1887

Abstract

A novel actinomycete strain, designated YIM 75904, was isolated from a soil sample that had been collected from a dry and hot river valley in Dongchuan county, Yunnan province, south-western China. The taxonomic position of the novel strain was investigated by a polyphasic approach. In phylogenetic analyses based on 16S rRNA gene sequences, strain YIM 75904 formed a distinct clade within the genus and appeared to be closely related to K24 (99.3 % sequence similarity). Strain YIM 75904 had a type-IV cell wall, with no detectable mycolic acids, and had MK-9(H) as its predominant menaquonine. Its cell wall contained -diaminopimelic acid, galactose, glucose and arabinose, and its major cellular fatty acids were iso-C, iso-C, anteiso-C and anteiso-C. The genomic DNA G+C content of the novel strain was 68.5 mol%. Based on the results of physiological and biochemical tests and DNA–DNA hybridizations, strain YIM 75904 represents a novel species of the genus for which the name sp. nov. is proposed. The type strain is YIM 75904 ( = CCTCC AA 2011016  = JCM 18054).

Funding
This study was supported by the:
  • Science and Technology Innovation Talents Program of the Universities of Henan Province (Award 2010HASTIT020)
  • Key Technologies R & D Program of Henan Province (Award 112102210106 and 112102310335)
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2012-11-01
2024-12-07
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References

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. 1990; Basic local alignment search tool. J Mol Biol 215:403–410[PubMed] [CrossRef]
    [Google Scholar]
  2. Bian J., Li Y., Wang J., Song F. H., Liu M., Dai H. Q., Ren B., Gao H., Hu X. et al. 2009; Amycolatopsis marina sp. nov., an actinomycete isolated from an ocean sediment. Int J Syst Evol Microbiol 59:477–481 [View Article][PubMed]
    [Google Scholar]
  3. Carlsohn M. R., Groth I., Tan G. Y. A., Schütze B., Saluz H. P., Munder T., Yang J., Wink J., Goodfellow M. 2007; 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]
  4. Chen J., Li Y., Su J. J., Wei Y. Z., Li Q. P., Yu L. Y., Liu H. Y., Zhang Y. Q., Zhang Y. Q. 2010; Amycolatopsis xylanica sp. nov., isolated from soil. Int J Syst Evol Microbiol 60:2124–2128 [View Article][PubMed]
    [Google Scholar]
  5. 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]
  6. Dong X. Z., Cai M. Y. 2001 Manual of Systematics and Identification of General Bacteria Beijing: Science Press;
    [Google Scholar]
  7. Embley T. M., Smida J., Stackebrandt E. 1988; The phylogeny of mycolate-less wall chemotype IV actinomycetes and the description of Pseudonocardiaceae fam. nov.. Syst Appl Microbiol 11:44–52 [View Article]
    [Google Scholar]
  8. 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 [View Article]
    [Google Scholar]
  9. Felsenstein J. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376 [View Article][PubMed]
    [Google Scholar]
  10. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–789 [View Article]
    [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 [View Article]
    [Google Scholar]
  12. Goodfellow M., Kim S. B., Minnikin D. E., Whitehead D., Zhou Z. H. A., Mattinson-Rose A. D. 2001; Amycolatopsis sacchari sp. nov., a moderately thermophilic actinomycete isolated from vegetable matter. Int J Syst Evol Microbiol 51:187–193[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 [View Article]
    [Google Scholar]
  14. Groth I., Tan G. Y. A., González J. M., Laiz L., Carlsohn M. R., Schütze B., Wink J., Goodfellow M. 2007; Amycolatopsis nigrescens sp. nov., an actinomycete isolated from a Roman catacomb. Int J Syst Evol Microbiol 57:513–519 [View Article][PubMed]
    [Google Scholar]
  15. Guan T. W., Xia Z. F., Tang S. K., Wu N., Chen Z. J., Huang Y., Ruan J. S., Li W. J., Zhang L. L. 2012; Amycolatopsis salitolerans sp. nov., a filamentous actinomycete isolated from a hypersaline habitat. Int J Syst Evol Microbiol 62:23–27 [View Article][PubMed]
    [Google Scholar]
  16. Guindon S., Gascuel O. 2003; A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704 [View Article][PubMed]
    [Google Scholar]
  17. He L., Li W., Huang Y., Wang L. M., Liu Z. H., Lanoot B. J., 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]
  18. Henssen A., Kothe H. W., Kroppenstedt R. M. 1987; Transfer of Pseudonocardia azurea and “Pseudonocardia fastidiosa” to the genus Amycolatopsis, with emended species description. Int J Syst Bacteriol 37:292–295 [View Article]
    [Google Scholar]
  19. Huang Y., Paściak M., Liu Z., Xie Q., Gamian A. 2004; Amycolatopsis palatopharyngis sp. nov., a potentially pathogenic actinomycete isolated from a human clinical source. Int J Syst Evol Microbiol 54:359–363 [View Article][PubMed]
    [Google Scholar]
  20. 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]
  21. Kim S. B., Goodfellow M. 1999; Reclassification of Amycolatopsis rugosa Lechevalier et al. 1986 as Prauserella rugosa gen. nov., comb. nov.. Int J Syst Bacteriol 49:507–512 [View Article][PubMed]
    [Google Scholar]
  22. Kim O.-S., Cho Y.-J., Lee K., Yoon S.-H., Kim M., Na H., Park S.-C., Jeon Y. S., Lee J.-H., Yi H., Won S., Chun J. 2012; Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721 [View Article][PubMed]
    [Google Scholar]
  23. Kimura M. 1983 The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; [CrossRef]
    [Google Scholar]
  24. Kroppenstedt R. M. 1982; Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 5:2359–2367 [View Article]
    [Google Scholar]
  25. Labeda D. P., Donahue J. M., Williams N. M., Sells S. F., Henton M. M. 2003; Amycolatopsis kentuckyensis sp. nov., Amycolatopsis lexingtonensis sp. nov. and Amycolatopsis pretoriensis sp. nov., isolated from equine placentas. Int J Syst Evol Microbiol 53:1601–1605 [View Article][PubMed]
    [Google Scholar]
  26. Lechevalier M. P., Prauser H., Labeda D. P., Ruan J. S. 1986; Two new genera of nocardioform actinomycetes: Amycolata gen. nov. and Amycolatopsis gen. nov.. Int J Syst Bacteriol 36:29–37 [View Article]
    [Google Scholar]
  27. Lee S. D. 2006; Amycolatopsis jejuensis sp. nov. and Amycolatopsis halotolerans sp. nov., novel actinomycetes isolated from a natural cave. Int J Syst Evol Microbiol 56:549–553 [View Article][PubMed]
    [Google Scholar]
  28. Lee S. D. 2009; Amycolatopsis ultiminotia sp. nov., isolated from rhizosphere soil, and emended description of the genus Amycolatopsis . Int J Syst Evol Microbiol 59:1401–1404 [View Article][PubMed]
    [Google Scholar]
  29. Lee S. D., Kinkel L. L., Samac D. A. 2006; Amycolatopsis minnesotensis sp. nov., isolated from a prairie soil. Int J Syst Evol Microbiol 56:265–269 [View Article][PubMed]
    [Google Scholar]
  30. Leifson E. 1960 Atlas of Bacterial Flagellation London: Academic Press;
    [Google Scholar]
  31. 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]
  32. Mann J. 2001; Natural products as immunosuppressive agents. Nat Prod Rep 18:417–430 [View Article][PubMed]
    [Google Scholar]
  33. Maskey R. P., Li F. C., Qin S., Fiebig H. H., Laatsch H. 2003; Chandrananimycins A-C: production of novel anticancer antibiotics from a marine Actinomadura sp. isolate M048 by variation of medium composition and growth conditions. J Antibiot (Tokyo) 56:622–629 [View Article][PubMed]
    [Google Scholar]
  34. Mertz F. P., Yao R. C. 1993; Amycolatopsis alba sp. nov., isolated from soil. Int J Syst Bacteriol 43:715–720 [View Article][PubMed]
    [Google Scholar]
  35. 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]
  36. Miao Q., Qin S., Bian G. K., Yuan B., Xing K., Zhang Y. J., Li Q., Tang S. K., Li W. J., Jiang J. H. 2011; Amycolatopsis endophytica sp. nov., a novel endophytic actinomycete isolated from oil-seed plant Jatropha curcas L.. Antonie van Leeuwenhoek 100:333–339 [View Article][PubMed]
    [Google Scholar]
  37. 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 [View Article]
    [Google Scholar]
  38. 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 [View Article]
    [Google Scholar]
  39. 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]
  40. Nascimento R. P., Coelho R. R. R., Marques S., Alves L., Girio F. M., Bon E. P. S., Amaral-Collaco M. T. 2002; Production and partial characterization of xylanase from Streptomyces sp. strain AMT-3 isolated from Brazilian cerrado soil. Enzyme Microb Technol 31:549–555 [View Article]
    [Google Scholar]
  41. Otoguro M., Yamamura H., Tamura T., Irzaldi R., Ratnakomala S., Ridwan R., Kartina G., Triana E., Nurkanto A. et al. 2011; Actinophytocola timorensis sp. nov. and Actinophytocola corallina sp. nov., isolated from soil. Int J Syst Evol Microbiol 61:834–838 [View Article][PubMed]
    [Google Scholar]
  42. Qin S., Li J., Chen H. H., Zhao G. Z., Zhu W. Y., Jiang C. L., Xu L. H., Li W. J. 2009a; Isolation, diversity, and antimicrobial activity of rare actinobacteria from medicinal plants of tropical rain forests in Xishuangbanna, China. Appl Environ Microbiol 75:6176–6186 [View Article][PubMed]
    [Google Scholar]
  43. Saddler G. S., Tavecchia P., Lociuro S., Zanol M., Colombo L., Selva E. 1991; Analysis of madurose and other actinomycete wholecell sugars by gas chromatography. J Microbiol Methods 14:185–191 [View Article]
    [Google Scholar]
  44. 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]
  45. Sasser M. 1990; Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 20:16
    [Google Scholar]
  46. Shirling E. B., Gottlieb D. 1966; Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340 [View Article]
    [Google Scholar]
  47. 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 [View Article]
    [Google Scholar]
  48. 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]
  49. 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]
  50. Tang S. K., Wang Y., Chen Y., Lou K., Cao L. L., Xu L. H., Li W. J. 2009a; Zhihengliuella alba sp. nov., and emended description of the genus Zhihengliuella . Int J Syst Evol Microbiol 59:2025–2031 [View Article][PubMed]
    [Google Scholar]
  51. Tang S. K., Wang Y., Lou K., Mao P. H., Xu L. H., Jiang C. L., Kim C. J., Li W. J. 2009b; Kocuria halotolerans sp. nov., an actinobacterium isolated from a saline soil in China. Int J Syst Evol Microbiol 59:1316–1320 [View Article][PubMed]
    [Google Scholar]
  52. Tang S. K., Wang Y., Guan T. W., Lee J. C., Kim C. J., Li W. J. 2010; Amycolatopsis halophila sp. nov., a halophilic actinomycete isolated from a salt lake. Int J Syst Evol Microbiol 60:1073–1078 [View Article][PubMed]
    [Google Scholar]
  53. 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]
  54. Waksman S. A. 1967 The Actinomycetes. A Summary of Current Knowledge New York: Ronald Press;
    [Google Scholar]
  55. 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 [View Article][PubMed]
    [Google Scholar]
  56. Williams S. T., Goodfellow M., Alderson G. 1989; Genus Streptomyces Waksman and Henrici 1943, 339AL . In Bergey’s Manual of Systematic Bacteriology vol. 4 pp. 2463–2468 Edited by Williams S. T., Sharpe M. E., Holt J. G. Baltimore: Williams & Wilkins;
    [Google Scholar]
  57. Yassin A. F., Haggenel B., Budzikiewicz H., Schaal K. P. 1993; Fatty acid and polar lipid composition of the genus Amycolatopsis: application of fast atom bombardment-mass spectrometry to structure analysis of underivatized phospholipids. Int J Syst Bacteriol 43:414–420 [View Article]
    [Google Scholar]
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