sp. nov., a potential plant-promoting endophytic bacterium isolated from rice roots Free

Abstract

A novel endophytic bacterium, strain ZYY112, isolated from rice roots, was characterized by a polyphasic approach. In phylogenetic analyses based on 16S rRNA gene sequences, ZYY112 showed highest sequence similarity to HU1-AH51 (97.2 %) and less than 97 % similarity with respect to other species with validly published names. The DNA G+C content of strain ZYY112 was 60.8 mol%. The level of DNA–DNA relatedness between strain ZYY112 and DSM 27057 was 33.7 % (reciprocal 5.2 %), which supported the suggestion that ZYY112 represented a novel species of the genus . Ubiquinone Q-10 was the unique respiratory quinone (100 %). The polar lipid profile contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, an unknown aminolipid and an unknown phospholipid. The major fatty acids of strain ZYY112 were summed feature 8 (consisting of Cω7 and/or Cω6c), summed feature 3 (consisting of Cω7 and/or Cω6), C 2-OH and C. The major polyamine of ZYY112 was spermidine, which is a characteristic trait of the genus Characterization by genotypic, chemotaxonomic and phenotypic analysis indicated that strain ZYY112 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is ZYY112 ( = ACCC 06131 = JCM 30537).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.000718
2016-01-01
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/1/302.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.000718&mimeType=html&fmt=ahah

References

  1. Addison S. L., Foote S. M., Reid N. M., Lloyd-Jones G. 2007; Novosphingobium nitrogenifigens sp. nov., a polyhydroxyalkanoate-accumulating diazotroph isolated from a New Zealand pulp and paper wastewater. Int J Syst Evol Microbiol 57:2467–2471 [View Article][PubMed]
    [Google Scholar]
  2. Baek S. H., Lim J. H., Jin L., Lee H. G., Lee S. T. 2011; Novosphingobium sediminicola sp. nov. isolated from freshwater sediment. Int J Syst Evol Microbiol 61:2464–2468 [View Article][PubMed]
    [Google Scholar]
  3. Balkwill D. L., Drake G. R., Reeves R. H., Fredrickson J. K., White D. C., Ringelberg D. B., Chandler D. P., Romine M. F., Kennedy D. W., Spadoni C. M. 1997; Taxonomic study of aromatic-degrading bacteria from deep-terrestrial-subsurface sediments and description of Sphingomonas aromaticivorans sp. nov., Sphingomonas subterranea sp. nov., and Sphingomonas stygia sp. nov. Int J Syst Bacteriol 47:191–201 [View Article][PubMed]
    [Google Scholar]
  4. Busse H.-J., Bunka S., Hensel A., Lubitz W. 1997; Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 47:698–708 [View Article]
    [Google Scholar]
  5. Cowan S. T., Steel K. J. 1965 Manual for the Identification of Medical Bacteria London: Cambridge University Press;
    [Google Scholar]
  6. De Ley J., Cattoir H., Reynaerts A. 1970; The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142 [View Article][PubMed]
    [Google Scholar]
  7. Fujii K., Satomi M., Morita N., Motomura T., Tanaka T., Kikuchi S. 2003; Novosphingobium tardaugens sp. nov., an oestradiol-degrading bacterium isolated from activated sludge of a sewage treatment plant in Tokyo. Int J Syst Evol Microbiol 53:47–52 [View Article][PubMed]
    [Google Scholar]
  8. Glaeser S. P., Kämpfer P., Busse H.-J., Langer S., Glaeser J. 2009; Novosphingobium acidiphilum sp. nov., an acidophilic salt-sensitive bacterium isolated from the humic acid-rich Lake Grosse Fuchskuhle. Int J Syst Evol Microbiol 59:323–330 [View Article][PubMed]
    [Google Scholar]
  9. Glaeser S. P., Bolte K., Martin K., Busse H.-J., Grossart H.-P., Kämpfer P., Glaeser J. 2013; Novosphingobium fuchskuhlense sp. nov., isolated from the north-east basin of Lake Grosse Fuchskuhle. Int J Syst Evol Microbiol 63:586–592 [View Article][PubMed]
    [Google Scholar]
  10. Gupta S. K., Lal D., Lal R. 2009; Novosphingobium panipatense sp. nov. and Novosphingobium mathurense sp. nov., from oil-contaminated soil. Int J Syst Evol Microbiol 59:156–161 [View Article][PubMed]
    [Google Scholar]
  11. Huss V. A., Festl H., Schleifer K. H. 1983; Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4:184–192 [View Article][PubMed]
    [Google Scholar]
  12. Kämpfer P., Witzenberger R., Denner E. B. M., Busse H.-J., Neef A. 2002; Novosphingobium hassiacum sp. nov., a new species isolated from an aerated sewage pond. Syst Appl Microbiol 25:37–45 [View Article][PubMed]
    [Google Scholar]
  13. Kämpfer P., Young C. C., Busse H. J., Lin S. Y., Rekha P. D., Arun A. B., Chen W. M., Shen F. T., Wu Y. H. 2011; Novosphingobium soli sp. nov., isolated from soil. Int J Syst Evol Microbiol 61:259–263 [View Article][PubMed]
    [Google Scholar]
  14. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H., other authors. 2012; Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721 [View Article][PubMed]
    [Google Scholar]
  15. Lane D. J. 1991; 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics pp 115–175Edited by Stackebrandt E., Goodfellow M. Chichester: Wiley;
    [Google Scholar]
  16. Lim Y. W., Moon E. Y., Chun J. 2007; Reclassification of Flavobacterium resinovorum Delaporte and Daste 1956 as Novosphingobium resinovorum comb. nov., with Novosphingobium subarcticum (Nohynek et al. 1996) Takeuchi et al. 2001 as a later heterotypic synonym. Int J Syst Evol Microbiol 57:1906–1908 [View Article][PubMed]
    [Google Scholar]
  17. Lin S. Y., Hameed A., Liu Y. C., Hsu Y. H., Lai W. A., Huang H. I., Young C. C. 2014; Novosphingobium arabidopsis sp. nov., a DDT-resistant bacterium isolated from the rhizosphere of Arabidopsis thaliana . Int J Syst Evol Microbiol 64:594–598 [View Article][PubMed]
    [Google Scholar]
  18. Liu Z. P., Wang B. J., Liu Y. H., Liu S. J. 2005; Novosphingobium taihuense sp. nov., a novel aromatic-compound-degrading bacterium isolated from Taihu Lake, China. Int J Syst Evol Microbiol 55:1229–1232 [View Article][PubMed]
    [Google Scholar]
  19. Marmur J. 1961; A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3:208–218 [View Article]
    [Google Scholar]
  20. 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]
  21. Minnikin D. E., O'Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J. H. 1984; An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241 [View Article]
    [Google Scholar]
  22. Niharika N., Moskalikova H., Kaur J., Sedlackova M., Hampl A., Damborsky J., Prokop Z., Lal R. 2013; Novosphingobium barchaimii sp. nov., isolated from hexachlorocyclohexane-contaminated soil. Int J Syst Evol Microbiol 63:667–672 [View Article][PubMed]
    [Google Scholar]
  23. Sasser M. 1990 Identification of bacteria by gas chromatography of cellular fatty acids MIDI Technical Note 101 Newark, DE: MIDI Inc;
    [Google Scholar]
  24. Sohn J. H., Kwon K. K., Kang J. H., Jung H. B., Kim S. J. 2004; Novosphingobium pentaromativorans sp. nov., a high-molecular-mass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment. Int J Syst Evol Microbiol 54:1483–1487 [View Article][PubMed]
    [Google Scholar]
  25. Suzuki S., Hiraishi A. 2007; Novosphingobium naphthalenivorans sp. nov., a naphthalene-degrading bacterium isolated from polychlorinated-dioxin-contaminated environments. J Gen Appl Microbiol 53:221–228 [View Article][PubMed]
    [Google Scholar]
  26. Taibi G., Schiavo M. R., Gueli M. C., Rindina P. C., Muratore R., Nicotra C. M. A. 2000; Rapid and simultaneous high-performance liquid chromatography assay of polyamines and monoacetylpolyamines in biological specimens. J Chromatogr B Biomed Sci Appl 745:431–437 [View Article][PubMed]
    [Google Scholar]
  27. Takeuchi M., Sakane T., Yanagi M., Yamasato K., Hamana K., Yokota A. 1995; Taxonomic study of bacteria isolated from plants: proposal of Sphingomonas rosa sp. nov., Sphingomonas pruni sp. nov., Sphingomonas asaccharolytica sp. nov., and Sphingomonas mali sp. nov. Int J Syst Bacteriol 45:334–341 [View Article][PubMed]
    [Google Scholar]
  28. Takeuchi M., Hamana K., Hiraishi A. 2001; Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 51:1405–1417 [View Article][PubMed]
    [Google Scholar]
  29. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. 2013; mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729 [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. Tiirola M. A., Busse H.-J., Kämpfer P., Männistö M. K. 2005; Novosphingobium lentum sp. nov., a psychrotolerant bacterium from a polychlorophenol bioremediation process. Int J Syst Evol Microbiol 55:583–588 [View Article][PubMed]
    [Google Scholar]
  32. 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 Evol Microbiol 37:463–464 [CrossRef]
    [Google Scholar]
  33. Yabuuchi E., Yano I., Oyaizu H., Hashimoto Y., Ezaki T., Yamamoto H. 1990; Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas . Microbiol Immunol 34:99–119 [View Article][PubMed]
    [Google Scholar]
  34. Yuan J., Lai Q., Zheng T., Shao Z. 2009; Novosphingobium indicum sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from a deep-sea environment. Int J Syst Evol Microbiol 59:2084–2088 [View Article][PubMed]
    [Google Scholar]
  35. 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]
  36. Zhang X. X., Gao J. S., Cao Y. H., Ma X. T., He J. Z. 2013; Long-term rice and green manure rotation alters the endophytic bacterial communities of the rice root. Microb Ecol 66:917–926 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.000718
Loading
/content/journal/ijsem/10.1099/ijsem.0.000718
Loading

Data & Media loading...

Supplements

Supplementary Data

PDF

Most cited Most Cited RSS feed