1887

Abstract

Bacterial strains ZYY136 and ZYY9 were isolated from surface-sterilized rice roots from a long-term experiment of rice–rice– rotation. The 16S rRNA gene sequences of strains ZYY136 and ZYY9 showed the highest similarity, of 97.0  %, to PL-41. Sequence analysis of the housekeeping genes , and clearly differentiated the isolates from currently described species of the genus . The DNA–DNA relatedness value between ZYY136 and ZYY9 was 82.3  %, and ZYY136 showed 34.0  % DNA–DNA relatedness with the most closely related type strain, PL-41. The DNA G+C content of strain ZYY136 was 58.1 mol%. The major cellular fatty acids were summed feature 8 (Cω7 and/or Cω6), C and C 3-OH. Strains ZYY136 and ZYY9 could be differentiated from the previously defined species of the genus by several phenotypic characteristics. Therefore, we conclude that strains ZYY136 and ZYY9 represent a novel species of the genus , for which the name sp. nov. is proposed (type strain ZYY136 = ACCC 05753 = KCTC 32088).

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2015-09-01
2020-11-30
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References

  1. Dakora F.D. ( 2003;). Defining new roles for plant and rhizobial molecules in sole and mixed plant cultures involving symbiotic legumes. New Phytol 158 3949 [CrossRef].
    [Google Scholar]
  2. De Ley J. ( 1970;). Reexamination of the association between melting point, buoyant density, and chemical base composition of deoxyribonucleic acid. J Bacteriol 101 738754 [PubMed].
    [Google Scholar]
  3. Dong X.-Z., Cai M.-Y. ( 2001;). Determination of biochemical properties. . In Manual for the Systematic Identification of General Bacteria, pp. 370398 Beijing: Science Press; (in Chinese) .
    [Google Scholar]
  4. Felsenstein J. ( 1985;). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 783791 [CrossRef].
    [Google Scholar]
  5. Frank B. ( 1889;). Ueber die Pilzsymbiose der Leguminosen. Ber Dtsch Bot Ges 7 332346 (in German) .
    [Google Scholar]
  6. Gao J.L., Sun J.G., Li Y., Wang E.T., Chen W.X. ( 1994;). Numerical taxonomy and DNA relatedness of tropical rhizobia isolated from Hainan Province. China. Int J Syst Bacteriol 44 151158 [CrossRef].
    [Google Scholar]
  7. García-Fraile P., Rivas R., Willems A., Peix A., Martens M., Martínez-Molina E., Mateos P.F., Velázquez E. ( 2007;). Rhizobium cellulosilyticum sp. nov., isolated from sawdust of Populus alba . Int J Syst Evol Microbiol 57 844848 [CrossRef] [PubMed] .
    [Google Scholar]
  8. Gevers D., Cohan F.M., Lawrence J.G., Spratt B.G., Coenye T., Feil E.J., Stackebrandt E., Van de Peer Y., Vandamme P., other authors. ( 2005;). Opinion: re-evaluating prokaryotic species. Nat Rev Microbiol 3 733739 [PubMed]. [CrossRef]
    [Google Scholar]
  9. Jordan D.C. ( 1984;). Genus I. Rhizobium Frank 1889, 338AL . . In Bergey's Manual of Systematic Bacteriology, pp. 235242. Edited by Krieg N. R., Holt J. G. vol. 1 Baltimore, MD: Williams & Wilkins;.
    [Google Scholar]
  10. 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 981993 [PubMed]. [CrossRef]
    [Google Scholar]
  11. Lane D.J. ( 1991;). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115175. Edited by Stackebrandt E., Goodfellow M. Chichester: Wiley;.
    [Google Scholar]
  12. Mano H., Morisaki H. ( 2008;). Endophytic bacteria in the rice plant. Microbes Environ 23 109117 [PubMed]. [CrossRef]
    [Google Scholar]
  13. Marmur J. ( 1961;). A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 3 208218. [CrossRef]
    [Google Scholar]
  14. Marmur J., Doty P. ( 1962;). Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 5 109118 [PubMed]. [CrossRef]
    [Google Scholar]
  15. Martens M., Delaere M., Coopman R., De Vos P., Gillis M., Willems A. ( 2007;). Multilocus sequence analysis of Ensifer and related taxa. Int J Syst Evol Microbiol 57 489503 [CrossRef] [PubMed] .
    [Google Scholar]
  16. Martens M., Dawyndt P., Coopman R., Gillis M., De Vos P., Willems A. ( 2008;). Advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium). Int J Syst Evol Microbiol 58 200214 [CrossRef] [PubMed] .
    [Google Scholar]
  17. Pagan J.D., Child J.J., Scowcroft W.R., Gibson A.H. ( 1975;). Nitrogen fixation by Rhizobium cultured on a defined medium. Nature 256 406407 [CrossRef].
    [Google Scholar]
  18. 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 25432549 [PubMed]. [CrossRef]
    [Google Scholar]
  19. Raja P., Uma S., Sundaram S. ( 2006;). Non-nodulating pink-pigmented facultative Methylobacterium sp. with a functional nifH gene. World J Microbiol Biotechnol 22 13811384 [CrossRef].
    [Google Scholar]
  20. Rashid M.H., Schäfer H., Gonzalez J., Wink M. ( 2012;). Genetic diversity of rhizobia nodulating lentil (Lens culinaris) in Bangladesh. Syst Appl Microbiol 35 98109 [CrossRef] [PubMed] .
    [Google Scholar]
  21. Sasser M. ( 1990)., Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101 Newark, DE: MIDI Inc;.
  22. Singh R.K., Mishra R.P., Jaiswal H.K., Kumar V., Pandey S.P., Rao S.B., Annapurna K. ( 2006;). Isolation and identification of natural endophytic rhizobia from rice (Oryza sativa L.) through rDNA PCR-RFLP and sequence analysis. Curr Microbiol 52 117122 [CrossRef] [PubMed] .
    [Google Scholar]
  23. Stackebrandt E., Frederiksen W., Garrity G.M., Grimont P.A., Kämpfer P., Maiden M.C.J., Nesme X., Rosselló-Mora R., Swings J., other authors. ( 2002;). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52 10431047 [CrossRef] [PubMed] .
    [Google Scholar]
  24. Sullivan J.T., Eardly B.D., van Berkum P., Ronson C.W. ( 1996;). Four unnamed species of nonsymbiotic rhizobia isolated from the rhizosphere of Lotus corniculatus . Appl Environ Microbiol 62 28182825 [PubMed].
    [Google Scholar]
  25. Sun L., Qiu F., Zhang X., Dai X., Dong X., Song W. ( 2008;). Endophytic bacterial diversity in rice (Oryza sativa L) roots estimated by 16S rDNA sequence analysis. Microb Ecol 55 415424 [PubMed]. [CrossRef]
    [Google Scholar]
  26. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. ( 2013;). mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30 27252729 [PubMed]. [CrossRef]
    [Google Scholar]
  27. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. ( 1997;). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25 48764882 [CrossRef] [PubMed] .
    [Google Scholar]
  28. Tighe S.W., de Lajudie P., Dipietro K., Lindström K., Nick G., Jarvis B.D. ( 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 787801 [CrossRef] [PubMed] .
    [Google Scholar]
  29. Turdahon M., Osman G., Hamdun M., Yusuf K., Abdurehim Z., Abaydulla G., Abdukerim M., Fang C., Rahman E. ( 2013;). Rhizobium tarimense sp. nov., isolated from soil in the ancient Khiyik River. Int J Syst Evol Microbiol 63 24242429 [CrossRef] [PubMed] .
    [Google Scholar]
  30. Vincent J. ( 1970;). A manual for the practical study of root-nodule bacteria. Oxford: Blackwell Scientific Pubilications, UK;.
  31. Vinuesa P., Silva C., Lorite M.J., Izaguirre-Mayoral M.L., Bedmar E.J., Martínez-Romero E. ( 2005;). Molecular systematics of rhizobia based on maximum likelihood and Bayesian phylogenies inferred from rrs, atpD, recA and nifH sequences, and their use in the classification of Sesbania microsymbionts from Venezuelan wetlands. Syst Appl Microbiol 28 702716 [CrossRef] [PubMed] .
    [Google Scholar]
  32. White L.O. ( 1972;). The taxonomy of the crown gall organism Agrobacterium tumefaciens and its relationship to rhizobia and other agrobacteria. J Gen Microbiol 72 565574 [CrossRef].
    [Google Scholar]
  33. Zhang X., Sun L., Ma X., Sui X.H., Jiang R. ( 2011;). Rhizobium pseudoryzae sp. nov., isolated from the rhizosphere of rice. Int J Syst Evol Microbiol 61 24252429 [CrossRef] [PubMed] .
    [Google Scholar]
  34. Zhang X., Li B., Wang H., Sui X., Ma X., Hong Q., Jiang R. ( 2012;). Rhizobium petrolearium sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 62 18711876 [CrossRef] [PubMed] .
    [Google Scholar]
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