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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 64, Issue Pt_1

sp. nov., isolated from sandy soil Free

Abstract

A novel, Gram-stain-negative, non-motile, non-spore-forming, short rod-shaped, aerobic bacterium designated H-12 was isolated from a mixed sandy soil sample collected from Xinjiang, China. Strain H-12 grew at 20–37 °C (optimum, 30 °C), pH 7.0–11.0 (optimum, pH 8.5) on TGY medium with 0–5 % NaCl (w/v). 16S rRNA gene sequence analysis indicated that strain H-12 shared sequence similarities with DSM 18850 (90.0 %). Strain H-12 showed a low level of DNA–DNA relatedness to DSM 18850 (45.5 %). The predominant isoprenoid quinone of strain H-12 was MK-7 and the major polar lipid was phosphatidylethanolamine. The predominant cellular fatty acids were Cω7 and/or Cω6, iso-C, iso-C 3-OH, C, C 3-OH and iso-C 3-OH. DNA G+C content of strain H-12 was 44.15 mol%. On the basis of phenotypic, genetic and phylogenetic data, strain H-12 is proposed to be a representative of a novel species of the genus , for which the name sp. nov. is suggested and the type strain is H-12 ( = ACCC 05758 = KCTC 32294).

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Funding
This study was supported by the:
  • Ministry of Science and Technology of China (Award 2010CB126504, 2013CB733903 and 2012AA063503)
  • Important National Science & Technology Specific Projects (Award 2013ZX08009-003 and 2013ZX08012-001)
  • National Natural Science Foundation of China (Award 31230004, 30925002 and 31170105)
  • Special Fund for Agro-scientific Research in the Public Interest
© 2014 IUMS
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2014-01-01
2024-04-19
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References

  1. Albert R. A., Waas N. E., Pavlons S. C., Pearson J. L., Ketelboeter L., Rosselló-Móra R., Busse H.-J. ( 2013 ). Sphingobacterium psychroaquaticum sp. nov., a psychrophilic bacterium isolated from Lake Michigan water. . Int J Syst Evol Microbiol 63, 952–958. [View Article] [PubMed]
    [Google Scholar]
  2. Choi H.-A., Lee S.-S. ( 2012 ). Sphingobacterium kyonggiense sp. nov., isolated from chloroethene-contaminated soil, and emended descriptions of Sphingobacterium daejeonense and Sphingobacterium mizutaii . . Int J Syst Evol Microbiol 62, 2559–2564. [View Article] [PubMed]
    [Google Scholar]
  3. Collins M. D., Jones D. ( 1980 ). Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. . J Appl Bacteriol 48, 459–470. [View Article]
    [Google Scholar]
  4. Cowan S. T., Barrow G. I., Steel K. J., Feltham R. K. A. ( 2003 ). Cowan and Steel’s Manual for the Identification of Medical Bacteria. Cambridge:: Cambridge University Press;.
     [Google Scholar]
  5. Duan S., Liu Z., Feng X., Zheng K., Cheng L. ( 2009 ). Sphingobacterium bambusae sp. nov., isolated from soil of bamboo plantation. . J Microbiol 47, 693–698. [View Article] [PubMed]
    [Google Scholar]
  6. Duan S., Liu Z., Feng X., Zheng K., Cheng L. ( 2010 ). Sphingobacterium bambusae sp. nov. In List of New Names And New Combinations Previously Effectively, but not Validly, Published, Validation List no. 134. . Int J Syst Evol Microbiol 60, 1477–1479. [View Article]
    [Google Scholar]
  7. Ezaki T., Hashimoto Y., Takeuchi N., Yamamoto H., Liu S. L., Miura H., Matsui K., Yabuuchi E. ( 1988 ). Simple genetic method to identify viridans group streptococci by colorimetric dot hybridization and fluorometric hybridization in microdilution wells. . J Clin Microbiol 26, 1708–1713.[PubMed]
    [Google Scholar]
  8. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783–791. [View Article]
    [Google Scholar]
  9. He X., Xiao T., Kuang H., Lan X., Tudahong M., Osman G., Fang C., Rahman E. ( 2010 ). Sphingobacterium shayense sp. nov., isolated from forest soil. . Int J Syst Evol Microbiol 60, 2377–2381. [View Article] [PubMed]
    [Google Scholar]
  10. Holmes B., Owen R. J., Hollis D. G. ( 1982 ). Flavobacterium spiritivorum, a new species isolated from human clinical specimens. . Int J Syst Bacteriol 32, 157–165. [View Article]
    [Google Scholar]
  11. Kämpfer P., Kroppenstedt R. M. ( 1996 ). Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. . Can J Microbiol 42, 989–1005. [View Article]
    [Google Scholar]
  12. Kämpfer P., Lodders N., Martin K., Avendaño-Herrera R. ( 2012 ). Flavobacterium chilense sp. nov. and Flavobacterium araucananum sp. nov., isolated from farmed salmonid fish. . Int J Syst Evol Microbiol 62, 1402–1408. [View Article] [PubMed]
    [Google Scholar]
  13. Kim K. H., Ten L. N., Liu Q. M., Im W. T., Lee S. T. ( 2006 ). Sphingobacterium daejeonense sp. nov., isolated from a compost sample. . Int J Syst Evol Microbiol 56, 2031–2036. [View Article] [PubMed]
    [Google Scholar]
  14. Kim S.-J., Weon H.-Y., Kim Y.-S., Yoo S.-H., Kim B.-Y., Anandham R., Kwon S.-W. ( 2010 ). Parapedobacter luteus sp. nov. and Parapedobacter composti sp. nov., isolated from cotton waste compost. . Int J Syst Evol Microbiol 60, 1849–1853. [View Article] [PubMed]
    [Google Scholar]
  15. Lee D.-H., Hur J. S., Kahng H.-Y. ( 2013 ). Sphingobacterium cladoniae sp. nov., isolated from lichen, Cladonia sp., and emended description of Sphingobacterium siyangense . . Int J Syst Evol Microbiol 63, 755–760. [View Article] [PubMed]
    [Google Scholar]
  16. Liu R., Liu H., Zhang C. X., Yang S. Y., Liu X. H., Zhang K. Y., Lai R. ( 2008 ). Sphingobacterium siyangense sp. nov., isolated from farm soil. . Int J Syst Evol Microbiol 58, 1458–1462. [View Article] [PubMed]
    [Google Scholar]
  17. Liu J., Yang L.-L., Xu C.-K., Xi J.-Q., Yang F.-X., Zhou F., Zhou Y., Mo M.-H., Li W.-J. ( 2012 ). Sphingobacterium nematocida sp. nov., a nematicidal endophytic bacterium isolated from tobacco. . Int J Syst Evol Microbiol 62, 1809–1813. [View Article] [PubMed]
    [Google Scholar]
  18. Ludwig W., Euzeby J., Whitman W. B. ( 2008 ). Draft Taxonomic Outline of the Bacteroidetes, Planctomycetes, Chlamydiae, Spirochaetes, Fibrobacteres, Fusobacteria, Acidobacteria, Verrucomicrobia, Dictyoglomi, and Gemmatimonadetes . . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 4, pp. 21–24. Edited by Krieg N. R., Staley J. T., Brown D. R., Hedlund B., Paster B. J., Ward N., Ludwig W., Whitman W. B. . New York:: Springer;.
    [Google Scholar]
  19. 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]
  20. Marqués A. M., Burgos-Díaz C., Aranda F. J., Teruel J. A., Manresa À., Ortiz A., Farfán M. ( 2012 ). Sphingobacterium detergens sp. nov., a surfactant-producing bacterium isolated from soil. . Int J Syst Evol Microbiol 62, 3036–3041. [View Article] [PubMed]
    [Google Scholar]
  21. Matsuyama H., Katoh H., Ohkushi T., Satoh A., Kawahara K., Yumoto I. ( 2008 ). Sphingobacterium kitahiroshimense sp. nov., isolated from soil. . Int J Syst Evol Microbiol 58, 1576–1579. [View Article] [PubMed]
    [Google Scholar]
  22. Mehnaz S., Weselowski B., Lazarovits G. ( 2007 ). Sphingobacterium canadense sp. nov., an isolate from corn roots. . Syst Appl Microbiol 30, 519–524. [View Article] [PubMed]
    [Google Scholar]
  23. Mehnaz S., Weselowski B., Lazarovits G. ( 2008 ). Sphingobacterium canadense sp. nov. In List of New Names And New Combinations Previously Effectively, but not Validly, Published, Validation List no. 119. . Int J Syst Evol Microbiol 58, 1–2. [View Article] [PubMed]
    [Google Scholar]
  24. 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]
  25. Ntougias S., Fasseas C., Zervakis G. I. ( 2007 ). Olivibacter sitiensis gen. nov., sp. nov., isolated from alkaline olive-oil mill wastes in the region of Sitia, Crete. . Int J Syst Evol Microbiol 57, 398–404. [View Article] [PubMed]
    [Google Scholar]
  26. Owen R. J., Lapage S. P. ( 1976 ). The thermal denaturation of partly purified bacterial deoxyribonucleic acid and its taxonomic applications. . J Appl Bacteriol 41, 335–340. [View Article] [PubMed]
    [Google Scholar]
  27. Park M., Ryu S. H., Vu T. H., Ro H.-S., Yun P.-Y., Jeon C. O. ( 2007 ). Flavobacterium defluvii sp. nov., isolated from activated sludge. . Int J Syst Evol Microbiol 57, 233–237. [View Article] [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. Schmidt V. S. J., Wenning M., Scherer S. ( 2012 ). Sphingobacterium lactis sp. nov. and Sphingobacterium alimentarium sp. nov., isolated from raw milk and a dairy environment. . Int J Syst Evol Microbiol 62, 1506–1511. [View Article] [PubMed]
    [Google Scholar]
  30. Shivaji S., Ray M. K., Shyamala Rao N., Saisree L., Jagannadham M. V., Seshu Kumar G., Reddy G. S. N., Bhargava P. M. ( 1992 ). Sphingobacterium antarcticus sp. nov., a psychrotrophic bacterium from the soils of Schirmacher Oasis, Antarctica. . Int J Syst Bacteriol 42, 102–106. [View Article]
    [Google Scholar]
  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. Steyn P. L., Segers P., Vancanneyt M., Sandra P., Kersters K., Joubert J. J. ( 1998 ). Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. proposal of the family Sphingobacteriaceae fam. nov.. Int J Syst Bacteriol 48, 165–177. [View Article] [PubMed]
    [Google Scholar]
  33. Takeuchi M., Yokota A. ( 1992 ). Proposals of Sphingobacterium faecium sp. nov., Sphingobacterium piscium sp. nov., Sphingobacterium heparinum comb. nov., Sphingobacterium thalpophilum comb. nov. and two genospecies of the genus Sphingobacterium, and synonymy of Flavobacterium yabuuchiae and Sphingobacterium spiritivorum . . J Gen Appl Microbiol 38, 465–482. [View Article]
    [Google Scholar]
  34. Takeuchi M., Yokota A. ( 1993 ). Sphingobacterium faecium sp. nov., Sphingobacterium piscium sp. nov. In Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB, List no. 47. . Int J Syst Bacteriol 43, 864–865. [View Article]
    [Google Scholar]
  35. Tamura K., Dudley J., Nei M., Kumar S. ( 2007 ). mega4: molecular evolutionary genetics analysis (mega) software version 4.0. . Mol Biol Evol 24, 1596–1599. [View Article] [PubMed]
    [Google Scholar]
  36. Ten L. N., Liu Q.-M., Im W.-T., Aslam Z., Lee S.-T. ( 2006 ). Sphingobacterium composti, sp. nov., a novel DNase producing bacterium isolated from compost. . J Microbiol Biotechnol 6, 1728–1733.
     [Google Scholar]
  37. 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 ). Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37, 463–464. [View Article]
    [Google Scholar]
  38. Wei W., Zhou Y., Wang X., Huang X., Lai R. ( 2008 ). Sphingobacterium anhuiense sp. nov., isolated from forest soil. . Int J Syst Evol Microbiol 58, 2098–2101. [View Article] [PubMed]
    [Google Scholar]
  39. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J. ( 1991 ). 16S ribosomal DNA amplification for phylogenetic study. . J Bacteriol 173, 697–703.[PubMed]
    [Google Scholar]
  40. Xiao T., He X., Cheng G., Kuang H. J., Ma X. R., Yusup K., Hamdun M., Gulsimay A., Fang C. X., Rahman E. ( 2013 ). Sphingobacterium hotanense sp. nov., isolated from soil of a Populus euphratica forest, and emended descriptions of Sphingobacterium daejeonense and Sphingobacterium shayense . . Int J Syst Evol Microbiol 63, 815–820. [View Article] [PubMed]
    [Google Scholar]
  41. Yabe S., Aiba Y., Sakai Y., Hazaka M., Kawahara K., Yokota A. ( 2013 ). Sphingobacterium thermophilum sp. nov., within the phylum Bacteroidetes isolated from compost. . Int J Syst Evol Microbiol 63, 1584–1588. [View Article] [PubMed]
    [Google Scholar]
  42. Yabuuchi E., Kaneko T., Yano I., Moss C. W., Miyoshi N. ( 1983 ). Sphingobacterium gen. nov., Sphingobacterium spiritivorum comb. nov., Sphingobacterium multivorum comb. nov., Sphingobacterium mizutae sp. nov., and Flavobacterium indologenes sp. nov.: glucose-nonfermenting gram-negative rods in CDC groups IIK-2 and IIb. . Int J Syst Bacteriol 33, 580–598. [View Article]
    [Google Scholar]
  43. Yoo S. H., Weon H. Y., Jang H. B., Kim B. Y., Kwon S. W., Go S. J., Stackebrandt E. ( 2007a ). Sphingobacterium composti sp. nov. In List of New Names And New Combinations Previously Effectively, but not Validly, Published, Validation List no. 116. . Int J Syst Evol Microbiol 57, 1371–1373. [View Article] [PubMed]
    [Google Scholar]
  44. Yoo S. H., Weon H. Y., Jang H. B., Kim B. Y., Kwon S. W., Go S. J., Stackebrandt E. ( 2007b ). Sphingobacterium composti sp. nov., isolated from cotton-waste composts. . Int J Syst Evol Microbiol 57, 1590–1593. [View Article] [PubMed]
    [Google Scholar]
  45. Zhang J., Zheng J.-W., Cho B. C., Hwang C. Y., Fang C. X., He J., Li S.-P. ( 2012 ). Sphingobacterium wenxiniae sp. nov., a cypermethrin-degrading species from activated sludge. . Int J Syst Evol Microbiol 62, 683–687. [View Article] [PubMed]
    [Google Scholar]
  46. Zhao J.-K., Li X.-M., Zhang M.-J., Jin J.-H., Jiang C.-Y., Liu S.-J. ( 2013 ). Parapedobacter pyrenivorans sp. nov., isolated from a pyrene-degrading microbial enrichment and emended description of the genus Parapedobacter . . Int J Syst Evol Microbiol 63, 3994–3999. [View Article] [PubMed]
    [Google Scholar]
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Sphingobacterium arenae sp. nov., isolated from sandy soil
Int J Syst Evol Microbiol 64, 248 (2014); https://doi.org/10.1099/ijs.0.051706-0
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