1887

Abstract

A novel Gram-stain-positive, aerobic, motile, non-spore-forming coccus-shaped actinomycete, designated strain YIM 121300, was isolated from alkaline sediment in Yuanjiang, Yunnan province, south-west China. Phylogenetic analyses based on the 16S rRNA gene sequence showed that strain YIM 121300 was affiliated to the genus , and was closely related to IFO 15268 (97.3 % similarity). 16S rRNA gene sequence similarity to other species of the genus was < 97 %. The cell wall contained -diaminopimelic acid as the diagnostic diamino acid. The whole-cell sugars contained arabinose, galactose, glucose, mannose and ribose. The predominant menaquinone was MK-9(H). Mycolic acids were not detected. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and an unknown phospholipid. The predominant fatty acids were anteiso-C and anteiso-C A. The G+C content of the genomic DNA was 75.1 mol%. DNA–DNA relatedness (55 ± 4 % to IFO 15268) and differential phenotypic data demonstrated that strain YIM 121300 was distinguished from all related species of the genus . On the basis of data from the present polyphasic study, the organism should be assigned to a novel species of the genus , for which the name sp. nov. is proposed. The type strain is YIM 121300 ( = CCTCC AA 2013232 = DSM 27627).

Funding
This study was supported by the:
  • , National Natural Science Foundation of China
  • , Yunnan Provincial Science and Technology Department
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.000478
2015-10-01
2021-02-27
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/10/3703.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.000478&mimeType=html&fmt=ahah

References

  1. Bian G.K., Feng Z.Z., Qin S., Xing K., Wang Z., Cao C.L., Liu C.H., Dai C.C., Jiang J.H. ( 2012;). Kineococcus endophytica sp. nov., a novel endophytic actinomycete isolated from a coastal halophyte in Jiangsu, China. Antonie van Leeuwenhoek 102 621628 [CrossRef] [PubMed].
    [Google Scholar]
  2. 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 10951102 [CrossRef] [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 459470 [CrossRef].
    [Google Scholar]
  4. Collins M.D., Pirouz T., Goodfellow M., Minnikin D.E. ( 1977;). Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100 221230 [CrossRef] [PubMed].
    [Google Scholar]
  5. Duangmal K., Thamchaipenet A., Ara I., Matsumoto A., Takahashi Y. ( 2008;). Kineococcus gynurae sp. nov., isolated from a Thai medicinal plant. Int J Syst Evol Microbiol 58 24392442 [CrossRef] [PubMed].
    [Google Scholar]
  6. Euzéby J. ( 2012;). List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 62 25492554 [CrossRef].
    [Google Scholar]
  7. Ezaki T., Hashimoto Y., Yabuuchi E. ( 1989;). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39 224229 [CrossRef].
    [Google Scholar]
  8. Felsenstein J. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 368376 [CrossRef] [PubMed].
    [Google Scholar]
  9. Felsenstein J. ( 1985;). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 783791 [CrossRef].
    [Google Scholar]
  10. Fitch W.M. ( 1971;). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20 406416 [CrossRef].
    [Google Scholar]
  11. Garrity G.M., Lilburn T.G., Cole J.R., Harrison S.H., Euzeby J., Tindall B.J. ( 2007;). Part 10—The Bacteria: phylum Actinobacteria: class ‘Actinobacteria’. In: The taxonomic outline of the Bacteria and Archaea . Release 7.7. http://www.taxonomicoutline.org/index.php/toba/article/view/187/219 .
  12. Hasegawa T., Takizawa M., Tanida S. ( 1983;). A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Microbiol 29 319322 [CrossRef].
    [Google Scholar]
  13. 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 19391944 [CrossRef] [PubMed].
    [Google Scholar]
  14. 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 26942698 [CrossRef] [PubMed].
    [Google Scholar]
  15. Jurado V., Laiz L., Ortiz-Martinez A., Groth I., Saiz-Jimenez C. ( 2011;). Pseudokineococcus lusitanus gen. nov., sp. nov., and reclassification of Kineococcus marinus Lee 2006 as Pseudokineococcus marinus comb. nov. Int J Syst Evol Microbiol 61 25152519 [CrossRef] [PubMed].
    [Google Scholar]
  16. Kelly A.T., Fulton M. ( 1953;). Use of triphenyl tetrazolium in motility test medium. Am J Clin Pathol 23 512 [PubMed].
    [Google Scholar]
  17. 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]
  18. Küster E., Williams S.T. ( 1964;). Selection of media for isolation of Streptomycetes. Nature 202 928929 [CrossRef] [PubMed].
    [Google Scholar]
  19. Lechevalier M.P., Lechevalier H. ( 1970;). Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 20 435443 [CrossRef].
    [Google Scholar]
  20. Lee S.D. ( 2006;). Kineococcus marinus sp. nov., isolated from marine sediment of the coast of Jeju, Korea. Int J Syst Evol Microbiol 56 12791283 [CrossRef] [PubMed].
    [Google Scholar]
  21. Lee S.D. ( 2009;). Kineococcus rhizosphaerae sp. nov., isolated from rhizosphere soil. Int J Syst Evol Microbiol 59 22042207 [CrossRef] [PubMed].
    [Google Scholar]
  22. Leifson E. ( 1960). Atlas of Bacterial Flagellation London: Academic Press;. [CrossRef]
    [Google Scholar]
  23. 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 14241428 [CrossRef] [PubMed].
    [Google Scholar]
  24. Liu M., Peng F., Wang Y., Zhang K., Chen G., Fang C. ( 2009;). Kineococcus xinjiangensis sp. nov., isolated from desert sand. Int J Syst Evol Microbiol 59 10901093 [CrossRef] [PubMed].
    [Google Scholar]
  25. Maszenan A.M., Tay J.H., Schumann P., Jiang H.L., Tay S.T.L. ( 2005;). Quadrisphaera granulorum gen. nov., sp. nov., a Gram-positive polyphosphate-accumulating coccus in tetrads or aggregates isolated from aerobic granules. Int J Syst Evol Microbiol 55 17711777 [CrossRef] [PubMed].
    [Google Scholar]
  26. 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 159167 [CrossRef].
    [Google Scholar]
  27. Minnikin D.E., Collins M.D., Goodfellow M. ( 1979;). Fatty acid and polar lipid composition in the classification of Cellulomonas . Oerskovia and related taxa. J Appl Bacteriol 47 8795 [CrossRef].
    [Google Scholar]
  28. Nie G.X., Ming H., Zhang J., Feng H.G., Li S., Yu T.T., Zhou E.M., Tang S.K., Li W.J. ( 2012;). Kineococcus glutineturens sp. nov., isolated from soil in Yunnan, south-west China. Antonie van Leeuwenhoek 102 239246 [CrossRef] [PubMed].
    [Google Scholar]
  29. Pagani H., Parenti F. ( 1978;). Kineosporia, a new genus of the order Actinomycetales . Int J Syst Bacteriol 28 401406 [CrossRef].
    [Google Scholar]
  30. Phillips R.W., Wiegel J., Berry C.J., Fliermans C., Peacock A.D., White D.C., Shimkets L.J. ( 2002;). Kineococcus radiotolerans sp. nov., a radiation-resistant, gram-positive bacterium. Int J Syst Evol Microbiol 52 933938 [CrossRef] [PubMed].
    [Google Scholar]
  31. Saitou N., Nei M. ( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 406425 [PubMed].
    [Google Scholar]
  32. Sasser M. ( 1990). Identification of bacteria by gas chromatography of cellular fatty acids MIDI Technical Note 101 Newark, DE: MIDI Inc;.
    [Google Scholar]
  33. Smibert R.M., Krieg N.R. ( 1994;). Phenotypic characterization. . In Methods for General and Molecular 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]
  34. Stackebrandt E., Goebel B.M. ( 1994;). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44 846849 [CrossRef].
    [Google Scholar]
  35. Tamaoka J., Katayama-Fujimura Y., Kuraishi H. ( 1983;). Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 54 3136 [CrossRef].
    [Google Scholar]
  36. Tamura T., Hayakawa M., Hatano K. ( 1998;). A new genus of the order Actinomycetales . Cryptosporangium gen. nov., with descriptions of Cryptosporangium arvum sp. nov. and Cryptosporangium japonicum sp. nov. Int J Syst Bacteriol 48 9951005 [CrossRef] [PubMed].
    [Google Scholar]
  37. Tamura T., Ishida Y., Otoguro M., Yamamura H., Hayakawa M., Suzuki K. ( 2010;). Angustibacter luteus gen. nov., sp. nov., isolated from subarctic forest soil. Int J Syst Evol Microbiol 60 24412445 [CrossRef] [PubMed].
    [Google Scholar]
  38. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. ( 2013). mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30 27252729 [CrossRef] [PubMed].
    [Google Scholar]
  39. Tang S.K., Wang Y., Chen Y., Lou K., Cao L.L., Xu L.H., Li W.J. ( 2009;). Zhihengliuella alba sp. nov., and emended description of the genus Zhihengliuella . Int J Syst Evol Microbiol 59 20252032 [CrossRef] [PubMed].
    [Google Scholar]
  40. 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]
  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 11491153 [CrossRef] [PubMed].
    [Google Scholar]
  42. Yokota A., Tamura T., Nishii T., Hasegawa T. ( 1993;). Kineococcus aurantiacus gen. nov., sp. nov., a new aerobic, Gram-positive, motile coccus with meso-diaminopimelic acid and arabinogalactan in the cell wall. Int J Syst Bacteriol 43 5257 [CrossRef].
    [Google Scholar]
  43. Zhi X.Y., Li W.J., Stackebrandt E. ( 2009;). An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 59 589608 [CrossRef] [PubMed].
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.000478
Loading
/content/journal/ijsem/10.1099/ijsem.0.000478
Loading

Data & Media loading...

Supplements

Supplementary Data

PDF

Most cited this month Most Cited RSS feed

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