1887

Abstract

An actinomycete, designated XMU 198, was isolated from the rhizosphere soil of a pharmaceutical plant, Engl., collected in Xiamen City, China. 16S rRNA gene sequence analysis showed that the isolate exhibited highest sequence similarities with KACC 20148, Q41 and YIM 31975 (98.7, 98.4 and 98.2 %, respectively). The chemotaxonomic characteristics further supported the assignment of strain XMU 198 to the genus : -diaminopimelic acid in the cell-wall peptidoglycan; glucose and galactose with minor amounts of ribose as the whole-cell sugars; polar lipids comprising phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol and unidentified phospholipids; a fatty acid profile characterized by the predominance of iso-C, iso-C and anteiso-C; and MK-9(H) as the main menaquinone. Gyrase subunit B gene () sequence analysis showed that the genetic distances between strain XMU 198 and all other members of the genus were greater than 0.014, the value used as the threshold for species delineation within this genus. A wide range of genotypic and phenotypic characteristics, as well as DNA–DNA relatedness between strain XMU 198 and DSM 17836 (41.18 %), Q41 (38.02 %) and DSM 15500 (50.58 %), distinguished the isolate from its closest phylogenetic neighbours. On the basis of the above data, a novel species of the genus , sp. nov., is proposed. The type strain is XMU 198 ( = DSM 24683 = NBRC 107914).

Funding
This study was supported by the:
  • National Sciences Foundation of China (Award 30973566)
  • Fundamental Research Funds for the Central Universities (Award 2010121092)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.033290-0
2012-05-01
2024-04-18
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/62/5/1081.html?itemId=/content/journal/ijsem/10.1099/ijs.0.033290-0&mimeType=html&fmt=ahah

References

  1. Carlsohn M. R., Groth I., Spröer C., Schütze B., Saluz H. P., Munder T., Stackebrandt E. 2007a; Kribbella aluminosa sp. nov., isolated from a medieval alum slate mine. Int J Syst Evol Microbiol 57:1943–1947 [View Article][PubMed]
    [Google Scholar]
  2. Carlsohn M. R., Groth I., Tan G. Y., Schütze B., Saluz H.-P., Munder T., Yang J., Wink J., Goodfellow M. 2007b; Amycolatopsis saalfeldensis sp. nov., a novel actinomycete isolated from a medieval alum slate mine. Int J Syst Evol Microbiol 57:1640–1646 [View Article][PubMed]
    [Google Scholar]
  3. Christensen H., Angen O., Mutters R., Olsen J. E., Bisgaard M. 2000; DNA–DNA hybridization determined in micro-wells using covalent attachment of DNA. Int J Syst Evol Microbiol 50:1095–1102 [View Article][PubMed]
    [Google Scholar]
  4. 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]
  5. Groth I., Schütze B., Boettcher T., Pullen C. B., Rodriguez C., Leistner E., Goodfellow M. 2003; Kitasatospora putterlickiae sp. nov., isolated from rhizosphere soil, transfer of Streptomyces kifunensis to the genus Kitasatospora as Kitasatospora kifunensis comb. nov., and emended description of Streptomyces aureofaciens Duggar 1948. Int J Syst Evol Microbiol 53:2033–2040 [View Article][PubMed]
    [Google Scholar]
  6. He L., Li W., Huang Y., Wang L., Liu Z., Lanoot B., Vancanneyt M., Swings J. 2005; Streptomyces jietaisiensis sp. nov., isolated from soil in northern China. Int J Syst Evol Microbiol 55:1939–1944 [View Article][PubMed]
    [Google Scholar]
  7. Jarerat A., Pranamuda H., Tokiwa Y. 2002; Poly(l-lactide)-degrading activity in various actinomycetes. Macromol Biosci 9:420–428 [CrossRef]
    [Google Scholar]
  8. Jiang Y., Tang S. K., Wiese J., Xu L.-H, Imhoff J. F., Jiang C.-L. 2007; Streptomyces hainanensis sp. nov., a novel member of the genus Streptomyces . Int J Syst Evol Microbiol 57:2694–2698[PubMed]
    [Google Scholar]
  9. 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]
  10. 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]
  11. Kimura M. 1980; A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120 [View Article][PubMed]
    [Google Scholar]
  12. Kirby B. M., Le Roes M., Meyers P. R. 2006; Kribbella karoonensis sp. nov. and Kribbella swartbergensis sp. nov., isolated from soil from the Western Cape, South Africa.. Int J Syst Evol Microbiol 56:1097–1101[PubMed]
    [Google Scholar]
  13. Kirby B. M., Everest G. J., Meyers P. R. 2010; Phylogenetic analysis of the genus Kribbella based on the gyrB gene: proposal of a gyrB-sequence threshold for species delineation in the genus Kribbella . Antonie van Leeuwenhoek 97:131–142 [View Article][PubMed]
    [Google Scholar]
  14. Kuykendall L. D., Roy M. A., O’Neill J. J., Devine T. E. 1988; Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum . Int J Syst Bacteriol 38:358–361 [View Article]
    [Google Scholar]
  15. Lechevalier M. P., Lechevalier H. A. 1970; Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 20:435–443 [View Article]
    [Google Scholar]
  16. Lechevalier M. P., De Bievre C., Lechevalier H. A. 1977; Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 5:249–260 [View Article]
    [Google Scholar]
  17. Li W. J., Wang D., Zhang Y. Q., Schumann P., Stackebrandt E., Xu L. H., Jiang C. L. 2004; Kribbella antibiotica sp. nov., a novel nocardioform actinomycete strain isolated from soil in Yunnan, China. Syst Appl Microbiol 27:160–165[PubMed]
    [Google Scholar]
  18. Li W. J., Wang D., Zhang Y. Q., Xu L. H., Jiang C. L. 2006; Kribbella yunnanensis sp. nov., Kribbella alba sp. nov., two novel species of genus Kribbella isolated from soils in Yunnan, China. Syst Appl Microbiol 29:29–35 [View Article][PubMed]
    [Google Scholar]
  19. Miller L. T. 1982; Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 16:584–586[PubMed]
    [Google Scholar]
  20. Park Y. H., Yoon J. H., Shin Y. K., Suzuki K., Kudo T., Seino A., Kim H. J., Lee J. S., Lee S. T. 1999; Classification of ‘Nocardioides fulvus’ IFO 14399 and Nocardioides sp. ATCC 39419 in Kribbella gen. nov., as Kribbella flavida sp. nov. and Kribbella sandramycini sp. nov.. Int J Syst Bacteriol 49:743–752 [View Article][PubMed]
    [Google Scholar]
  21. 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]
  22. Shirling E. B., Gottlieb D. 1966; Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340 [View Article]
    [Google Scholar]
  23. Stackebrandt E. 1988; Phylogenetic relationships vs. phenotypic diversity: how to achieve a phylogenetic classification system of the eubacteria. Can J Microbiol 34:552–556 [View Article][PubMed]
    [Google Scholar]
  24. Staneck J. L., Roberts G. D. 1974; Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28:226–231[PubMed]
    [Google Scholar]
  25. Tamaoka J., Komagata K. 1984; Determination of DNA base composition by reverse-phase high-performance liquid chromatography. FEMS Microbiol Lett 25:125–128 [View Article]
    [Google Scholar]
  26. 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]
  27. 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]
  28. Tindall B. J. 1990a; A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13:128–130 [View Article]
    [Google Scholar]
  29. Tindall B. J. 1990b; Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 66:199–202 [View Article]
    [Google Scholar]
  30. Tindall B. J., Sikorski J., Smibert R. M., Krieg N. R. 2007; Phenotypic characterization and the principles of comparative systematics. In Methods for General and Molecular Microbiology, 3rd edn. pp. 330–393 Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G., Schmidt T. M., Snyder L. R. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  31. Trujillo M. E., Kroppenstedt R. M., Schumann P., Martínez-Molina E. 2006; Kribbella lupini sp. nov., isolated from the roots of Lupinus angustifolius . Int J Syst Evol Microbiol 56:407–411 [View Article][PubMed]
    [Google Scholar]
  32. Wu Y., Lu C., Qian X., Huang Y., Shen Y. 2009; Diversities within genotypes, bioactivity and biosynthetic genes of endophytic actinomycetes isolated from three pharmaceutical plants. Curr Microbiol 59:475–482 [View Article][PubMed]
    [Google Scholar]
  33. Xu C., Wang L., Cui Q., Huang Y., Liu Z., Zheng G., Goodfellow M. 2006; Neutrotolerant acidophilic Streptomyces species isolated from acidic soils in China: Streptomyces guanduensis sp. nov., Streptomyces paucisporeus sp. nov., Streptomyces rubidus sp. nov. and Streptomyces yanglinensis sp. nov.. Int J Syst Evol Microbiol 56:1109–1115 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.033290-0
Loading
/content/journal/ijsem/10.1099/ijs.0.033290-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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