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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 65, Issue Pt_5

sp. nov., an actinobacterium isolated from desert soil Free

Abstract

A rod- or coccus-shaped, non-spore-forming actinobacterium, designated strain SC8A-24, was isolated from a soil sample collected from the rhizosphere of on the southern edge of the Taklimakan desert, Xinjiang, China, and examined by a polyphasic approach to clarify its taxonomic position. This actinobacterium was Gram-staining-positive and aerobic. Substrate and aerial mycelia were not observed, and no diffusible pigments were observed on the media tested. Strain SC8A-24 grew optimally without NaCl at 28–30 °C and pH 7.0–8.0. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain SC8A-24 belonged to the genus and shared the highest 16S rRNA gene sequence similarity with CL-Z59 (96.51 %), OS4 (96.43 %) and BX5-10 (96.37 %). The DNA G+C content of strain SC8A-24 was 71 mol%. The cell-wall peptidoglycan contained -2,6-diaminopimelic acid, and MK-8(H) was the predominant menaquinone. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid and an unidentified phospholipid. The major fatty acids were Cω8, 10-methyl C and Cω9. On the basis of phylogenetic analysis and phenotypic and chemotaxonomic characteristics, strain SC8A-24 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is SC8A-24 ( = DSM 26045 = CGMCC 4.7183).

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Funding
This study was supported by the:
  • National Natural Sciences Foundation of China (Award 81172963 and 81373308)
  • National Science and Technology Major Project from the Ministry of Science and Technology of China (Award 2012ZX09301-002-001-018)
  • Specialized Research Fund for the Doctoral Programme of Higher Education from the Ministry of Education of China (Award 20111106110032)
© 2015 IUMS
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2015-05-01
2024-05-02
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References

  1. Cappuccino J. G., Sherman N. ( 2002 ). Microbiology: a Laboratory Manual, , 6th edn.. San Francisco:: Benjamin Cummings Pearson Education;.
     [Google Scholar]
  2. Cho Y., Jang G. I., Cho B. C. ( 2013 a). Nocardioides marinquilinus sp. nov., isolated from coastal seawater. . Int J Syst Evol Microbiol 63, 2594–2599. [View Article] [PubMed]
    [Google Scholar]
  3. Cho Y., Jang G. I., Hwang C. Y., Kim E.-H., Cho B. C. ( 2013 b). Nocardioides salsibiostraticola sp. nov., isolated from biofilm formed in coastal seawater. . Int J Syst Evol Microbiol 63, 3800–3806. [View Article] [PubMed]
    [Google Scholar]
  4. Choi D. H., Kim H. M., Noh J.-H., Cho B. C. ( 2007 ). Nocardioides marinus sp. nov.. Int J Syst Evol Microbiol 57, 775–779. [View Article] [PubMed]
    [Google Scholar]
  5. Chou J.-H., Cho N.-T., Arun A. B., Young C. C., Chen W.-M. ( 2008 ). Nocardioides fonticola sp. nov., a novel actinomycete isolated from spring water. . Int J Syst Evol Microbiol 58, 1864–1868. [View Article] [PubMed]
    [Google Scholar]
  6. Chun J., Lee J.-H., Jung Y., Kim M., Kim S., Kim B. K., Lim Y.-W. ( 2007 ). EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. . Int J Syst Evol Microbiol 57, 2259–2261. [View Article] [PubMed]
    [Google Scholar]
  7. Collins M. D., Pirouz T., Goodfellow M., Minnikin D. E. ( 1977 ). Distribution of menaquinones in actinomycetes and corynebacteria. . J Gen Microbiol 100, 221–230. [View Article] [PubMed]
    [Google Scholar]
  8. Collins M. D., Cockcroft S., Wallbanks S. ( 1994 ). Phylogenetic analysis of a new ll-diaminopimelic acid-containing coryneform bacterium from herbage, Nocardioides plantarum sp. nov.. Int J Syst Bacteriol 44, 523–526. [View Article] [PubMed]
    [Google Scholar]
  9. Dastager S. G., Lee J.-C., Ju Y.-J., Park D.-J., Kim C.-J. ( 2009 ). Nocardioides sediminis sp. nov., isolated from a sediment sample. . Int J Syst Evol Microbiol 59, 280–284. [View Article] [PubMed]
    [Google Scholar]
  10. Dong Y.-P., Guo L., Habden X., Liu J.-M., Chen C., Jiang Z.-K., Li X., Zhu X.-L., Cao C.-W. et al. ( 2013 ). Study on diversity and bioactivity of actinomycetes isolated from the south edge of the Taklamakan Desert. . Chin J Antibiot 38, 241–247.
     [Google Scholar]
  11. Euzéby J. P. ( 1997 ). List of bacterial names with standing in nomenclature: a folder available on the Internet. . Int J Syst Bacteriol 47, 590–592. [View Article] [PubMed]
    [Google Scholar]
  12. Evtushenko L. I., Krausova V. I., Yoon J.-H. ( 2012 ). Genus I. Nocardioides Prauser 1976, 61AL . . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 5, pp. 1197–1251. Edited by Whitman W. B., Goodfellow M., Kämpfer P., Busse H.-J., Trujillo M. E., Ludwig W., Suzuki K., Parte A. . New York:: Springer;.
     [Google Scholar]
  13. Fan X., Qiao Y., Gao X., Zhang X.-H. ( 2014 ). Nocardioides pacificus sp. nov., isolated from deep sub-seafloor sediment. . Int J Syst Evol Microbiol 64, 2217–2222. [View Article] [PubMed]
    [Google Scholar]
  14. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368–376. [View Article] [PubMed]
    [Google Scholar]
  15. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783–791. [View Article]
    [Google Scholar]
  16. Fitch W. M. ( 1971 ). Toward defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20, 406–416. [View Article]
    [Google Scholar]
  17. Gonzalez C., Gutierrez C., Ramirez C. ( 1978 ). Halobacterium vallismortis sp. nov. An amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. . Can J Microbiol 24, 710–715. [View Article] [PubMed]
    [Google Scholar]
  18. Gordon R. E., Smith M. M. ( 1955 ). Proposed group of characters for the separation of Streptomyces and Nocardia . . J Bacteriol 69, 147–150.[PubMed]
    [Google Scholar]
  19. Kelly K. L. ( 1964 ). Inter-Society Color Council-National Bureau of Standards Color Name Charts Illustrated with Centroid Colors. Washington, DC:: US Government Printing Office;.
     [Google Scholar]
  20. Kim K.-H., Roh S. W., Chang H.-W., Nam Y.-D., Yoon J.-H., Jeon C. O., Oh H.-M., Bae J.-W. ( 2009 ). Nocardioides basaltis sp. nov., isolated from black beach sand. . Int J Syst Evol Microbiol 59, 42–47. [View Article] [PubMed]
    [Google Scholar]
  21. Kimura M. ( 1983 ). The Neutral Theory of Molecular Evolution. Cambridge:: Cambridge University Press;. [View Article]
    [Google Scholar]
  22. Lawson P. A., Collins M. D., Schumann P., Tindall B. J., Hirsch P., Labrenz M. ( 2000 ). New ll-diaminopimelic acid-containing actinomycetes from hypersaline, heliothermal and meromictic Antarctic Ekho Lake: Nocardioides aquaticus sp. nov. and Friedmannielly lacustris sp. nov.. Syst Appl Microbiol 23, 219–229. [View Article] [PubMed]
    [Google Scholar]
  23. Lee S. D. ( 2007 ). Nocardioides furvisabuli sp. nov., isolated from black sand. . Int J Syst Evol Microbiol 57, 35–39. [View Article] [PubMed]
    [Google Scholar]
  24. Lee D. W., Hyun C.-G., Lee S. D. ( 2007 ). Nocardioides marinisabuli sp. nov., a novel actinobacterium isolated from beach sand. . Int J Syst Evol Microbiol 57, 2960–2963. [View Article] [PubMed]
    [Google Scholar]
  25. Lee S.-H., Liu Q.-M., Lee S.-T., Kim S.-C., Im W.-T. ( 2012 ). Nocardioides ginsengagri sp. nov., isolated from the soil of a ginseng field. . Int J Syst Evol Microbiol 62, 591–595. [View Article] [PubMed]
    [Google Scholar]
  26. Li W.-J., Xu P., Schumann P., Zhang Y.-Q., Pukall R., Xu L.-H., Stackebrandt E., Jiang C.-L. ( 2007 ). Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia . . Int J Syst Evol Microbiol 57, 1424–1428. [View Article] [PubMed]
    [Google Scholar]
  27. Magee C. M., Rodeheaver G., Edgerton M. T., Edlich R. F. ( 1975 ). A more reliable gram staining technic for diagnosis of surgical infections. . Am J Surg 130, 341–346. [View Article] [PubMed]
    [Google Scholar]
  28. Marmur J. ( 1961 ). A procedure for the isolation of deoxyribonucleic acid from microorganisms. . J Mol Biol 3, 208–218. [View Article]
    [Google Scholar]
  29. Mesbah M., Premachandran U., Whitman W. B. ( 1989 ). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. . Int J Syst Bacteriol 39, 159–167. [View Article]
    [Google Scholar]
  30. 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]
  31. Park S. C., Baik K. S., Kim M. S., Chun J., Seong C. N. ( 2008 ). Nocardioides dokdonensis sp. nov., an actinomycete isolated from sand sediment. . Int J Syst Evol Microbiol 58, 2619–2623. [View Article] [PubMed]
    [Google Scholar]
  32. Prauser H. ( 1976 ). Nocardioides, a new genus of the order Actinomycetales. . Int J Syst Bacteriol 26, 58–65. [View Article]
    [Google Scholar]
  33. 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]
  34. Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
  35. Schleifer K. H., Kandler O. ( 1972 ). Peptidoglycan types of bacterial cell walls and their taxonomic implications. . Bacteriol Rev 36, 407–477.[PubMed]
    [Google Scholar]
  36. Shirling E. B., Gottlieb D. ( 1966 ). Methods for characterization of Streptomyces species. . Int J Syst Bacteriol 16, 313–340. [View Article]
    [Google Scholar]
  37. 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]
  38. 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]
  39. Waksman S. A. ( 1961 ). The Actinomycetes, vol. 2. Baltimore:: Williams & Wilkins;.
     [Google Scholar]
  40. Wu C., Lu X., Qin M., Wang Y., Ruan J. ( 1989 ). Analysis of menaquinone compound in microbial cells by HPLC. . Microbiology [English translation of Microbiology (Beijing)] 16, 176–178.
     [Google Scholar]
  41. Xu P., Li W.-J., Tang S.-K., Zhang Y.-Q., Chen G.-Z., Chen H.-H., Xu L.-H., Jiang C.-L. ( 2005 ). Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China. . Int J Syst Evol Microbiol 55, 1149–1153. [View Article] [PubMed]
    [Google Scholar]
  42. Yi H., Chun J. ( 2004 a). Nocardioides ganghwensis sp. nov., isolated from tidal flat sediment. . Int J Syst Evol Microbiol 54, 1295–1299. [View Article] [PubMed]
    [Google Scholar]
  43. Yi H., Chun J. ( 2004 b). Nocardioides aestuarii sp. nov., isolated from tidal flat sediment. . Int J Syst Evol Microbiol 54, 2151–2154. [View Article] [PubMed]
    [Google Scholar]
  44. Yoon J.-H., Kim I.-G., Lee M.-H., Lee C.-H., Oh T.-K. ( 2005 a). Nocardioides alkalitolerans sp. nov., isolated from an alkaline serpentinite soil in Korea. . Int J Syst Evol Microbiol 55, 809–814. [View Article] [PubMed]
    [Google Scholar]
  45. Yoon J.-H., Kim I.-G., Lee M.-H., Oh T.-K. ( 2005 b). Nocardioides kribbensis sp. nov., isolated from an alkaline soil. . Int J Syst Evol Microbiol 55, 1611–1614. [View Article] [PubMed]
    [Google Scholar]
  46. Yoon J.-H., Lee C.-H., Oh T.-K. ( 2005 c). Nocardioides dubius sp. nov., isolated from an alkaline soil. . Int J Syst Evol Microbiol 55, 2209–2212. [View Article] [PubMed]
    [Google Scholar]
  47. Yoon J.-H., Lee C.-H., Oh T.-K. ( 2006 ). Nocardioides lentus sp. nov., isolated from an alkaline soil. . Int J Syst Evol Microbiol 56, 271–275. [View Article] [PubMed]
    [Google Scholar]
  48. Zhang D.-F., Zhong J.-M., Zhang X.-M., Jiang Z., Zhou E.-M., Tian X.-P., Zhang S., Li W.-J. ( 2014 ). Nocardioides nanhaiensis sp. nov., an actinobacterium isolated from a marine sediment sample. . Int J Syst Evol Microbiol 64, 2718–2722. [View Article] [PubMed]
    [Google Scholar]
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Nocardioides deserti sp. nov., an actinobacterium isolated from desert soil
Int J Syst Evol Microbiol 65, 1604 (2015); https://doi.org/10.1099/ijs.0.000147
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