1887

Abstract

A Gram-positive, non-motile actinobacterium, designated YIM 65754, was isolated from the stem of L., collected from Yunnan province, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM 65754 comprised an evolutionary lineage within the genus . The isolate clustered with PDB9, W 4937 and DSM 43241, with which it shared 98.4, 97.9 and 97.8 % 16S rRNA gene sequence similarities, respectively. However, DNA–DNA relatedness demonstrated that strain YIM 65754 was distinct from its closest phylogenetic neighbours. The cell-wall peptidoglycan contained -diaminopimelic acid, arabinose, galactose, mannose and glucose (cell-wall chemotype IV). The major menaquinone was MK-8(H) and the predominant fatty acids were C (27.83 %), iso-C 2-OH and/or Cω7 (20.21 %) and 10-methyl C (17.50 %). The DNA G+C content was 66.2 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic evidence, the isolate represents a novel species of the genus , for which the name sp. nov. is proposed; the type strain is YIM 65754 ( = CCTCC AA 209042 = DSM 45380).

Funding
This study was supported by the:
  • , National Basic Research Program of China , (Award 2010CB833801)
  • , National Natural Science Foundation of China , (Award U0932601)
  • , Yunnan Provincial Natural Science Foundation , (Award 2009DA002)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.031930-0
2012-04-01
2020-08-14
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/62/4/900.html?itemId=/content/journal/ijsem/10.1099/ijs.0.031930-0&mimeType=html&fmt=ahah

References

  1. Bell K. S., Philp J. C., Aw D. W., Christofi N. 1998; The genus Rhodococcus . J Appl Microbiol 85:195–210 [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 50:1095–1102 [CrossRef][PubMed]
    [Google Scholar]
  3. 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 [CrossRef][PubMed]
    [Google Scholar]
  4. Collins M. D., Jones D. 1980; Lipids in the classification and identification of coryneform bacteria containing peptidoglycan based on 2,4-diaminobutyric acid. J Appl Bacteriol 48:459–470 [CrossRef]
    [Google Scholar]
  5. Collins M. D., Pirouz T., Goodfellow M., Minnikin D. E. 1977; Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230[PubMed] [CrossRef]
    [Google Scholar]
  6. 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 39:224–229 [CrossRef]
    [Google Scholar]
  7. Felsenstein J. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  8. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–789 [CrossRef]
    [Google Scholar]
  9. Felsenstein J. 2002; phylip (phylogeny inference package), version 3.6a. Distributed by the author. Department of Genome Science, University of Washington, Seattle, USA.
  10. Finnerty W. R. 1992; The biology and genetics of the genus Rhodococcus . Annu Rev Microbiol 46:193–218 [CrossRef][PubMed]
    [Google Scholar]
  11. Fitch W. M. 1971; Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416 [CrossRef]
    [Google Scholar]
  12. Ghosh A., Paul D., Prakash D., Mayilraj S., Jain R. K. 2006; Rhodococcus imtechensis sp. nov., a nitrophenol-degrading actinomycete. Int J Syst Evol Microbiol 56:1965–1969 [CrossRef][PubMed]
    [Google Scholar]
  13. Gordon R. E., Barnett D. A., Handerhan J. E., Pang C. H.-N. 1974; Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 24:54–63 [CrossRef]
    [Google Scholar]
  14. Guindon S., Gascuel O. 2003; A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704 [CrossRef][PubMed]
    [Google Scholar]
  15. Gürtler V., Mayall B. C., Seviour R. 2004; Can whole genome analysis refine the taxonomy of the genus Rhodococcus?. FEMS Microbiol Rev 28:377–403 [CrossRef][PubMed]
    [Google Scholar]
  16. Hasegawa T., Takizawa M., Tanida S. 1983; A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Microbiol 29:319–322 [CrossRef]
    [Google Scholar]
  17. 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 [CrossRef][PubMed]
    [Google Scholar]
  18. Jones A. L., Brown J. M., Mishra V., Perry J. D., Steigerwalt A. G., Goodfellow M. 2004; Rhodococcus gordoniae sp. nov., an actinomycete isolated from clinical material and phenol-contaminated soil. Int J Syst Evol Microbiol 54:407–411 [CrossRef][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. Lányí B. 1987; Classical and rapid identification methods for medically important bacteria. Methods Microbiol 19:1–67 [CrossRef]
    [Google Scholar]
  21. 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 [CrossRef]
    [Google Scholar]
  22. Lechevalier M. P., De Bièvre C., Lechevalier H. A. 1977; Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 5:249–260 [CrossRef]
    [Google Scholar]
  23. Leifson E. 1960 Atlas of Bacterial Flagellation London: Academic Press;
    [Google Scholar]
  24. 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 [CrossRef][PubMed]
    [Google Scholar]
  25. Li J., Zhao G.-Z., Chen H.-H., Qin S., Xu L.-H., Jiang C.-L., Li W.-J. 2008; Rhodococcus cercidiphylli sp. nov., a new endophytic actinobacterium isolated from a Cercidiphyllum japonicum leaf. Syst Appl Microbiol 31:108–113 [CrossRef][PubMed]
    [Google Scholar]
  26. Mayilraj S., Krishnamurthi S., Saha P., Saini H. S. 2006; Rhodococcus kroppenstedtii sp. nov., a novel actinobacterium isolated from a cold desert of the Himalayas, India. Int J Syst Evol Microbiol 56:979–982 [CrossRef][PubMed]
    [Google Scholar]
  27. 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 [CrossRef]
    [Google Scholar]
  28. Miché L., Balandreau J. 2001; Effects of rice seed surface sterilization with hypochlorite on inoculated Burkholderia vietnamiensis . Appl Environ Microbiol 67:3046–3052 [CrossRef][PubMed]
    [Google Scholar]
  29. 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 47:87–95 [CrossRef]
    [Google Scholar]
  30. Minnikin D. E., Hutchinson I. G., Caldicott A. B., Goodfellow M. 1980; Thin layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromatogr A 188:221–233 [CrossRef]
    [Google Scholar]
  31. Qin S., Li J., Chen H.-H., Zhao G.-Z., Zhu W.-Y., Jiang C.-L., Xu L.-H., Li W.-J. 2009; Isolation, diversity, and antimicrobial activity of rare actinobacteria from medicinal plants of tropical rain forests in Xishuangbanna, China. Appl Environ Microbiol 75:6176–6186 [CrossRef][PubMed]
    [Google Scholar]
  32. Rainey F. A., Burghardt J., Kroppenstedt R. M., Klatte S., Stackebrandt E. 1995; Phylogenetic analysis of the genera Rhodococcus and Nocardia and evidence for the evolutionary origin of the genus Nocardia from within the radiation of Rhodococcus species. Microbiology 141:523–528 [CrossRef]
    [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. Shirling E. B., Gottlieb D. 1966; Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340 [CrossRef]
    [Google Scholar]
  35. 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]
  36. 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 44:846–849 [CrossRef]
    [Google Scholar]
  37. Stackebrandt E., Rainey F. A., Ward-Rainey N. L. 1997; Proposal for a new hierarchic classification system, Actinobacteria classis nov.. Int J Syst Bacteriol 47:479–491 [CrossRef]
    [Google Scholar]
  38. Strobel G., Daisy B. 2003; Bioprospecting for microbial endophytes and their natural products. Microbiol Mol Biol Rev 67:491–502 [CrossRef][PubMed]
    [Google Scholar]
  39. Tamaoka J., Katayama-Fujimura Y., Kuraishi H. 1983; Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 54:31–36 [CrossRef]
    [Google Scholar]
  40. 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 [CrossRef][PubMed]
    [Google Scholar]
  41. 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 59:2025–2032 [CrossRef][PubMed]
    [Google Scholar]
  42. 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 [CrossRef][PubMed]
    [Google Scholar]
  43. Wang Z., Xu J., Li Y., Wang K., Wang Y., Hong Q., Li W.-J., Li S.-P. 2010; Rhodococcus jialingiae sp. nov., an actinobacterium isolated from sludge of a carbendazim wastewater treatment facility. Int J Syst Evol Microbiol 60:378–381 [CrossRef][PubMed]
    [Google Scholar]
  44. Warhurst A. M., Fewson C. A. 1994; Biotransformations catalyzed by the genus Rhodococcus . Crit Rev Biotechnol 14:29–73 [CrossRef][PubMed]
    [Google Scholar]
  45. 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 [CrossRef][PubMed]
    [Google Scholar]
  46. Xu J.-L., He J., Wang Z.-C., Wang K., Li W.-J., Tang S.-K., Li S.-P. 2007; Rhodococcus qingshengii sp. nov., a carbendazim-degrading bacterium. Int J Syst Evol Microbiol 57:2754–2757 [CrossRef][PubMed]
    [Google Scholar]
  47. Yassin A. F. 2005; Rhodococcus triatomae sp. nov., isolated from a blood-sucking bug. Int J Syst Evol Microbiol 55:1575–1579 [CrossRef][PubMed]
    [Google Scholar]
  48. Zhang Y.-Q., Li W.-J., Kroppenstedt R. M., Kim C.-J., Chen G.-Z., Park D.-J., Xu L.-H., Jiang C.-L. 2005; Rhodococcus yunnanensis sp. nov., a mesophilic actinobacterium isolated from forest soil. Int J Syst Evol Microbiol 55:1133–1137 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.031930-0
Loading
/content/journal/ijsem/10.1099/ijs.0.031930-0
Loading

Data & Media loading...

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