1887

Abstract

Five strains isolated from root nodules of and grown in the Anhui and Sichuan provinces of China were classified as members of the genus . These strains had identical 16S rRNA gene sequences which shared 99.48 %, 99.48 % and 99.22 % similarity with the most closely related strains of PAC68, PAC48 and USDA 76, respectively. A study using a polyphasic approach, including 16S rRNA gene RFLP, IGS-RFLP, BOX-PCR, comparative sequence analysis of the 16S–23S rRNA intergenic spacer (IGS) and the , and genes, DNA–DNA hybridization and phenotypic tests, showed that the five strains clustered into a coherent group that differentiated them from all recognized species of the genus . Sequencing of and genes and cross-nodulation tests showed that the representative strains CCBAU 23086, CCBAU 23160 and CCBAU 61434, isolated from different plants, had identical and gene sequences and were all able to nodulate , and . Based upon these results, the name sp. nov. is proposed for this novel species and strain CCBAU 23086 ( = LMG 25572 = HAMBI 3052) is designated as the type strain. The DNA GC mol% is 60.14 ( ).

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2011-10-01
2020-01-23
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References

  1. Chen Q. , Zhang X. , Terefework Z. , Kaijalainen S. , Li D. , Lindström K. . ( 2003; ). Diversity and compatibility of peanut (Arachis hypogaea L.) bradyrhizobia and their host plants. . Plant Soil 255:, 605–617. [CrossRef]
    [Google Scholar]
  2. de Bruijn F. J. . ( 1992; ). Use of repetitive (repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus) sequences and the polymerase chain reaction to fingerprint the genomes of Rhizobium meliloti isolates and other soil bacteria. . Appl Environ Microbiol 58:, 2180–2187.[PubMed]
    [Google Scholar]
  3. de Lajudie P. , Willems A. , Nick G. , Moreira F. , Molouba F. , Hoste B. , Torck U. , Neyra M. , Collins M. D. et al. & other authors ( 1998; ). Characterization of tropical tree rhizobia and description of Mesorhizobium plurifarium sp. nov.. Int J Syst Bacteriol 48:, 369–382.[PubMed] [CrossRef]
    [Google Scholar]
  4. De Ley J. , Cattoir H. , Reynaerts A. . ( 1970; ). The quantitative measurement of DNA hybridization from renaturation rates. . Eur J Biochem 12:, 133–142. [CrossRef] [PubMed]
    [Google Scholar]
  5. El-Akhal M. , Rincon A. , Arenal F. , Lucas M. , El Mourabit N. , Barrijal S. , Pueyo J. . ( 2008; ). Genetic diversity and symbiotic efficiency of rhizobial isolates obtained from nodules of Arachis hypogaea in northwestern Morocco. . Soil Biol Biochem 40:, 2911–2914. [CrossRef]
    [Google Scholar]
  6. El-Akhal M. R. , Rincon A. , Mourabit N. E. , Pueyo J. J. , Barrijal S. . ( 2009; ). Phenotypic and genotypic characterizations of rhizobia isolated from root nodules of peanut (Arachis hypogaea L.) grown in Moroccan soils. . J Basic Microbiol 49:, 415–425. [CrossRef] [PubMed]
    [Google Scholar]
  7. Felsenstein J. . ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39:, 783–791. [CrossRef]
    [Google Scholar]
  8. Gao J. , Sun J. , Li Y. , Wang E. , Chen W. . ( 1994; ). Numerical taxonomy and DNA relatedness of tropical rhizobia isolated from Hainan Province, China. . Int J Syst Bacteriol 44:, 151–158. [CrossRef]
    [Google Scholar]
  9. Graham P. , Sadowsky M. , Keyser H. , Barnet Y. , Bradley R. , Cooper J. , De Ley D. , Jarvis B. , Roslycky E. et al. & other authors ( 1991; ). Proposed minimal standards for the description of new genera and species of root-and stem-nodulating bacteria. . Int J Syst Evol Microbiol 41:, 582–587.
    [Google Scholar]
  10. Guindon S. , Gascuel O. . ( 2003; ). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. . Syst Biol 52:, 696–704. [CrossRef] [PubMed]
    [Google Scholar]
  11. Hurek T. , Wagner B. , Reinhold-Hurek B. . ( 1997; ). Identification of N2-fixing plant- and fungus-associated Azoarcus species by PCR-based genomic fingerprints. . Appl Environ Microbiol 63:, 4331–4339.[PubMed]
    [Google Scholar]
  12. Islam M. S. , Kawasaki H. , Muramatsu Y. , Nakagawa Y. , Seki T. . ( 2008; ). Bradyrhizobium iriomotense sp. nov., isolated from a tumor-like root of the legume Entada koshunensis from Iriomote Island in Japan. . Biosci Biotechnol Biochem 72:, 1416–1429. [CrossRef] [PubMed]
    [Google Scholar]
  13. Jukes T. H. , Cantor C. R. . ( 1969; ). Evolution of protein molecules. . In Mammalian Protein Metabolism, vol. 3, pp. 21–132. Edited by Munro H. N. . . New York:: Academic Press;.
    [Google Scholar]
  14. Kumar S. , Tamura K. , Nei M. . ( 1994; ). mega: Molecular evolutionary genetics analysis software for microcomputers. . Comput Appl Biosci 10:, 189–191.[PubMed]
    [Google Scholar]
  15. Kumar S. , Nei M. , Dudley J. , Tamura K. . ( 2008; ). mega: A biologist-centric software for evolutionary analysis of DNA and protein sequences. . Brief Bioinform 9:, 299–306. [CrossRef] [PubMed]
    [Google Scholar]
  16. Kuykendall L. D. , Saxena B. , Devine T. E. , Udell S. E. . ( 1992; ). Genetic diversity in Bradyrhizobium japonicum Jordan 1982 and a proposal for Bradyrhizobium elkanii sp. nov. . Can J Microbiol 38:, 501–505.[CrossRef]
    [Google Scholar]
  17. Kwon S. W. , Park J. Y. , Kim J. S. , Kang J. W. , Cho Y. H. , Lim C. K. , Parker M. A. , Lee G. B. . ( 2005; ). Phylogenetic analysis of the genera Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium on the basis of 16S rRNA gene and internally transcribed spacer region sequences. . Int J Syst Evol Microbiol 55:, 263–270. [CrossRef] [PubMed]
    [Google Scholar]
  18. Laguerre G. , Mavingui P. , Allard M. R. , Charnay M. P. , Louvrier P. , Mazurier S. I. , Rigottier-Gois L. , Amarger N. . ( 1996; ). Typing of rhizobia by PCR DNA fingerprinting and PCR-restriction fragment length polymorphism analysis of chromosomal and symbiotic gene regions: application to Rhizobium leguminosarum and its different biovars. . Appl Environ Microbiol 62:, 2029–2036.[PubMed]
    [Google Scholar]
  19. Laguerre G. , Nour S. M. , Macheret V. , Sanjuan J. , Drouin P. , Amarger N. . ( 2001; ). Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts. . Microbiology 147:, 981–993.[PubMed]
    [Google Scholar]
  20. Marmur J. . ( 1961; ). A procedure for the isolation of deoxyribonucleic acid from microorganisms. . J Mol Biol 3:, 208–218. [CrossRef]
    [Google Scholar]
  21. Morrison N. , Trinick M. , Rolfe B. . ( 1986; ). Comparison of the host range of fast-growing R. japonicum strains with a fast-growing isolates from Lablab . . Plant Soil 92:, 313–317. [CrossRef]
    [Google Scholar]
  22. Murphy A. , Colucci P. . ( 1999; ). A tropical forage solution to poor quality ruminant diets: A review of Lablab purpureus . . Livestock Res Rural Dev 11. http://www.lrrd.org/lrrd11/2/colu112.htm
    [Google Scholar]
  23. Nick G. , Lindstrom K. . ( 1994; ). Use of repetitive sequences and the polymerase chain reaction to fingerprint the genomic DNA of Rhizobium galegae strains and to identify the DNA obtained by sonicating the liquid cultures and root nodules. . Syst Appl Microbiol 17:, 265–273.[CrossRef]
    [Google Scholar]
  24. Nick G. , de Lajudie P. , Eardly B. D. , Suomalainen S. , Paulin L. , Zhang X. , Gillis M. , Lindström K. . ( 1999; ). Sinorhizobium arboris sp. nov. and Sinorhizobium kostiense sp. nov., isolated from leguminous trees in Sudan and Kenya. . Int J Syst Bacteriol 49:, 1359–1368. [CrossRef] [PubMed]
    [Google Scholar]
  25. Posada D. , Crandall K. A. . ( 1998; ). MODELTEST: testing the model of DNA substitution. . Bioinformatics 14:, 817–818. [CrossRef] [PubMed]
    [Google Scholar]
  26. Quan Z. X. , Bae H. S. , Baek J. H. , Chen W. F. , Im W. T. , Lee S. T. . ( 2005; ). Rhizobium daejeonense sp. nov. isolated from a cyanide treatment bioreactor. . Int J Syst Evol Microbiol 55:, 2543–2549. [CrossRef] [PubMed]
    [Google Scholar]
  27. Ramírez-Bahena M. H. , Peix A. , Rivas R. , Camacho M. , Rodríguez-Navarro D. N. , Mateos P. F. , Martínez-Molina E. , Willems A. , Velázquez E. . ( 2009; ). Bradyrhizobium pachyrhizi sp. nov. and Bradyrhizobium jicamae sp. nov., isolated from effective nodules of Pachyrhizus erosus . . Int J Syst Evol Microbiol 59:, 1929–1934. [CrossRef] [PubMed]
    [Google Scholar]
  28. Saitou N. , Nei M. . ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4:, 406–425.[PubMed]
    [Google Scholar]
  29. Sarita S. , Sharma P. K. , Priefer U. B. , Prell J. . ( 2005; ). Direct amplification of rhizobial nodC sequences from soil total DNA and comparison to nodC diversity of root nodule isolates. . FEMS Microbiol Ecol 54:, 1–11. [CrossRef] [PubMed]
    [Google Scholar]
  30. Sasser M. . ( 1990; ). Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids. Technical Note 101. . Newark, DE:: Microbial MIDI Inc;.
  31. Smibert R. M. , Krieg N. R. . ( 1994; ). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607–654. Edited by Gerhardt P. , Murray R. G. E. , Wood W. A. , Krieg N. R. . . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  32. Tan Z. Y. , Xu X. D. , Wang E. T. , Gao J. L. , Martinez-Romero E. , Chen W. X. . ( 1997; ). Phylogenetic and genetic relationships of Mesorhizobium tianshanense and related rhizobia. . Int J Syst Bacteriol 47:, 874–879. [CrossRef] [PubMed]
    [Google Scholar]
  33. Taurian T. , Ibanez F. , Fabra A. , Aguilar O. . ( 2006; ). Genetic diversity of rhizobia nodulating Arachis hypogaea L. in central Argentinean soils. . Plant Soil 282:, 41–52. [CrossRef]
    [Google Scholar]
  34. Terefework Z. , Kaijalainen S. , Lindström K. . ( 2001; ). AFLP fingerprinting as a tool to study the genetic diversity of Rhizobium galegae isolated from Galega orientalis and Galega officinalis . . J Biotechnol 91:, 169–180. [CrossRef] [PubMed]
    [Google Scholar]
  35. Tighe S. W. , de Lajudie P. , Dipietro K. , Lindström K. , Nick G. , Jarvis B. D. W. . ( 2000; ). Analysis of cellular fatty acids and phenotypic relationships of Agrobacterium, Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium species using the Sherlock Microbial Identification System. . Int J Syst Evol Microbiol 50:, 787–801. [CrossRef] [PubMed]
    [Google Scholar]
  36. Trinick M. . ( 1980; ). Relationships amongst the fast-growing rhizobia of Lablab purpureus, Leucaena leucocephala, Mimosa spp., Acacia farnesiana and Sesbania grandiflora and their affinities with other rhizobial groups. . J Appl Microbiol 49:, 39–53. [CrossRef]
    [Google Scholar]
  37. Versalovic J. , Schneider M. , de Bruijn F. J. , Lupski J. R. . ( 1994; ). Genomic fingerprinting of bacteria using repetitive sequence based PCR (rep-PCR). . Methods Mol Cell Biol 5:, 25–40.
    [Google Scholar]
  38. Vincent J. M. . ( 1970; ). The cultivation, isolation and maintenance of rhizobia. . In A Manual for the Practical Study of the Root-Nodule Bacteria, pp. 1–13. Edited by Vincent J. M. . . Oxford:: Blackwell Scientific;.
    [Google Scholar]
  39. Vinuesa P. , Silva C. , Werner D. , Martínez-Romero E. . ( 2005; ). Population genetics and phylogenetic inference in bacterial molecular systematics: the roles of migration and recombination in Bradyrhizobium species cohesion and delineation. . Mol Phylogenet Evol 34:, 29–54. [CrossRef] [PubMed]
    [Google Scholar]
  40. Wayne L. , Brenner D. , Colwell R. , Grimont P. A. D. , Kandler O. , Krichevsky M. I. , Moore L. H. , Moore W. E. C. , Murray R. G. E. et al. & other authors ( 1987; ). Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37:, 463–464. [CrossRef]
    [Google Scholar]
  41. Willems A. , Coopman R. , Gillis M. . ( 2001; ). Comparison of sequence analysis of 16S-23S rDNA spacer regions, AFLP analysis and DNA-DNA hybridizations in Bradyrhizobium . . Int J Syst Evol Microbiol 51:, 623–632.[PubMed]
    [Google Scholar]
  42. Willems A. , Munive A. , de Lajudie P. , Gillis M. . ( 2003; ). In most Bradyrhizobium groups sequence comparison of 16S-23S rDNA internal transcribed spacer regions corroborates DNA-DNA hybridizations. . Syst Appl Microbiol 26:, 203–210. [CrossRef] [PubMed]
    [Google Scholar]
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