Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 64, Issue Pt_4

sp. nov., isolated from rice roots Free

Abstract

Two strains (J3-AN59 and J3-N84) of Gram-stain-negative, aerobic and rod-shaped bacteria were isolated from the roots of fresh rice plants. The 16S rRNA gene sequence similarity results showed that the similarity between strains J3-AN59 and J3-N84 was 100 %. Both strains were phylogenetically related to members of the genus , and they were most closely related to ACCC 06128 (97.43 %). Similarities in the sequences of housekeeping genes between strains J3-AN59 and J3-N84 and those of recognized species of the genus were less than 90 %. The polar lipid profiles of both strains were predominantly composed of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unknown aminophospholipid. The major cellular fatty acids were summed feature 8 (Cω7 and/or Cω6) and C. The DNA G+C contents of J3-AN59 and J3-N84 were 55.7 and 57.1 mol%, respectively. The DNA–DNA relatedness value between J3-AN59 and J3-N84 was 89 %, and strain J3-AN59 showed 9 % DNA–DNA relatedness to ACCC 06128, the most closely related strain. Based on this evidence, we found that J3-AN59 and J3-N84 represent a novel species in the genus and we propose the name sp. nov. The type strain is J3-AN59 ( = ACCC 05916 = KCTC 23652).

  • Published Online:
Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 41271273)
  • National High Technology Research and Development Program (863) of China (Award 2013AA102802)
  • Special Scientific Research Funds for Commonwealth Agricultural Industry (Award 201103005-01)
© 2014 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.056325-0
2014-04-01
2025-04-21
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/64/4/1373.html?itemId=/content/journal/ijsem/10.1099/ijs.0.056325-0&mimeType=html&fmt=ahah

References

  1. Antoun H., Beauchamp C. J., Goussard N., Chabot R., Lalande R. ( 1998 ). Potential of Rhizobium and Bradyrhizobium species as plant growth promoting rhizobacteria on non-legumes: Effect on radishes (Raphanus sativus L.). . Plant Soil 204, 57–67. [View Article]
    [Google Scholar]
  2. Bellone S. C. D., Bellone C. H. ( 2006 ). Presence of endophytic diazotrophs in sugarcane juice. . World J Microbiol Biotechnol 22, 1065–1068. [View Article]
    [Google Scholar]
  3. Chaintreuil C., Giraud E., Prin Y., Lorquin J., Bâ A., Gillis M., de Lajudie P., Dreyfus B. ( 2000 ). Photosynthetic bradyrhizobia are natural endophytes of the African wild rice Oryza breviligulata . . Appl Environ Microbiol 66, 5437–5447. [View Article] [PubMed]
    [Google Scholar]
  4. Collins M. D., Jones D. ( 1980 ). Lipids in the classification and identification of coryneform bacteria containing peptidoglycan based on 2, 4-diaminobutyric acid. . J Appl Bacteriol 48, 459–470. [View Article]
    [Google Scholar]
  5. Dakora F. D. ( 2003 ). Defining new roles for plant and rhizobial molecules in sole and mixed plant cultures involving symbiotic legumes. . New Phytol 158, 39–49. [View Article]
    [Google Scholar]
  6. De Ley J. ( 1970 ). Reexamination of the association between melting point, buoyant density, and chemical base composition of deoxyribonucleic acid. . J Bacteriol 101, 738–754.[PubMed]
    [Google Scholar]
  7. Dong X.-Z., Cai M.-Y. (editors) ( 2001 ). Determination of biochemical properties. . In Manual for the Systematic Identification of General Bacteria, pp. 370–398. Beijing:: Science Press (in Chinese);.
     [Google Scholar]
  8. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783–791. [View Article]
    [Google Scholar]
  9. Frank B. ( 1889 ). Über die Pilzsymbiose der Leguminosen. Berichte der Deutschen Botanischen Gesellschaft. , 7, 332–346. [View Article]
    [Google Scholar]
  10. Gao J. L., Turner S. L., Kan F. L., Wang E. T., Tan Z. Y., Qiu Y. H., Gu J., Terefework Z., Young J. P. W. & other authors ( 2004 ). Mesorhizobium septentrionale sp. nov. and Mesorhizobium temperatum sp. nov., isolated from Astragalus adsurgens growing in the northern regions of China. . Int J Syst Evol Microbiol 54, 2003–2012. [View Article] [PubMed]
    [Google Scholar]
  11. Graham P. H., Sadowsky M. J., Keyser H. H., Barnet Y. M., Bradley R. S., Cooper J. E., De Ley D. J., Jarvis B. D. W., Roslycky E. B. & other authors ( 1991 ). Proposed minimal standards for the description of new genera and species of root- and stem-nodulating bacteria. . Int J Syst Bacteriol 41, 582–587. [View Article]
    [Google Scholar]
  12. Gutiérrez-Zamora M. L., Martínez-Romero E. ( 2001 ). Natural endophytic association between Rhizobium etli and maize (Zea mays L.). . J Biotechnol 91, 117–126. [View Article] [PubMed]
    [Google Scholar]
  13. 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]
  14. Lane D. J. ( 1991 ). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115–175. Edited by Stackebrandt E., Goodfellow M. . Chichester:: Wiley;.
     [Google Scholar]
  15. Mano H., Morisaki H. ( 2008 ). Endophytic bacteria in the rice plant. . Microbes Environ 23, 109–117. [View Article] [PubMed]
    [Google Scholar]
  16. Marmur J. ( 1961 ). A procedure for the isolation of deoxyribonucleic acid from micro-organisms. . J Mol Biol 3, 208–218. [View Article]
    [Google Scholar]
  17. Marmur J., Doty P. ( 1962 ). Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. . J Mol Biol 5, 109–118. [View Article] [PubMed]
    [Google Scholar]
  18. 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, 489–503. [View Article] [PubMed]
    [Google Scholar]
  19. McInroy J. A., Kloepper J. W. ( 1995 ). Population dynamics of endophytic bacteria in field-grown sweet corn and cotton. . Can J Microbiol 41, 895–901. [View Article]
    [Google Scholar]
  20. Minnikin D. E., Collins M. D., Goodfellow M. ( 1979 ). Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. . J Appl Bacteriol 47, 87–95. [View Article]
    [Google Scholar]
  21. Parshetti G., Saratale G., Telke A., Govindwar S. ( 2009 ). Biodegradation of hazardous triphenylmethane dye methyl violet by Rhizobium radiobacter (MTCC 8161). . J Basic Microbiol 49 (Suppl 1), S36–S42. [View Article] [PubMed]
    [Google Scholar]
  22. Peng G., Yuan Q., Li H., Zhang W., Tan Z. ( 2008 ). Rhizobium oryzae sp. nov., isolated from the wild rice Oryza alta . . Int J Syst Evol Microbiol 58, 2158–2163. [View Article] [PubMed]
    [Google Scholar]
  23. Raja P., Uma S., Sundaram S. ( 2006 ). Non-nodulating pink-pigmented facultative Methylobacterium sp. with a functional nifH gene. . World J Microbiol Biotechnol 22, 1381–1384. [View Article]
    [Google Scholar]
  24. 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]
  25. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE:: MIDI Inc;.
     [Google Scholar]
  26. Sharma P. K., Sarita S., Prell J. ( 2005 ). Isolation and characterization of an endophytic bacterium related to Rhizobium/Agrobacterium from wheat (Triticum aestivum L.) roots. . Curr Sci 89, 608–610.
     [Google Scholar]
  27. 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, 117–122. [View Article] [PubMed]
    [Google Scholar]
  28. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. ( 2011 ). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28, 2731–2739. [View Article] [PubMed]
    [Google Scholar]
  29. Tan Z., Hurek T., Vinuesa P., Müller P., Ladha J. K., Reinhold-Hurek B. ( 2001 ). Specific detection of Bradyrhizobium and Rhizobium strains colonizing rice (Oryza sativa) roots by 16S-23S ribosomal DNA intergenic spacer-targeted PCR. . Appl Environ Microbiol 67, 3655–3664. [View Article] [PubMed]
    [Google Scholar]
  30. 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, 4876–4882. [View Article] [PubMed]
    [Google Scholar]
  31. 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, 787–801. [View Article] [PubMed]
    [Google Scholar]
  32. 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, 2424–2429. [View Article] [PubMed]
    [Google Scholar]
  33. Ueda T., Suga Y., Yahiro N., Matsuguchi T. ( 1995 ). Remarkable N2-fixing bacterial diversity detected in rice roots by molecular evolutionary analysis of nifH gene sequences. . J Bacteriol 177, 1414–1417.[PubMed]
    [Google Scholar]
  34. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E. & other authors ( 1987 ). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37, 463–464. [View Article]
    [Google Scholar]
  35. Yanni Y. G., Rizk R. Y., Corich V., Squartini A., Ninke K., Philip-Hollingsworth S., Orgambide G., de Bruijn F., Stoltzfus J. & other authors ( 1997 ). Natural endophytic association between Rhizobium leguminosarum bv. trifolii and rice roots and assessment of its potential to promote rice growth. . Plant Soil 194, 99–114. [View Article]
    [Google Scholar]
  36. 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, 2425–2429. [View Article] [PubMed]
    [Google Scholar]
  37. 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, 1871–1876. [View Article] [PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijs.0.056325-0
Loading
Rhizobium rhizoryzae sp. nov., isolated from rice roots
Int J Syst Evol Microbiol 64, 1373 (2014); https://doi.org/10.1099/ijs.0.056325-0
/content/journal/ijsem/10.1099/ijs.0.056325-0
/content/journal/ijsem/10.1099/ijs.0.056325-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error