1887

Abstract

A bacterial strain, designated D75, was isolated from the rhizosphere soil of . Phylogenetic analysis based on the complete 16S rRNA gene sequence revealed that strain D75 was a member of the genus . High levels of 16S rRNA gene sequence similarity were found between strain D75 and DS-1 (99.2 %), B538 (97.5 %) and Ch-32 (97.2 %). The chemotaxonomic properties of strain D75 were consistent with those of the genus : the cell-wall peptidoglycan type was based on -diaminopimelic acid (A1γ), the predominant menaquinone was MK-7, and the major fatty acids were anteiso-C, iso-C and C. However, levels of DNA–DNA relatedness between strain D75 and NBRC 16618, DSM 16970 and DSM 19417 were 35, 20 and 18 %, respectively. On the basis of phenotypic and chemotaxonomic analyses, phylogenetic data and DNA–DNA relatedness values, strain D75 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is D75 ( = DSM 24714 = CGMCC 1.10784).

Funding
This study was supported by the:
  • , Fundamental Research Funds for the Central Universities , (Award YX2011-25 and TD2012-03)
  • , Beijing Nova Program , (Award 2011033)
  • , Forestry Industry Research Special Funds for Public Welfare Projects , (Award 201304409)
  • , National Science and Technology Ministry , (Award 2012BAC09B03)
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2013-05-01
2020-11-23
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References

  1. Ash C., Priest F. G., Collins M. D. ( 1993 ). Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. . Antonie van Leeuwenhoek 64, 253260. [CrossRef] [PubMed]
    [Google Scholar]
  2. Bae J. Y., Kim K. Y., Kim J. H., Lee K., Cho J. C., Cha C. J. ( 2010 ). Paenibacillus aestuarii sp. nov., isolated from an estuarine wetland. . Int J Syst Evol Microbiol 60, 644647. [CrossRef] [PubMed]
    [Google Scholar]
  3. Baek S. H., Yi T. H., Lee S. T., Im W. T. ( 2010 ). Paenibacillus pocheonensis sp. nov., a facultative anaerobe isolated from soil of a ginseng field. . Int J Syst Evol Microbiol 60, 11631167. [CrossRef] [PubMed]
    [Google Scholar]
  4. Baik K. S., Lim C. H., Choe H. N., Kim E. M., Seong C. N. ( 2011 ). Paenibacillus rigui sp. nov., isolated from a freshwater wetland. . Int J Syst Evol Microbiol 61, 529534. [CrossRef] [PubMed]
    [Google Scholar]
  5. Benardini J. N., Vaishampayan P. A., Schwendner P., Swanner E., Fukui Y., Osman S., Satomi M., Venkateswaran K. ( 2011 ). Paenibacillus phoenicis sp. nov., isolated from the Phoenix Lander assembly facility and a subsurface molybdenum mine. . Int J Syst Evol Microbiol 61, 13381343. [CrossRef] [PubMed]
    [Google Scholar]
  6. Claus D., Berkeley R. C. W. ( 1986 ). Genus Bacillus Cohn 1872, 174AL. . In Bergey’s Manual of Systematic Bacteriology, vol. 2, pp. 11051139. Edited by Sneath P. H. A., Mair N. S., Sharpe M. E., Holt J. G. . Baltimore:: Williams & Wilkins;.
    [Google Scholar]
  7. Collins M. D. ( 1985 ). Analysis of isoprenoid quinones. . Methods Microbiol 18, 329366. [CrossRef]
    [Google Scholar]
  8. Cowan S. T., Steel K. J. ( 1965 ). Manual for the Identification of Medical Bacteria. London:: Cambridge University Press;.
    [Google Scholar]
  9. Daane L. L., Harjono I., Barns S. M., Launen L. A., Palleron N. J., Häggblom M. M. ( 2002 ). PAH-degradation by Paenibacillus spp. and description of Paenibacillus naphthalenovorans sp. nov., a naphthalene-degrading bacterium from the rhizosphere of salt marsh plants. . Int J Syst Evol Microbiol 52, 131139.[PubMed]
    [Google Scholar]
  10. De Ley J., Cattoir H., Reynaerts A. ( 1970 ). The quantitative measurement of DNA hybridization from renaturation rates. . Eur J Biochem 12, 133142. [CrossRef] [PubMed]
    [Google Scholar]
  11. Embley T. M., Wait R. ( 1994 ). Structural lipids of eubacteria. . In Chemical Methods in Prokaryotic Systematics, pp. 121161. Edited by Goodfellow M., O’Donnell A. G. . Chichester:: Wiley;.
    [Google Scholar]
  12. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [CrossRef]
    [Google Scholar]
  13. Fitch W. M. ( 1971 ). Toward defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20, 406416. [CrossRef]
    [Google Scholar]
  14. Gordon R. E., Haynes W. C., Pang C. H.-N. ( 1973 ). The Genus Bacillus. US Department of Agriculture Handbook no. 427. Washington, DC:: Agricultural Research Service;.
    [Google Scholar]
  15. Huss V. A. R., Festl H., Schleifer K. H. ( 1983 ). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. . Syst Appl Microbiol 4, 184192. [CrossRef] [PubMed]
    [Google Scholar]
  16. Jin H. J., Lv J., Chen S. F. ( 2011 ). Paenibacillus sophorae sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Sophora japonica . . Int J Syst Evol Microbiol 61, 767771. [CrossRef] [PubMed]
    [Google Scholar]
  17. Kim K. K., Lee K. C., Yu H., Ryoo S., Park Y., Lee J. S. ( 2010 ). Paenibacillus sputi sp. nov., isolated from the sputum of a patient with pulmonary disease. . Int J Syst Evol Microbiol 60, 23712376. [CrossRef] [PubMed]
    [Google Scholar]
  18. 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, 716721. [CrossRef] [PubMed]
    [Google Scholar]
  19. Kishore K. H., Begum Z., Pathan A. A. K., Shivaji S. ( 2010 ). Paenibacillus glacialis sp. nov., isolated from the Kafni glacier of the Himalayas, India. . Int J Syst Evol Microbiol 60, 19091913. [CrossRef] [PubMed]
    [Google Scholar]
  20. Komagata K., Suzuki K. ( 1987 ). Lipid and cell-wall analysis in bacterial systematics. . Methods Microbiol 19, 161207. [CrossRef]
    [Google Scholar]
  21. Kumar S., Tamura K., Jakobsen I.-B., Nei M. ( 2001 ). mega2: molecular evolutionary genetics analysis software. . Bioinformatics 17, 12441245. [CrossRef] [PubMed]
    [Google Scholar]
  22. Lim J. M., Jeon C. O., Park D. J., Xu L. H., Jiang C. L., Kim C. J. ( 2006 ). Paenibacillus xinjiangensis sp. nov., isolated from Xinjiang province in China. . Int J Syst Evol Microbiol 56, 25792582. [CrossRef] [PubMed]
    [Google Scholar]
  23. Liu Y., Liu L., Qiu F., Schumann P., Shi Y., Zou Y., Zhang X., Song W. ( 2010 ). Paenibacillus hunanensis sp. nov., isolated from rice seeds. . Int J Syst Evol Microbiol 60, 12661270. [CrossRef] [PubMed]
    [Google Scholar]
  24. Logan N. A., Berge O., Bishop A. H., Busse H.-J., De Vos P., Fritze D., Heyndrickx M., Kämpfer P., Rabinovitch L. & other authors ( 2009 ). Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. . Int J Syst Evol Microbiol 59, 21142121. [CrossRef] [PubMed]
    [Google Scholar]
  25. Ma Y. C., Chen S. F. ( 2008 ). Paenibacillus forsythiae sp. nov., a nitrogen-fixing species isolated from rhizosphere soil of Forsythia mira . . Int J Syst Evol Microbiol 58, 319323. [CrossRef] [PubMed]
    [Google Scholar]
  26. Ma Y., Xia Z., Liu X., Chen S. ( 2007a ). Paenibacillus sabinae sp. nov., a nitrogen-fixing species isolated from the rhizosphere soils of shrubs. . Int J Syst Evol Microbiol 57, 611. [CrossRef] [PubMed]
    [Google Scholar]
  27. Ma Y., Zhang J., Chen S. ( 2007b ). Paenibacillus zanthoxyli sp. nov., a novel nitrogen-fixing species isolated from the rhizosphere of Zanthoxylum simulans . . Int J Syst Evol Microbiol 57, 873877. [CrossRef] [PubMed]
    [Google Scholar]
  28. Minnikin D. E., Alshamaony L., Goodfellow M. ( 1975 ). Differentiation of Mycobacterium, Nocardia, and related taxa by thin layer chromatographic analysis of whole-cell methanolysates. . J Gen Microbiol 88, 200204. [CrossRef]
    [Google Scholar]
  29. Minnikin D., O’Donnell A., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J. ( 1984 ). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. . J Microbiol Methods 2, 233241. [CrossRef]
    [Google Scholar]
  30. Montes M. J., Mercadé E., Bozal N., Guinea J. ( 2004 ). Paenibacillus antarcticus sp. nov., a novel psychrotolerant organism from the Antarctic environment. . Int J Syst Evol Microbiol 54, 15211526. [CrossRef] [PubMed]
    [Google Scholar]
  31. Moon J. C., Jung Y. J., Jung J. H., Jung H. S., Cheong Y. R., Jeon C. O., Lee K. O., Lee S. Y. ( 2011 ). Paenibacillus sacheonensis sp. nov., a xylanolytic and cellulolytic bacterium isolated from tidal flat sediment. . Int J Syst Evol Microbiol 61, 27532757. [CrossRef] [PubMed]
    [Google Scholar]
  32. Oh H. W., Kim B. C., Lee K. H., Kim Y., Park D. S., Park H. M., Bae K. S. ( 2008 ). Paenibacillus camelliae sp. nov., isolated from fermented leaves of Camellia sinensis . . J Microbiol 46, 530534. [CrossRef] [PubMed]
    [Google Scholar]
  33. Park D. S., Jeong W. J., Lee K. H., Oh H. W., Kim B. C., Bae K. S., Park H. Y. ( 2009 ). Paenibacillus pectinilyticus sp. nov., isolated from the gut of Diestrammena apicalis . . Int J Syst Evol Microbiol 59, 13421347. [CrossRef] [PubMed]
    [Google Scholar]
  34. Park M. H., Traiwan J., Jung M. Y., Nam Y. S., Jeong J. H., Kim W. ( 2011 ). Paenibacillus chungangensis sp. nov., isolated from a tidal-flat sediment. . Int J Syst Evol Microbiol 61, 281285. [CrossRef] [PubMed]
    [Google Scholar]
  35. Priest F. G., Goodfellow M., Todd C. ( 1981 ). The genus Bacillus: a numerical analysis. . In The Aerobic Endospore-Forming Bacteria. Classification and Identification, pp. 91103. Edited by Berkeley R. C. W., Goodfellow M. . London:: Academic Press;.
    [Google Scholar]
  36. Rhodes-Roberts M. ( 1981 ). The taxonomy of some nitrogen-fixing Bacillus species with special reference to nitrogen fixation. . In The Aerobic Endospore-Forming Bacteria. Classification and Identification, pp. 315335. Edited by Berkeley R. C. W., Goodfellow M. . London:: Academic Press;.
    [Google Scholar]
  37. Rivas R., Mateos P. F., Martínez-Molina E., Velázquez E. ( 2005 ). Paenibacillus xylanilyticus sp. nov., an airborne xylanolytic bacterium. . Int J Syst Evol Microbiol 55, 405408. [CrossRef] [PubMed]
    [Google Scholar]
  38. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  39. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. . Newark, DE:: MIDI Inc.;
  40. Slepecky E. B., Hemphill E. ( 1991 ). The genus Bacillus nonmedical. . In The Prokaryotes, vol. 2, pp. 16631696. Edited by Balows A., Truper H. G., Dworkin M., Harder W., Schleifer K.-H. . New York:: Springer;.
    [Google Scholar]
  41. Šmerda J., Sedlácek I., Pácová Z., Durnová E., Smísková A., Havel L. ( 2005 ). Paenibacillus mendelii sp. nov., from surface-sterilized seeds of Pisum sativum L.. Int J Syst Evol Microbiol 55, 23512354. [CrossRef] [PubMed]
    [Google Scholar]
  42. Smibert R. M., Krieg N. R. ( 1994 ). Phenotypic characterization. . In Manual of Methods for General and Microbiology Bacteriology, pp. 607654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  43. Tamaoka J., Komagata K. ( 1984 ). Determination of DNA base composition by reverse-phase high-performance liquid chromatography. . FEMS Microbiol Lett 25, 125128. [CrossRef]
    [Google Scholar]
  44. Tamura K., Nei M. ( 1993 ). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. . Mol Biol Evol 10, 512526.[PubMed]
    [Google Scholar]
  45. 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, 27312739. [CrossRef] [PubMed]
    [Google Scholar]
  46. Tang Q. Y., Yang N., Wang J., Xie Y. Q., Ren B., Zhou Y. G., Gu M. Y., Mao J., Li W. J. & other authors ( 2011 ). Paenibacillus algorifonticola sp. nov., isolated from a cold spring. . Int J Syst Evol Microbiol 61, 21672172. [CrossRef] [PubMed]
    [Google Scholar]
  47. 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]
  48. Tindall B. J., Rosselló-Móra R., Busse H.-J., Ludwig W., Kämpfer P. ( 2010 ). Notes on the characterization of prokaryote strains for taxonomic purposes. . Int J Syst Evol Microbiol 60, 249266. [CrossRef] [PubMed]
    [Google Scholar]
  49. Traiwan J., Park M. H., Kim W. ( 2011 ). Paenibacillus puldeungensis sp. nov., isolated from a grassy sandbank. . Int J Syst Evol Microbiol 61, 670673. [CrossRef] [PubMed]
    [Google Scholar]
  50. Vaz-Moreira I., Figueira V., Lopes A. R., Pukall R., Spröer C., Schumann P., Nunes O. C., Manaia C. M. ( 2010 ). Paenibacillus residui sp. nov., isolated from urban waste compost. . Int J Syst Evol Microbiol 60, 24152419. [CrossRef] [PubMed]
    [Google Scholar]
  51. 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, 463464. [CrossRef]
    [Google Scholar]
  52. Yanagi M., Yamasato K. ( 1993 ). Phylogenetic analysis of the family Rhizobiaceae and related bacteria by sequencing of 16S rRNA gene using PCR and DNA sequencer. . FEMS Microbiol Lett 107, 115120. [CrossRef] [PubMed]
    [Google Scholar]
  53. Yoon J.-H., Kim H., Kim S.-B., Kim H.-J., Kim W. Y., Lee S. T., Goodfellow M., Park Y.-H. ( 1996 ). Identification of Saccharomonospora strains by the use of genomic DNA fragments and rRNA gene probes. . Int J Syst Bacteriol 46, 502505. [CrossRef]
    [Google Scholar]
  54. Yoon J.-H., Kang S.-J., Yeo S.-H., Oh T.-K. ( 2005 ). Paenibacillus alkaliterrae sp. nov., isolated from an alkaline soil in Korea. . Int J Syst Evol Microbiol 55, 23392344. [CrossRef] [PubMed]
    [Google Scholar]
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