: 10.1016/j.syapm.2018.09.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/30/2018] [Accepted: 09/10/2018] [Indexed: 01/05/2023]
Abstract
We describe for the first time a non-symbiotic species of the recently described genus Neorhizobium, lacking nodulation or nitrogen fixation genes. The strains were isolated from a dryland agricultural soil in southern Spain where no record of legume cultivation is available, thus we propose the name Neorhizobium tomejilense sp. nov. (type strain T17_20T, LMG 30623T and CECT 9621T). N. tomejilense exhibit a clear distinct lineage from the other Neorhizobium species, Neorhizobium galegae, Neorhizobium alkalisoli and Neorhizobium huautlense, based on polyphasic evidence. Phylogenetic marker analysis of 16S rDNA, atpD, glnII, recA, rpoB and thrC genes and genomic identity data derived from the draft genomic sequences showed that N. tomejilense strains clearly separated from the other Neorhizobium species and that N. galegae represents the closest species, with Average Nucleotide Identities (ANIb) ranging from 90% (for type strain HAMBI 540T) to just under 95.0% (for two N. galegae sv. officinalis strains). Genomes from N. galegae and N. tomejilense, however, clearly differed in important traits, such as the number of rRNA operon copies or the number of tRNAs. Phenotypic characterisation of N. tomejilense also displayed differences with the other Neorhizobium species. Whole-cell matrix-assisted laser-desorption time-of-flight mass spectrometry (WC MALDI-TOF-MS) fingerprint analysis and the dendrogram derived from the fingerprint profiles, showed a clearly distinct group formed by the three N. tomejilense isolates (T17_20T, T20_22 and T11_12) from the other Neorhizobium especies.
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Affiliation(s)
- Amalia Soenens
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Margarita Gomila
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
| | - Juan Imperial
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, 28223 Pozuelo de Alarcón, Madrid, Spain; Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain.
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Soenens A, Imperial J. Novel, non-symbiotic isolates of Neorhizobium from a dryland agricultural soil. PeerJ 2018; 6:e4776. [PMID: 29785349 PMCID: PMC5960266 DOI: 10.7717/peerj.4776] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 04/25/2018] [Indexed: 12/21/2022] Open
Abstract
Semi-selective enrichment, followed by PCR screening, resulted in the successful direct isolation of fast-growing Rhizobia from a dryland agricultural soil. Over 50% of these isolates belong to the genus Neorhizobium, as concluded from partial rpoB and near-complete 16S rDNA sequence analysis. Further genotypic and genomic analysis of five representative isolates confirmed that they form a coherent group within Neorhizobium, closer to N. galegae than to the remaining Neorhizobium species, but clearly differentiated from the former, and constituting at least one new genomospecies within Neorhizobium. All the isolates lacked nod and nif symbiotic genes but contained a repABC replication/maintenance region, characteristic of rhizobial plasmids, within large contigs from their draft genome sequences. These repABC sequences were related, but not identical, to repABC sequences found in symbiotic plasmids from N. galegae, suggesting that the non-symbiotic isolates have the potential to harbor symbiotic plasmids. This is the first report of non-symbiotic members of Neorhizobium from soil.
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Affiliation(s)
- Amalia Soenens
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, Madrid, Spain
| | - Juan Imperial
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, Madrid, Spain.,Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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Kang W, Shi S, Xu L. Diversity and symbiotic divergence of endophytic and non-endophytic rhizobia of Medicago sativa. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1333-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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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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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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12
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Tena W, Wolde-Meskel E, Degefu T, Walley F. Genetic and phenotypic diversity of rhizobia nodulating chickpea (Cicer arietinum L.) in soils from southern and central Ethiopia. Can J Microbiol 2017; 63:690-707. [PMID: 28499096 DOI: 10.1139/cjm-2016-0776] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Forty-two chickpea-nodulating rhizobia were isolated from soil samples collected from diverse agro-ecological locations of Ethiopia and were characterized on the basis of 76 phenotypic traits. Furthermore, 18 representative strains were selected and characterized using multilocus sequence analyses of core and symbiotic gene loci. Numerical analysis of the phenotypic characteristics grouped the 42 strains into 4 distinct clusters. The analysis of the 16S rRNA gene of the 18 strains showed that they belong to the Mesorhizobium genus. On the basis of the phylogenetic tree constructed from the combined genes sequences (recA, atpD, glnII, and gyrB), the test strains were distributed into 4 genospecies (designated as genospecies I-IV). Genospecies I, II, and III could be classified with Mesorhizobium ciceri, Mesorhizobium abyssinicae, and Mesorhizobium shonense, respectively, while genospecies IV might represent an unnamed Mesorhizobium genospecies. Phylogenetic reconstruction based on the symbiosis-related (nifH and nodA) genes supported a single cluster together with a previously described symbiont of chickpea (M. ciceri and Mesorhizobium mediterraneum). Overall, our results corroborate earlier findings that Ethiopian soils harbor phylogenetically diverse Mesorhizobium species, justifying further explorative studies. The observed differences in symbiotic effectiveness indicated the potential to select effective strains for use as inoculants and to improve the productivity of chickpea in the country.
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Affiliation(s)
- Wondwosen Tena
- a Department of Plant Science, Debre Berhan University, P.O. Box 445, Debre Berhan, Ethiopia
| | | | - Tulu Degefu
- c Department of Biology, Hawassa University, P.O. Box 05, Hawassa, Ethiopia
| | - Fran Walley
- d Department of Soil Science, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
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13
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Andrews M, Andrews ME. Specificity in Legume-Rhizobia Symbioses. Int J Mol Sci 2017; 18:E705. [PMID: 28346361 PMCID: PMC5412291 DOI: 10.3390/ijms18040705] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 03/19/2017] [Accepted: 03/21/2017] [Indexed: 11/24/2022] Open
Abstract
Most species in the Leguminosae (legume family) can fix atmospheric nitrogen (N₂) via symbiotic bacteria (rhizobia) in root nodules. Here, the literature on legume-rhizobia symbioses in field soils was reviewed and genotypically characterised rhizobia related to the taxonomy of the legumes from which they were isolated. The Leguminosae was divided into three sub-families, the Caesalpinioideae, Mimosoideae and Papilionoideae. Bradyrhizobium spp. were the exclusive rhizobial symbionts of species in the Caesalpinioideae, but data are limited. Generally, a range of rhizobia genera nodulated legume species across the two Mimosoideae tribes Ingeae and Mimoseae, but Mimosa spp. show specificity towards Burkholderia in central and southern Brazil, Rhizobium/Ensifer in central Mexico and Cupriavidus in southern Uruguay. These specific symbioses are likely to be at least in part related to the relative occurrence of the potential symbionts in soils of the different regions. Generally, Papilionoideae species were promiscuous in relation to rhizobial symbionts, but specificity for rhizobial genus appears to hold at the tribe level for the Fabeae (Rhizobium), the genus level for Cytisus (Bradyrhizobium), Lupinus (Bradyrhizobium) and the New Zealand native Sophora spp. (Mesorhizobium) and species level for Cicer arietinum (Mesorhizobium), Listia bainesii (Methylobacterium) and Listia angolensis (Microvirga). Specificity for rhizobial species/symbiovar appears to hold for Galega officinalis (Neorhizobium galegeae sv. officinalis), Galega orientalis (Neorhizobium galegeae sv. orientalis), Hedysarum coronarium (Rhizobium sullae), Medicago laciniata (Ensifer meliloti sv. medicaginis), Medicago rigiduloides (Ensifer meliloti sv. rigiduloides) and Trifolium ambiguum (Rhizobium leguminosarum sv. trifolii). Lateral gene transfer of specific symbiosis genes within rhizobial genera is an important mechanism allowing legumes to form symbioses with rhizobia adapted to particular soils. Strain-specific legume rhizobia symbioses can develop in particular habitats.
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Affiliation(s)
- Mitchell Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, PO Box 84, Lincoln 7647, New Zealand.
| | - Morag E Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, PO Box 84, Lincoln 7647, New Zealand.
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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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15
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HANNANE FZ, KACEM M, KAID HARCHE M. Preliminary characterization of slow growing rhizobial strains isolated from Retama monosperma (L.) Boiss. root nodules from Northwest coast of Algeria. ACTA ACUST UNITED AC 2016. [DOI: 10.5897/ajb2016.15226] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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16
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Li Y, Li X, Liu Y, Wang ET, Ren C, Liu W, Xu H, Wu H, Jiang N, Li Y, Zhang X, Xie Z. Genetic diversity and community structure of rhizobia nodulating Sesbania cannabina in saline-alkaline soils. Syst Appl Microbiol 2016; 39:195-202. [PMID: 27061259 DOI: 10.1016/j.syapm.2016.02.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 02/26/2016] [Accepted: 02/28/2016] [Indexed: 11/16/2022]
Abstract
Sesbania cannabina is a plant that grows naturally along the seashores in Rudong County, China (RDC) and it has been introduced into the Yellow River Delta (YRD) as a pioneer plant to improve the saline-alkaline soils. In order to investigate the diversity of S. cannabina rhizobia in these soils, a total of 198 rhizobial isolates were characterized and phylogenetic trees were constructed based on data from multilocus sequence analysis (MLSA) of the housekeeping genes recA, atpD and glnII, as well as 16S rRNA. Symbiotic features were also studied by establishing the phylogeny of the symbiotic genes nodA and nifH, and by performing nodulation assays. The isolates had highly conserved symbiotic genes and were classified into nine genospecies belonging to the genera Ensifer, Agrobacterium, Neorhizobium and Rhizobium. A unique community structure was detected in the rhizobia associated with S. cannabina in the saline-alkaline soils that was characterized by five novel genospecies and four defined species. In addition, Ensifer sp. I was the predominant rhizobia in YRD, whereas Ensifer meliloti and Neorhizobium huautlense were the dominant species in RDC. Therefore, the study demonstrated for the first time that this plant strongly selected the symbiotic gene background but not the genomic background of its microsymbionts. In addition, biogeographic patterns existed in the rhizobial populations associated with S. cannabina, which were mainly correlated with pH and salinity, as well as the mineral nutrient contents. This study provided novel information concerning the interaction between soil conditions, host plant and rhizobia, in addition to revealing the diversity of S. cannabina rhizobia in saline-alkaline soils.
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Affiliation(s)
- Yan Li
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, China
| | - Xiangyue Li
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, China
| | - Yajing Liu
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 Mexico City, D.F., Mexico
| | - Chenggang Ren
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, China
| | - Wei Liu
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, China
| | - Hualing Xu
- Dongying Institute of Agriculture Sciences, 257000 Dongying, China
| | - Hailong Wu
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, China
| | - Nan Jiang
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, China
| | - Yunzhao Li
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, China
| | - Xiaoli Zhang
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, China
| | - Zhihong Xie
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, China.
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17
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Naamala J, Jaiswal SK, Dakora FD. Antibiotics Resistance in Rhizobium: Type, Process, Mechanism and Benefit for Agriculture. Curr Microbiol 2016; 72:804-16. [DOI: 10.1007/s00284-016-1005-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/07/2016] [Indexed: 11/29/2022]
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18
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Korenblum E, Jiménez DJ, van Elsas JD. Succession of lignocellulolytic bacterial consortia bred anaerobically from lake sediment. Microb Biotechnol 2016; 9:224-34. [PMID: 26875750 PMCID: PMC4767288 DOI: 10.1111/1751-7915.12338] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Revised: 10/23/2015] [Accepted: 11/08/2015] [Indexed: 11/28/2022] Open
Abstract
Anaerobic bacteria degrade lignocellulose in various anoxic and organically rich environments, often in a syntrophic process. Anaerobic enrichments of bacterial communities on a recalcitrant lignocellulose source were studied combining polymerase chain reaction-denaturing gradient gel electrophoresis, amplicon sequencing of the 16S rRNA gene and culturing. Three consortia were constructed using the microbiota of lake sediment as the starting inoculum and untreated switchgrass (Panicum virgatum) (acid or heat) or treated (with either acid or heat) as the sole source of carbonaceous compounds. Additionally, nitrate was used in order to limit sulfate reduction and methanogenesis. Bacterial growth took place, as evidenced from 3 to 4 log unit increases in the 16S rRNA gene copy numbers as well as direct cell counts through three transfers on cleaned and reused substrate placed in fresh mineral medium. After 2 days, Aeromonas bestiarum-like organisms dominated the enrichments, irrespective of the substrate type. One month later, each substrate revealed major enrichments of organisms affiliated with different species of Clostridium. Moreover, only the heat-treated substrate selected Dysgonomonas capnocytophagoides-affiliated bacteria (Bacteroidetes). Towards the end of the experiment, members of the Proteobacteria (Aeromonas, Rhizobium and/or Serratia) became dominant in all three types of substrates. A total of 160 strains was isolated from the enrichments. Most of the strains tested (78%) were able to grow anaerobically on carboxymethyl cellulose and xylan. The final consortia yield attractive biological tools for the depolymerization of recalcitrant lignocellulosic materials and are proposed for the production of precursors of biofuels.
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Affiliation(s)
- Elisa Korenblum
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Diego Javier Jiménez
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
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19
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Miranda-Sánchez F, Rivera J, Vinuesa P. Diversity patterns ofRhizobiaceaecommunities inhabiting soils, root surfaces and nodules reveal a strong selection of rhizobial partners by legumes. Environ Microbiol 2015; 18:2375-91. [DOI: 10.1111/1462-2920.13061] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 09/17/2015] [Indexed: 10/23/2022]
Affiliation(s)
- Fabiola Miranda-Sánchez
- Programa de Ingeniería Genómica; Centro de Ciencias Genómicas; Universidad Nacional Autónoma de México; Cuernavaca Morelos 62210 Mexico
| | - Javier Rivera
- Programa de Ingeniería Genómica; Centro de Ciencias Genómicas; Universidad Nacional Autónoma de México; Cuernavaca Morelos 62210 Mexico
| | - Pablo Vinuesa
- Programa de Ingeniería Genómica; Centro de Ciencias Genómicas; Universidad Nacional Autónoma de México; Cuernavaca Morelos 62210 Mexico
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20
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The diversity of rhizobia nodulating the Medicago, Melilotus and Trigonella inoculation group in Egypt is marked by the dominance of two genetic types. Symbiosis 2015. [DOI: 10.1007/s13199-015-0365-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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21
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Lin SY, Hung MH, Hameed A, Liu YC, Hsu YH, Wen CZ, Arun AB, Busse HJ, Glaeser SP, Kämpfer P, Young CC. Rhizobium capsici sp. nov., isolated from root tumor of a green bell pepper (Capsicum annuum var. grossum) plant. Antonie van Leeuwenhoek 2015; 107:773-84. [PMID: 25555455 DOI: 10.1007/s10482-014-0371-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 12/23/2014] [Indexed: 10/24/2022]
Abstract
A novel, Gram-staining-negative, rod-shaped, aerobic and motile bacterium, designated strain CC-SKC2(T), was isolated from the root tumor of a green bell pepper (Capsicum annuum var. grossum) plant in Taiwan. Cells were positive for oxidase and catalase activities and exhibited growth at 25-37 °C, pH 4.0-9.0 and tolerated NaCl concentrations up to 4.0 % (w/v). Strain CC-SKC2(T) is able to trigger nodulation in soybean (Glycine max Merr.), but not in Capsicum annuum var. grossum, red bean (Vigna angularis), sesbania (Sesbania roxburghii Merr.) or alfalfa (Medicago varia Martin.). The novel strain shared highest 16S rRNA gene sequence similarity to Rhizobium rhizoryzae KCTC 23652(T) and Rhizobium straminoryzae CC-LY845(T) (both 97.5 %) followed by Rhizobium lemnae L6-16(T) (97.3 %), Rhizobium pseudoryzae KCTC 23294(T) (97.1 %), and Rhizobium paknamense NBRC 109338(T) (97.0 %), whereas other Rhizobium species shared <96.7 % similarity. The DNA-DNA relatedness values of strain CC-SKC2(T) with R. rhizoryzae KCTC 23652(T), R. pseudoryzae KCTC 23294(T) and R. paknamense NBRC 109338(T) were 11.4, 17.2 and 17.0 %, respectively (reciprocal values were 11.1, 28.3 and 24.0 %, respectively). Phylogenetic analysis based on 16S rRNA, atpD and recA genes revealed a distinct taxonomic position attained by strain CC-SKC2(T) with respect to other Rhizobium species. The major fatty acids in strain CC-SKC2(T) were C16:0, C19:0 cyclo ω8c, C14:0 3-OH and/or C16:1 iso I and C18:1 ω7c and/or C18:1 ω6c. The polyamine pattern showed predominance of spermidine and moderate amounts of sym-homospermidine. The predominant quinone system was ubiquinone (Q-10) and the DNA G+C content was 60.5 mol%. On the basis of polyphasic taxonomic evidence presented here, strain CC-SKC2(T) is proposed to represent a novel species within the genus Rhizobium, for which the name Rhizobium capsici sp. nov. is proposed. The type strain is CC-SKC2(T) (=BCRC 80699(T) = JCM 19535(T)).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 250, Kuo Kuang Rd., Taichung, 402, Taiwan
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22
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Chen W, Sheng XF, He LY, Huang Z. Rhizobium yantingense sp. nov., a mineral-weathering bacterium. Int J Syst Evol Microbiol 2014; 65:412-417. [PMID: 25376852 DOI: 10.1099/ijs.0.064428-0] [Citation(s) in RCA: 24] [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 Gram-stain-negative, rod-shaped bacterial strain, H66(T), was isolated from the surfaces of weathered rock (purple siltstone) found in Yanting, Sichuan Province, PR China. Cells of strain H66(T) were motile with peritrichous flagella. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain H66(T) belongs to the genus Rhizobium. It is closely related to Rhizobium huautlense SO2(T) (98.1 %), Rhizobium alkalisoli CCBAU 01393(T) (98.0 %) and Rhizobium cellulosilyticum ALA10B2(T) (98.0 %). Analysis of the housekeeping genes, recA, glnII and atpD, showed low levels of sequence similarity (<92.0 %) between strain H66(T) and other recognized species of the genus Rhizobium. The predominant components of the cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The G+C content of strain H66(T) was 60.3 mol%. Strain H66(T) is suggested to be a novel species of the genus Rhizobium based on the low levels of DNA-DNA relatedness (ranging from 14.3 % to 40.0 %) with type strains of species of the genus Rhizobium and on its unique phenotypic characteristics. The namehttp://dx.doi.org/10.1601/nm.1279Rhizobium yantingense sp. nov. is proposed for this novel species. The type strain is H66(T) ( = CCTCC AB 2014007(T) = LMG 28229(T)).
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Affiliation(s)
- Wei Chen
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xia-Fang Sheng
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Lin-Yan He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Zhi Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
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23
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Zhang L, Shi X, Si M, Li C, Zhu L, Zhao L, Shen X, Wang Y. Rhizobium smilacinae sp. nov., an endophytic bacterium isolated from the leaf of Smilacina japonica. Antonie van Leeuwenhoek 2014; 106:715-23. [DOI: 10.1007/s10482-014-0241-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 07/18/2014] [Indexed: 11/29/2022]
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24
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Rhizobium
paknamense sp. nov., isolated from lesser duckweeds (Lemna aequinoctialis). Int J Syst Evol Microbiol 2013; 63:3823-3828. [DOI: 10.1099/ijs.0.051888-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped bacterium was isolated and designated strain L6-8T during a study of endophytic bacterial communities in lesser duckweed (Lemna aequinoctialis). Cells of strain L6-8T were motile with peritrichous flagella. The analysis of the nearly complete 16S rRNA gene sequence indicated that strain L6-8T was phylogenetically related to species of the genus
Rhizobium
. Its closest relatives were
Rhizobium borbori
DN316T (97.6 %),
Rhizobium oryzae
Alt 505T (97.3 %) and
Rhizobium pseudoryzae
J3-A127T (97.0 %). The sequence similarity analysis of housekeeping genes recA, glnII, atpD and gyrB showed low levels of sequence similarity (<91.5 %) between strain L6-8T and other species of the genus
Rhizobium
with validly published names. The pH range for growth was 4.0–9.0 (optimum 6.0–7.0), and the temperature range for growth was 20–45 °C (optimum 30 °C). Strain L6-8T tolerated NaCl up to 2 % (w/v) (optimum 1 % NaCl). The predominant components of cellular fatty acids were C19 : 0 cyclo ω8c (31.32 %), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 25.39 %) and C16 : 0 (12.03 %). The DNA G+C content of strain L6-8T was 60.4 mol% (T
m). nodC and nifH were not amplified in strain L6-8T. DNA–DNA relatedness between strain L6-8T and
R. borbori
DN316T,
R. oryzae
Alt505T and
R. pseudoryzae
J3-A127T was between 11.2 and 18.3 %. Based on the sequence similarity analyses, phenotypic, biochemical and physiological characteristics and DNA–DNA hybridization, strain L6-8T could be readily distinguished from its closest relatives and represents a novel species of the genus
Rhizobium
, for which the name
Rhizobium
paknamense sp. nov. is proposed. The type strain is L6-8T ( = NBRC 109338T = BCC 55142T).
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Rhizobium pongamiae sp. nov. from root nodules of Pongamia pinnata. BIOMED RESEARCH INTERNATIONAL 2013; 2013:165198. [PMID: 24078904 PMCID: PMC3783817 DOI: 10.1155/2013/165198] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 06/06/2013] [Indexed: 11/17/2022]
Abstract
Pongamia pinnata has an added advantage of N2-fixing ability and tolerance to stress conditions as compared with other biodiesel crops. It harbours “rhizobia” as an endophytic bacterial community on its root nodules. A gram-negative, nonmotile, fast-growing, rod-shaped, bacterial strain VKLR-01T was isolated from root nodules of Pongamia that grew optimal at 28°C, pH 7.0 in presence of 2% NaCl. Isolate VKLR-01 exhibits higher tolerance to the prevailing adverse conditions, for example, salt stress, elevated temperatures and alkalinity. Strain VKLR-01T has the major cellular fatty acid as C18:1
ω7c (65.92%). Strain VKLR-01T was found to be a nitrogen fixer using the acetylene reduction assay and PCR detection of a nifH gene. On the basis of phenotypic, phylogenetic distinctiveness and molecular data (16S rRNA, recA, and atpD gene sequences, G + C content, DNA-DNA hybridization etc.), strain VKLR-01T = (MTCC 10513T = MSCL 1015T) is considered to represent a novel species of the genus Rhizobium for which the name Rhizobium pongamiae sp. nov. is proposed. Rhizobium pongamiae may possess specific traits that can be transferred to other rhizobia through biotechnological tools and can be directly used as inoculants for reclamation of wasteland; hence, they are very important from both economic and environmental prospects.
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26
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Gurkanli CT, Ozkoc I, Gunduz I. Genetic diversity of rhizobia nodulating common bean (Phaseolus vulgaris L.) in the Central Black Sea Region of Turkey. ANN MICROBIOL 2012. [DOI: 10.1007/s13213-012-0551-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Patel U, Sinha S. Rhizobia species: A Boon for "Plant Genetic Engineering". Indian J Microbiol 2012; 51:521-7. [PMID: 23024417 DOI: 10.1007/s12088-011-0149-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Accepted: 10/05/2009] [Indexed: 10/18/2022] Open
Abstract
Since past three decades new discoveries in plant genetic engineering have shown remarkable potentials for crop improvement. Agrobacterium Ti plasmid based DNA transfer is no longer the only efficient way of introducing agronomically important genes into plants. Recent studies have explored a novel plant genetic engineering tool, Rhizobia sp., as an alternative to Agrobacterium, thereby expanding the choice of bacterial species in agricultural plant biotechnology. Rhizobia sp. serve as an open license source with no major restrictions in plant biotechnology and help broaden the spectrum for plant biotechnologists with respect to the use of gene transfer vehicles in plants. New efficient transgenic plants can be produced by transferring genes of interest using binary vector carrying Rhizobia sp. Studies focusing on the interactions of Rhizobia sp. with their hosts, for stable and transient transformation and expression of genes, could help in the development of an adequate gene transfer vehicle. Along with being biologically beneficial, it may also bring a new means for fast economic development of transgenic plants, thus giving rise to a new era in plant biotechnology, viz. "Rhizobia mediated transformation technology."
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Affiliation(s)
- Urmi Patel
- Institute of Science, Nirma University, Sarkhej-Gandhinagar Highway, Ahmedabad, 382481 Gujarat India
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Genetic diversity of rhizobia nodulating lentil (Lens culinaris) in Bangladesh. Syst Appl Microbiol 2012; 35:98-109. [DOI: 10.1016/j.syapm.2011.11.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 11/17/2011] [Accepted: 11/20/2011] [Indexed: 11/23/2022]
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Yao LJ, Shen YY, Zhan JP, Xu W, Cui GL, Wei GH. Rhizobium taibaishanense sp. nov., isolated from a root nodule of Kummerowia striata. Int J Syst Evol Microbiol 2012; 62:335-341. [DOI: 10.1099/ijs.0.029108-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During a study of the diversity and phylogeny of rhizobia in the root nodules of Kummerowia striata grown in north-western China, four strains were classified in the genus Rhizobium on the basis of their 16S rRNA gene sequences. The 16S rRNA gene sequences of three of these strains were identical and that of the other strain, which was the only one isolated in Yangling, differed from the others by just 1 bp. The16S rRNA gene sequences of the four strains showed a mean similarity of 99.3 % with the most closely related, recognized species, Rhizobium vitis. The corresponding recA and glnA gene sequences showed similarities with established species of Rhizobium of less than 86.5 % and less than 89.6 %, respectively. These low similarities indicated that the four strains represented a novel species of the genus Rhizobium. The strains were also found to be distinguishable from the closest related, established species (R. vitis) by rep-PCR DNA fingerprinting, analysis of cellular fatty acid profiles and from the results of a series of phenotypic tests. The level of DNA–DNA relatedness between the representative strain CCNWSX 0483T and Rhizobium vitis IAM 14140T was only 40.13 %. Therefore, a novel species, Rhizobium taibaishanense sp. nov., is proposed, with strain CCNWSX 0483T ( = ACCC 14971T = HAMBI 3214T) as the type strain. In nodulation and pathogenicity tests, none of the four strains of Rhizobium taibaishanense sp. nov. was able to induce any nodule or tumour formation on plants. As no amplicons were detected when DNA from the strains was run in PCR with primers for the detection of nodA, nifH and virC gene sequences, the strains probably do not carry sym or vir genes.
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Affiliation(s)
- Li Juan Yao
- College of Life Sciences, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A & F University, Yangling Shaanxi 712100, PR China
| | - Yao Yao Shen
- College of Life Sciences, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A & F University, Yangling Shaanxi 712100, PR China
| | - Jun Peng Zhan
- College of Life Sciences, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A & F University, Yangling Shaanxi 712100, PR China
| | - Wei Xu
- College of Life Sciences, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A & F University, Yangling Shaanxi 712100, PR China
| | - Guang Ling Cui
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production and Construction Group, Alar Xinjiang 843300, PR China
- College of Life Sciences, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A & F University, Yangling Shaanxi 712100, PR China
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López-López A, Rogel-Hernández MA, Barois I, Ortiz Ceballos AI, Martínez J, Ormeño-Orrillo E, Martínez-Romero E. Rhizobium grahamii sp. nov., from nodules of Dalea leporina, Leucaena leucocephala and Clitoria ternatea, and Rhizobium mesoamericanum sp. nov., from nodules of Phaseolus vulgaris, siratro, cowpea and Mimosa pudica. Int J Syst Evol Microbiol 2011; 62:2264-2271. [PMID: 22081714 DOI: 10.1099/ijs.0.033555-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel related Rhizobium species, Rhizobium grahamii sp. nov. and Rhizobium mesoamericanum sp. nov., were identified by a polyphasic approach using DNA-DNA hybridization, whole-genome sequencing and phylogenetic and phenotypic characterization including nodulation of Leucaena leucocephala and Phaseolus vulgaris (bean). As similar bacteria were found in the Los Tuxtlas rainforest in Mexico and in Central America, we suggest the existence of a Mesoamerican microbiological corridor. The type strain of Rhizobium grahamii sp. nov. is CCGE 502(T) (= ATCC BAA-2124(T) = CFN 242(T) = Dal4(T) = HAMBI 3152(T)) and that of Rhizobium mesoamericanum sp. nov. is CCGE 501(T) (= ATCC BAA-2123(T) = HAMBI 3151(T) = CIP 110148(T) = 1847(T)).
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Affiliation(s)
- Aline López-López
- Centro de Ciencias Genómicas, UNAM, Chamilpa 62210, Cuernavaca, Morelos, Mexico
| | | | - Isabelle Barois
- Departamento de Biología de Suelos, Instituto de Ecología AC, AP 63, Veracruz 91000, Xalapa, Mexico
| | | | - Julio Martínez
- Centro de Ciencias Genómicas, UNAM, Chamilpa 62210, Cuernavaca, Morelos, Mexico
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31
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Zhang YM, Li Y, Chen WF, Wang ET, Tian CF, Li QQ, Zhang YZ, Sui XH, Chen WX. Biodiversity and biogeography of rhizobia associated with soybean plants grown in the North China Plain. Appl Environ Microbiol 2011; 77:6331-42. [PMID: 21784912 PMCID: PMC3187167 DOI: 10.1128/aem.00542-11] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 07/09/2011] [Indexed: 11/20/2022] Open
Abstract
As the putative center of origin for soybean and the second largest region of soybean production in China, the North China Plain covers temperate and subtropical regions with diverse soil characteristics. However, the soybean rhizobia in this plain have not been sufficiently studied. To investigate the biodiversity and biogeography of soybean rhizobia in this plain, a total of 309 isolates of symbiotic bacteria from the soybean nodules collected from 16 sampling sites were studied by molecular characterization. These isolates were classified into 10 genospecies belonging to the genera Sinorhizobium and Bradyrhizobium, including four novel groups, with S. fredii (68.28%) as the dominant group. The phylogeny of symbiotic genes nodC and nifH defined four lineages among the isolates associated with Sinorhizobium fredii, Bradyrhizobium elkanii, B. japonicum, and B. yuanmingense, demonstrating the different origins of symbiotic genes and their coevolution with the chromosome. The possible lateral transfer of symbiotic genes was detected in several cases. The association between soil factors (available N, P, and K and pH) and the distribution of genospecies suggest clear biogeographic patterns: Sinorhizobium spp. were superdominant in sampling sites with alkaline-saline soils, while Bradyrhizobium spp. were more abundant in neutral soils. This study clarified the biodiversity and biogeography of soybean rhizobia in the North China Plain.
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Affiliation(s)
- Yan Ming Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Ying Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Wen Feng Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México D.F., México
| | - Chang Fu Tian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Qin Qin Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Yun Zeng Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Xin Hua Sui
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Wen Xin Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
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Ferreira L, Sánchez-Juanes F, García-Fraile P, Rivas R, Mateos PF, Martínez-Molina E, González-Buitrago JM, Velázquez E. MALDI-TOF mass spectrometry is a fast and reliable platform for identification and ecological studies of species from family Rhizobiaceae. PLoS One 2011; 6:e20223. [PMID: 21655291 PMCID: PMC3105015 DOI: 10.1371/journal.pone.0020223] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 04/21/2011] [Indexed: 11/19/2022] Open
Abstract
Family Rhizobiaceae includes fast growing bacteria currently arranged into three genera, Rhizobium, Ensifer and Shinella, that contain pathogenic, symbiotic and saprophytic species. The identification of these species is not possible on the basis of physiological or biochemical traits and should be based on sequencing of several genes. Therefore alternative methods are necessary for rapid and reliable identification of members from family Rhizobiaceae. In this work we evaluated the suitability of Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) for this purpose. Firstly, we evaluated the capability of this methodology to differentiate among species of family Rhizobiaceae including those closely related and then we extended the database of MALDI Biotyper 2.0 including the type strains of 56 species from genera Rhizobium, Ensifer and Shinella. Secondly, we evaluated the identification potential of this methodology by using several strains isolated from different sources previously identified on the basis of their rrs, recA and atpD gene sequences. The 100% of these strains were correctly identified showing that MALDI-TOF MS is an excellent tool for identification of fast growing rhizobia applicable to large populations of isolates in ecological and taxonomic studies.
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Affiliation(s)
- Laura Ferreira
- Unidad de Investigación, Hospital Universitario de Salamanca, Salamanca, Spain
| | | | - Paula García-Fraile
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Raúl Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Pedro F. Mateos
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | | | - José Manuel González-Buitrago
- Unidad de Investigación, Hospital Universitario de Salamanca, Salamanca, Spain
- Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, Salamanca, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- * E-mail:
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López-López A, Rogel MA, Ormeño-Orrillo E, Martínez-Romero J, Martínez-Romero E. Phaseolus vulgaris seed-borne endophytic community with novel bacterial species such as Rhizobium endophyticum sp. nov. Syst Appl Microbiol 2010; 33:322-7. [DOI: 10.1016/j.syapm.2010.07.005] [Citation(s) in RCA: 144] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Revised: 06/25/2010] [Accepted: 07/01/2010] [Indexed: 11/17/2022]
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34
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Ren DW, Wang ET, Chen WF, Sui XH, Zhang XX, Liu HC, Chen WX. Rhizobium herbae sp. nov. and Rhizobium giardinii-related bacteria, minor microsymbionts of various wild legumes in China. Int J Syst Evol Microbiol 2010; 61:1912-1920. [PMID: 20833881 DOI: 10.1099/ijs.0.024943-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seven Rhizobium strains associated with various legume species grown in different geographical regions of China were defined into four genomic groups related to Rhizobium giardinii, based upon ribosomal intergenic spacer RFLP, phylogenies of 16S rRNA and housekeeping (atpD, recA and glnII) genes, and DNA relatedness. Three strains in group I were classified as R. giardinii, as they showed high gene sequence similarities (>97 %) and DNA relatedness (64.3-67.5 %) to R. giardinii H152(T). Groups II, III and IV differed from all defined Rhizobium species based upon the consensus of all analyses. As group II contained two strains that originated from two distinct populations, we propose this group as a novel species, Rhizobium herbae sp. nov., with strain CCBAU 83011(T) ( = LMG 25718(T) = HAMBI 3117(T)) as the type strain.
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Affiliation(s)
- Da Wei Ren
- State Key Laboratories for Agrobiotechnology/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.,State Key Laboratories for Agrobiotechnology/College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Wen Feng Chen
- State Key Laboratories for Agrobiotechnology/College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Xin Hua Sui
- State Key Laboratories for Agrobiotechnology/College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Xiao Xia Zhang
- Agricultural Culture Collection of China, Institute of Agricultural Resource and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 10081, PR China
| | - Hong Can Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Wen Xin Chen
- State Key Laboratories for Agrobiotechnology/College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
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35
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Han TX, Tian CF, Wang ET, Chen WX. Associations among rhizobial chromosomal background, nod genes, and host plants based on the analysis of symbiosis of indigenous rhizobia and wild legumes native to Xinjiang. MICROBIAL ECOLOGY 2010; 59:311-323. [PMID: 19730765 DOI: 10.1007/s00248-009-9577-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Accepted: 08/07/2009] [Indexed: 05/28/2023]
Abstract
The associations among rhizobia chromosomal background, nodulation genes, legume plants, and geographical regions are very attractive but still unclear. To address this question, we analyzed the interactions among rhizobia rDNA genotypes, nodC genotypes, legume genera, as well as geographical regions in the present study. Complex relationships were observed among them, which may be the genuine nature of their associations. The statistical analyses indicate that legume plant is the key factor shaping both rhizobia genetic and symbiotic diversity. In the most cases of our results, the nodC lineages are clearly associated with rhizobial genomic species, demonstrating that nodulation genes have co-evolved with chromosomal background, though the lateral transfer of nodulation genes occurred in some cases in a minority. Our results also support the hypothesis that the endemic rhizobial populations to a certain geographical area prefer to have a wide spectrum of hosts, which might be an important event for the success of both legumes and rhizobia in an isolated region.
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Affiliation(s)
- Tian Xu Han
- State Key Laboratory of Agrobiotechnology, 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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36
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López-López A, Rosenblueth M, Martínez J, Martínez-Romero E. Rhizobial Symbioses in Tropical Legumes and Non-Legumes. SOIL BIOLOGY 2010. [DOI: 10.1007/978-3-642-05076-3_8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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37
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Shen L, Zheng LP, Liu H, Liu R, Zhang KY, Lai R. Rhizobium kunmingense sp. nov., isolated from rhizosphere soil of Camptotheca acuminata Decne. J GEN APPL MICROBIOL 2010; 56:143-9. [DOI: 10.2323/jgam.56.143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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38
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Rivas R, García-Fraile P, Velázquez E. Taxonomy of Bacteria Nodulating Legumes. Microbiol Insights 2009. [DOI: 10.4137/mbi.s3137] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Over the years, the term “rhizobia” has come to be used for all the bacteria that are capable of nodulation and nitrogen fixation in association with legumes but the taxonomy of rhizobia has changed considerably over the last 30 year. Recently, several non-rhizobial species belonging to alpha and beta subgroup of Proteobacteria have been identified as nitrogen-fixing legume symbionts. Here we provide an overview of the history of the rhizobia and the widespread phylogenetic diversity of nitrogen-fixing legume symbionts.
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Affiliation(s)
- Raúl Rivas
- Departamento de Microbiología y Genética, Laboratorio 209, Edificio Departamental de Biología, Doctores de la Reina s/n, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Paula García-Fraile
- Departamento de Microbiología y Genética, Laboratorio 209, Edificio Departamental de Biología, Doctores de la Reina s/n, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genética, Laboratorio 209, Edificio Departamental de Biología, Doctores de la Reina s/n, Universidad de Salamanca, 37007 Salamanca, Spain
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Elbanna K, Elbadry M, Gamal-Eldin H. Genotypic and phenotypic characterization of rhizobia that nodulate snap bean (Phaseolus vulgaris L.) in Egyptian soils. Syst Appl Microbiol 2009; 32:522-30. [PMID: 19682816 DOI: 10.1016/j.syapm.2009.07.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Indexed: 11/16/2022]
Abstract
Snap bean fields in 12 of the 25 governorates of Egypt were surveyed to determine the distribution and taxonomy of snap bean-nodulating rhizobia. Nodulation rates in the field were very low, indicating that Egyptian soils do not have sufficient numbers of snap bean-compatible Rhizobium spp. A total of 87 rhizobial isolates were assayed on the most commonly grown cultivars in order to identify the most effective strains. The five most effective isolates (R11, R13, R28, R49 and R52) were fast-growing and utilized a wide range of carbon and nitrogen sources. A phylogenetic assignment of these strains by analysis of the 16S ribosomal RNA gene suggested that all fell within the Rhizobium etli-Rhizobium leguminosarum group. Strains R11, R49 and R52 all clustered with other identified R. etli strains, while strains R13 and R28 were more distinct. The distinctness of R13 and R28 was supported by physiological characteristics, such as their ability to utilize citrate, erythritol, dulcitol and lactate. Strains R13 and R28 also yielded the highest plant nitrogen content of all isolates. The highly effective strains isolated in this study, in particular strains R13 and R28, are promising candidates for improving crop yields. The data also suggested that these two strains represented a novel sub-group within the R. etli-R. leguminosarum group. As snap bean is a crop of great economic value to Egypt, the identification of highly effective rhizobial strains adapted to Egyptian soils, such as strains R13 and R28, is of great interest.
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Affiliation(s)
- Khaled Elbanna
- Department of Agricultural Microbiology, Faculty of Agriculture, Fayoum University, Egypt.
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Yoon JH, Kang SJ, Yi HS, Oh TK, Ryu CM. Rhizobium soli sp. nov., isolated from soil. Int J Syst Evol Microbiol 2009; 60:1387-1393. [PMID: 19671727 DOI: 10.1099/ijs.0.013094-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, non-motile, pale-yellow, rod-shaped bacterial strain, DS-42(T), was isolated from a soil in Korea and its taxonomic position was investigated by a polyphasic study. Strain DS-42(T) grew optimally at 25 degrees C and pH 7.0-8.0. Strain DS-42(T) did not form nodules on three different legumes, and the nodD and nifH genes were also not detected by PCR. Strain DS-42(T) contained Q-10 as the predominant ubiquinone. The major cellular fatty acid was C(18 : 1)omega7c. The DNA G+C content was 60.8 mol%. Phylogenetic analyses based on 16S rRNA, atpD and recA gene sequences showed that strain DS-42(T) belonged to the genus Rhizobium. Strain DS-42(T) showed 16S rRNA gene sequence similarity of 94.1-97.7 % to the type strains of recognized Rhizobium species. DNA-DNA relatedness between strain DS-42(T) and the type strains of Rhizobium huautlense, R. galegae, R. loessense and R. cellulosilyticum was 13-19 %, indicating that strain DS-42(T) was distinct from them genetically. Strain DS-42(T) can also be differentiated from these four phylogenetically related Rhizobium species by various phenotypic properties. On the basis of phenotypic properties, phylogenetic distinctiveness and genetic data, strain DS-42(T) is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium soli sp. nov. is proposed. The type strain is DS-42(T) (=KCTC 12873(T) =JCM 14591(T)).
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Affiliation(s)
- Jung-Hoon Yoon
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Republic of Korea
| | - So-Jung Kang
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Republic of Korea
| | - Hwe-Su Yi
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Republic of Korea
| | - Tae-Kwang Oh
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Republic of Korea
| | - Choong-Min Ryu
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Republic of Korea
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Lu YL, Chen WF, Wang ET, Guan SH, Yan XR, Chen WX. Genetic diversity and biogeography of rhizobia associated with Caragana species in three ecological regions of China. Syst Appl Microbiol 2009; 32:351-61. [DOI: 10.1016/j.syapm.2008.10.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Revised: 10/03/2008] [Accepted: 10/09/2008] [Indexed: 11/17/2022]
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42
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Rhizobium alkalisoli sp. nov., isolated from Caragana intermedia growing in saline-alkaline soils in the north of China. Int J Syst Evol Microbiol 2009; 59:3006-11. [DOI: 10.1099/ijs.0.007237-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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43
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Cummings SP, Gyaneshwar P, Vinuesa P, Farruggia FT, Andrews M, Humphry D, Elliott GN, Nelson A, Orr C, Pettitt D, Shah GR, Santos SR, Krishnan HB, Odee D, Moreira FMS, Sprent JI, Young JPW, James EK. Nodulation of Sesbania species by Rhizobium (Agrobacterium) strain IRBG74 and other rhizobia. Environ Microbiol 2009; 11:2510-25. [PMID: 19555380 PMCID: PMC7163632 DOI: 10.1111/j.1462-2920.2009.01975.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Concatenated sequence analysis with 16S rRNA, rpoB and fusA genes identified a bacterial strain (IRBG74) isolated from root nodules of the aquatic legume Sesbania cannabina as a close relative of the plant pathogen Rhizobium radiobacter (syn. Agrobacterium tumefaciens). However, DNA:DNA hybridization with R. radiobacter, R. rubi, R. vitis and R. huautlense gave only 44%, 5%, 8% and 8% similarity respectively, suggesting that IRBG74 is potentially a new species. Additionally, it contained no vir genes and lacked tumour‐forming ability, but harboured a sym‐plasmid containing nifH and nodA genes similar to those in other Sesbania symbionts. Indeed, IRBG74 effectively nodulated S. cannabina and seven other Sesbania spp. that nodulate with Ensifer (Sinorhizobium)/Rhizobium strains with similar nodA genes to IRBG74, but not species that nodulate with Azorhizobium or Mesorhizobium. Light and electron microscopy revealed that IRBG74 infected Sesbania spp. via lateral root junctions under flooded conditions, but via root hairs under non‐flooded conditions. Thus, IRBG74 is the first confirmed legume‐nodulating symbiont from the Rhizobium (Agrobacterium) clade. Cross‐inoculation studies with various Sesbania symbionts showed that S. cannabina could form fully effective symbioses with strains in the genera Rhizobium and Ensifer, only ineffective ones with Azorhizobium strains, and either partially effective (Mesorhizobium huakii) or ineffective (Mesorhizobium plurifarium) symbioses with Mesorhizobium. These data are discussed in terms of the molecular phylogeny of Sesbania and its symbionts.
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Affiliation(s)
- Stephen P Cummings
- School of Applied Sciences, Ellison Building, University of Northumbria, Newcastle-upon-Tyne, UK
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Wei GH, Zhang ZX, Chen C, Chen WM, Ju WT. Phenotypic and genetic diversity of rhizobia isolated from nodules of the legume genera Astragalus, Lespedeza and Hedysarum in northwestern China. Microbiol Res 2008; 163:651-62. [PMID: 17207980 DOI: 10.1016/j.micres.2006.09.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2006] [Revised: 08/04/2006] [Accepted: 09/19/2006] [Indexed: 12/01/2022]
Abstract
Twenty-nine rhizobial isolates from root nodules of the wild Legumes Astragalus, Lespedeza and Hedysarum growing in the northwestern region of China, were characterized by numerical taxonomy, RFLP and sequencing of PCR-amplified 16S rDNA genes, and cross-nodulation with selected Legume species. Based on the results from numerical taxonomy, the isolates could be divided into two main groups (Clusters 1 and 2) and some single isolates at 82% similarity. CLuster 1 contained six isolates from Astragalus, Lespedeza and Hedysarum spp. Cluster 2 consisted of nine isolates from Astragalus and Hedysarum species. The phytogenetic analysis based on 16S rRNA gene sequences showed that SH199, representing cluster 1, belonged to the Rhizobium-Agrobacterium group, and SH290B, representing cluster 2, was closely related to R. galegae and R. huautlense.
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Affiliation(s)
- Ge Hong Wei
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Life Sciences, Northwest A&F University, Yangling Shaanxi 712100, PR China.
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Han TX, Wang ET, Han LL, Chen WF, Sui XH, Chen WX. Molecular diversity and phylogeny of rhizobia associated with wild legumes native to Xinjiang, China. Syst Appl Microbiol 2008; 31:287-301. [DOI: 10.1016/j.syapm.2008.04.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2008] [Revised: 04/16/2008] [Accepted: 04/17/2008] [Indexed: 11/16/2022]
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46
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Peng G, Yuan Q, Li H, Zhang W, Tan Z. Rhizobium oryzae sp. nov., isolated from the wild rice Oryza alta. Int J Syst Evol Microbiol 2008; 58:2158-63. [PMID: 18768622 DOI: 10.1099/ijs.0.65632-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During a study of endophytic nitrogen-fixing bacteria present in the wild rice species Oryza alta, eight novel isolates were obtained from surface-sterilized roots and classified in the genus Rhizobium on the basis of almost-complete 16S rRNA gene sequence analysis. These strains can nodulate Phaseolus vulgaris and Glycine max. The highly similar protein patterns, DNA fingerprint patterns of insertion sequence-based PCR (IS-PCR) and DNA-DNA hybridizations showed that these novel isolates were members of the same species. The closest phylogenetic relatives of the representative strain Alt 505(T) of the novel group were Rhizobium etli CFN 42(T) and Rhizobium indigoferae CCBAU 71714(T), with 96.2 and 96.0% 16S rRNA gene sequence similarity, respectively. Low DNA-DNA relatedness with the type strains of R. etli, R. indigoferae, Rhizobium hainanense, Rhizobium mongolense and Rhizobium galegae and differences in IS-PCR fingerprinting patterns, SDS-PAGE of proteins, antibiotic resistance, phenotypic tests and comparison of cellular fatty acids with Rhizobium species indicated that the novel group of isolates were distinct from previously described species. Based on these results, we propose to place them in a novel species, as Rhizobium oryzae sp. nov. The type strain is Alt 505(T) (=LMG 24253(T) =CGMCC 1.7048(T)).
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MESH Headings
- Bacterial Proteins/analysis
- Bacterial Typing Techniques
- DNA Fingerprinting
- DNA Transposable Elements
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Drug Resistance, Bacterial
- Electrophoresis, Polyacrylamide Gel
- Genes, rRNA
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Oryza/microbiology
- Phylogeny
- Plant Roots/microbiology
- Polymerase Chain Reaction/methods
- Proteome/analysis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Rhizobium/classification
- Rhizobium/genetics
- Rhizobium/isolation & purification
- Rhizobium/physiology
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Glycine max/microbiology
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Affiliation(s)
- Guixiang Peng
- College of Resources and Environment, South China Agricultural University, Guangzhou 510642, PR China
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47
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García-Fraile P, Rivas R, Willems A, Peix A, Martens M, Martínez-Molina E, Mateos PF, Velázquez E. Rhizobium cellulosilyticum sp. nov., isolated from sawdust of Populus alba. Int J Syst Evol Microbiol 2007; 57:844-848. [PMID: 17392217 DOI: 10.1099/ijs.0.64680-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During a study of polysaccharide-hydrolysing bacteria present in different plant sources, two strains were isolated from pulverized decaying wood of Populus alba and classified in the genus Rhizobium on basis of their almost complete 16S rRNA gene sequences. Their closest phylogenetic relatives were Rhizobium galegae USDA 4128T and Rhizobium huautlense S02T, with 98.2 and 98.1 % 16S rRNA gene sequence similarity, respectively. recA and atpD sequence analysis showed that these species have less than 88 and 92 % similarity, respectively, to the novel strains. In contrast to their closest phylogenetic relatives, the two strains showed strong cellulase activity on plates containing CM-cellulose as a carbon source. They were also distinguishable from these species on the basis of other phenotypic characteristics. The strains were able to induce ineffective nodules on Medicago sativa and the sequence of their nodD gene was phylogenetically close to that of Ensifer meliloti 1021 (99.6 % similarity). DNA–DNA hybridization values ranged from 10 to 22 % with respect to R. galegae USDA 4128T and 14 to 25 % with respect to R. huautlense S02T, showing that the strains from this study belong to a novel species, for which the name Rhizobium cellulosilyticum sp. nov. is proposed. The type strain is ALA10B2T (=LMG 23642T=DSM 18291T=CECT 7176T).
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Affiliation(s)
| | - Raúl Rivas
- Laboratorium voor Microbiologie, Vakgroep Biochemie, Fysiologie en Microbiologie, Universiteit Gent, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
- Departamento de Microbiología y Genética, Universidad de Salamanca, Spain
| | - Anne Willems
- Laboratorium voor Microbiologie, Vakgroep Biochemie, Fysiologie en Microbiologie, Universiteit Gent, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Alvaro Peix
- Instituto de Recursos Naturales y Agrobiología, IRNA-CSIC, Salamanca, Spain
| | - Miet Martens
- Laboratorium voor Microbiologie, Vakgroep Biochemie, Fysiologie en Microbiologie, Universiteit Gent, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | | | - Pedro F Mateos
- Departamento de Microbiología y Genética, Universidad de Salamanca, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Spain
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Baimiev AK, Baimiev AK, Gubaidullin II, Kulikova OL, Chemeris AV. Phylogeny and genetic diversity of the Astragalus cicer root nodule bacterial symbionts. Microbiology (Reading) 2007. [DOI: 10.1134/s002626170701016x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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49
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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: 30] [Impact Index Per Article: 1.7] [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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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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