1887

Abstract

A Gram-positive, aerobic, actinobacterial strain with rod-shaped spores, designated YIM 63158, was isolated from the surface-sterilized roots of L. collected from Yunnan province, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 63158 belonged to the genus . The closest neighbours were ‘’ KLBMP 1115 (99.9 % 16S rRNA gene sequence similarity), EUM 221 (99.1 %) and DSM 44774 (98.8 %); sequence similarities to other members of the genus ranged from 98.6 to 94.4 %. The chemotaxonomic characteristics, such as the cell-wall diaminopimelic acid, whole-cell sugars, fatty acid components and major menaquinones, suggested that the isolate belonged to the genus . The G+C content of the genomic DNA was 73.3 mol%. On the basis of physiological, biochemical and chemotaxonomic data, including low DNA–DNA relatedness between the isolate and other members of the genus , it is proposed that strain YIM 63158 represents a novel species in this genus, with the name sp. nov. The type strain is YIM 63158 ( = DSM 45301  = CCTCC AA 208081).

Erratum
This article contains a correction applying to the following content:
sp. nov., an actinobacterium isolated from surface-sterilized roots of L.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.027607-0
2011-09-01
2019-10-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/61/9/2292.html?itemId=/content/journal/ijsem/10.1099/ijs.0.027607-0&mimeType=html&fmt=ahah

References

  1. Ara I. , Tsetseg B. , Daram D. , Suto M. , Ando K. . ( 2011; ). Pseudonocardia mongoliensis sp. nov. and Pseudonocardia khuvsgulensis sp. nov., isolated from soil. . Int J Syst Evol Microbiol 61:, 747–756. [CrossRef]
    [Google Scholar]
  2. Chen H.-H. , Qin S. , Li J. , Zhang Y.-Q. , Xu L.-H. , Jiang C.-L. , Kim C.-J. , Li W.-J. . ( 2009; ). Pseudonocardia endophytica sp. nov., isolated from the pharmaceutical plant Lobelia clavata . . Int J Syst Evol Microbiol 59:, 559–563. [CrossRef] [PubMed]
    [Google Scholar]
  3. 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]
  4. 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]
  5. Dong X. Z. , Cai M. Y. . ( 2001; ). Manual for the Systematic Identification of General Bacteria. Beijing:: Science Press; (in Chinese).
    [Google Scholar]
  6. Duangmal K. , Thamchaipenet A. , Matsumoto A. , Takahashi Y. . ( 2009; ). Pseudonocardia acaciae sp. nov., isolated from roots of Acacia auriculiformis A. Cunn. ex Benth. . Int J Syst Evol Microbiol 59:, 1487–1491. [CrossRef] [PubMed]
    [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, WA, USA..
  10. 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]
  11. 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]
  12. Gu Q. , Luo H. , Zheng W. , Liu Z. , Huang Y. . ( 2006; ). Pseudonocardia oroxyli sp. nov., a novel actinomycete isolated from surface-sterilized Oroxylum indicum root. . Int J Syst Evol Microbiol 56:, 2193–2197. [CrossRef] [PubMed]
    [Google Scholar]
  13. 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]
  14. 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]
  15. Hayakawa M. , Nonomura H. . ( 1987; ). Humic acid-vitamin agar, a new medium for selective isolation of soil actinomycetes. . J Ferment Technol 65:, 501–509. [CrossRef]
    [Google Scholar]
  16. Henssen A. . ( 1957; ). Beiträge zur Morphologie und Systematic der thermophilen Actinomyceten. . Arch Mikrobiol 26:, 373–414 (in German). [CrossRef]
    [Google Scholar]
  17. Huang Y. , Wang L. , Lu Z. , Hong L. , Liu Z. , Tan G. Y. A. , Goodfellow M. . ( 2002; ). Proposal to combine the genera Actinobispora and Pseudonocardia in an emended genus Pseudonocardia, and description of Pseudonocardia zijingensis sp. nov.. Int J Syst Evol Microbiol 52:, 977–982. [CrossRef] [PubMed]
    [Google Scholar]
  18. Kaewkla O. , Franco C. M. M. . ( 2010; ). Pseudonocardia adelaidensis sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of a grey box tree (Eucalyptus microcarpa). . Int J Syst Evol Microbiol 60:, 2818–2822. [CrossRef] [PubMed]
    [Google Scholar]
  19. Kaewkla O. , Franco C. M. M. . ( 2011; ). Pseudonocardia eucalypti sp. nov., an endophytic actinobacterium with a unique knobby spore surface, isolated from roots of a native Australian eucalyptus tree. . Int J Syst Evol Microbiol 61:, 742–746. ; [CrossRef]
    [Google Scholar]
  20. Kämpfer P. , Kohlweyer U. , Thiemer B. , Andreesen J. R. . ( 2006; ). Pseudonocardia tetrahydrofuranoxydans sp. nov.. Int J Syst Evol Microbiol 56:, 1535–1538. [CrossRef] [PubMed]
    [Google Scholar]
  21. 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]
  22. 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]
  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. , Wang H. B. , Qin S. , Zhu W. Y. , Xu L. H. , Jiang C. L. , Li W. J. . ( 2008; ). Antitumour and antimicrobial activities of endophytic streptomycetes from pharmaceutical plants in rainforest. . Lett Appl Microbiol 47:, 574–580. [CrossRef] [PubMed]
    [Google Scholar]
  26. McVeigh H. P. , Munro J. , Embley T. M. . ( 1994; ). The phylogenetic position of Pseudoamycolata halophobica (Akimov et al. 1989) and a proposal to reclassify it as Pseudonocardia halophobica . . Int J Syst Bacteriol 44:, 300–302. [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. 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]
  29. 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]
  30. Park S. W. , Park S. T. , Lee J. E. , Kim Y. M. . ( 2008; ). Pseudonocardia carboxydivorans sp. nov., a carbon monoxide-oxidizing actinomycete, and an emended description of the genus Pseudonocardia . . Int J Syst Evol Microbiol 58:, 2475–2478. [CrossRef] [PubMed]
    [Google Scholar]
  31. Prabahar V. , Dube S. , Reddy G. S. N. , Shivaji S. . ( 2004; ). Pseudonocardia antarctica sp. nov. an actinomycetes from McMurdo Dry Valleys, Antarctica. . Syst Appl Microbiol 27:, 66–71. [CrossRef] [PubMed]
    [Google Scholar]
  32. Qin S. , Zhu W.-Y. , Jiang J.-H. , Klenk H.-P. , Li J. , Zhao G.-Z. , Xu L.-H. , Li W.-J. . ( 2010; ). Pseudonocardia tropica sp. nov., an endophytic actinomycete isolated from the stem of Maytenus austroyunnanensis . . Int J Syst Evol Microbiol 60:, 2524–2528. [CrossRef]
    [Google Scholar]
  33. Qin S. , Xing K. , Fei S. M. , Lin Q. , Chen X. M. , Cao C. L. , Sun Y. , Wang Y. , Li W. J. , Jiang J. H. . ( 2011; ). Pseudonocardia sichuanensis sp. nov., a novel endophytic actinomycete isolated from the root of Jatropha curcas L.. Antonie van Leeuwenhoek 99:, 395–401. [PubMed] [CrossRef]
    [Google Scholar]
  34. Reichert K. , Lipski A. , Pradella S. , Stackebrandt E. , Altendorf K. . ( 1998; ). Pseudonocardia asaccharolytica sp. nov. and Pseudonocardia sulfidoxydans sp. nov., two new dimethyl disulfide-degrading actinomycetes and emended description of the genus Pseudonocardia . . Int J Syst Bacteriol 48:, 441–449.[PubMed] [CrossRef]
    [Google Scholar]
  35. 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]
  36. Sakiyama Y. , Thao N. K. N. , Vinh H. V. , Giang N. M. , Miyadoh S. , Hop D. V. , Ando K. . ( 2010; ). Pseudonocardia babensis sp. nov., isolated from plant litter. . Int J Syst Evol Microbiol 60:, 2336–2340. [CrossRef] [PubMed]
    [Google Scholar]
  37. Schäfer J. , Busse H. J. , Kämpfer P. . ( 2009; ). Pseudonocardia parietis sp. nov., from the indoor environment. . Int J Syst Evol Microbiol 59:, 2449–2452. [CrossRef] [PubMed]
    [Google Scholar]
  38. Shirling E. B. , Gottlieb D. . ( 1966; ). Methods for characterization of Streptomyces species. . Int J Syst Bacteriol 16:, 313–340. [CrossRef]
    [Google Scholar]
  39. 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]
  40. 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]
  41. 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]
  42. 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]
  43. 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]
  44. 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]
  45. Warwick S. , Bowen T. , McVeigh H. P. , Embley T. M. . ( 1994; ). A phylogenetic analysis of the family Pseudonocardiaceae and the genera Actinokineospora and Saccharothrix with 16S rRNA sequences and a proposal to combine the genera Amycolata and Pseudonocardia in an emended genus Pseudonocardia . . Int J Syst Bacteriol 44:, 293–299. [CrossRef] [PubMed]
    [Google Scholar]
  46. 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]
  47. Zhao G.-Z. , Li J. , Qin S. , Huang H.-Y. , Zhu W.-Y. , Xu L.-H. , Li W.-J. . ( 2010; ). Streptomyces artemisiae sp. nov., isolated from surface-sterilized tissue of Artemisia annua L.. Int J Syst Evol Microbiol 60:, 27–32. [CrossRef] [PubMed]
    [Google Scholar]
  48. Zhao G.-Z. , Li J. , Huang H.-Y. , Zhu W.-Y. , Zhao L.-X. , Tang S.-K. , Xu L.-H. , Li W.-J. . ( 2011; ). Pseudonocardia artemisiae sp. nov., a novel actinobacterium isolated from surface-sterilized Artemisia annua L.. Int J Syst Evol Microbiol 61:, 1061–1065. [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.027607-0
Loading
/content/journal/ijsem/10.1099/ijs.0.027607-0
Loading

Data & Media loading...

Supplements

vol. , part 9, pp. 2292–2297

Scanning electron micrograph of cells of strain YIM 63158

Cultural characteristics of sp. nov.

Fatty acid compositions of sp. nov. and its closest phylogenetic neighbours

[ Single PDF file] (189 KB)



PDF

Most Cited This Month

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