1887

Abstract

A novel actinomycete strain, YIM 0006, was isolated from soil of a tropical rainforest in northern Thailand. The isolate displayed the following characteristics: aerial mycelium is absent, short spore chains are formed directly on the substrate mycelium, contains -diaminopimelic acid, arabinose and galactose (cell-wall chemotype IV), the diagnostic phospholipid is phosphatidylcholine, MK-9(H) is the predominant menaquinone and the G+C content of the genomic DNA is 69.0 mol%. Phylogenetic analysis and phenotypic characteristics showed that strain YIM 0006 belongs to the family but can be distinguished from representatives of all genera classified in the family. The novel genus and species gen. nov., sp. nov. are proposed, with strain YIM 0006 (=CCTCC AA 205017 =DSM 45062) as the type strain of .

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2008-02-01
2024-04-20
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References

  1. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J.(1997). Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25, 3389–3402.[CrossRef] [Google Scholar]
  2. Dong, X.-Z. & Cai, M.-Y. (editors)(2001). Determination of biochemical properties. In Manual for the Systematic Identification of General Bacteria, pp. 370–398. Beijing: Science Press (in Chinese).
  3. Embley, M. T., Smida, J. & Stackebrandt, E.(1988). The phylogeny of mycolate-less wall chemotype IV actinomycetes and description of Pseudonocardiaceae fam. nov. Syst Appl Microbiol 11, 16–19.[CrossRef] [Google Scholar]
  4. Felsenstein, J.(1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef] [Google Scholar]
  5. Gochnauer, M. B., Leppard, G. G., Komaratat, P., Kates, M., Novitsky, T. & Kushner, D. J.(1975). Isolation and characterization of Actinopolyspora halophila, gen. et sp. nov., an extremely halophilic actinomycete. Can J Microbiol 21, 1500–1511.[CrossRef] [Google Scholar]
  6. Gordon, R. E.(1967). The taxonomy of soil bacteria. In The Ecology of Soil Bacteria, pp. 293–321. Edited by T. R. G. Gray & D. Parkinson. Liverpool: Liverpool University Press.
  7. Guindon, S., Lethiec, F., Duroux, P. & Gascuel, O.(2005).phyml Online – a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res 33, W557–W559.[CrossRef] [Google Scholar]
  8. Hayakawa, M. & Nonomura, H.(1987). Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. J Ferment Technol 65, 501–509.[CrossRef] [Google Scholar]
  9. Henssen, A.(1957). Beiträge zur Morphologie und Systematik der thermophilen Actinomyceten. Arch Mikrobiol 26, 373–414 (in German).[CrossRef] [Google Scholar]
  10. Huang, Y., Wang, L. M., Lu, Z. T., Hong, L., Liu, Z. H., 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] [Google Scholar]
  11. Jiang, Y., Duan, S. R., Tang, S. K., Cheng, H. H., Li, W. J. & Xu, L. H.(2006). Isolation methods of rare actinomycetes. Microbiology (Beijing) 33, 181–183. [Google Scholar]
  12. Kämpfer, P., Kroppenstedt, R. M. & Dott, W.(1991). A numerical classification of the genera Streptomyces and Streptoverticillium using miniaturized physiological tests. J Gen Microbiol 137, 1831–1891.[CrossRef] [Google Scholar]
  13. Kämpfer, P., Kohlmeyer, U., Thiemer, B. & Andreesen, J. R.(2006).Pseudonocardia tetrahydrofuranoxydans sp. nov. Int J Syst Evol Microbiol 56, 1535–1538.[CrossRef] [Google Scholar]
  14. 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.
  15. 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.[CrossRef] [Google Scholar]
  16. 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.[CrossRef] [Google Scholar]
  17. Kimura, M.(1983).The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
  18. Korn-Wendisch, F., Rainey, F., Kroppenstedt, R. M., Kempf, A., Majazza, A., Kutzner, H. J. & Stackebrandt, E.(1995).Thermocrispum gen. nov., a new genus of the order Actinomycetales, and description of Thermocrispum municipale sp. nov. and Thermocrispum agreste sp. nov. Int J Syst Bacteriol 45, 67–77.[CrossRef] [Google Scholar]
  19. 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.[CrossRef] [Google Scholar]
  20. Kroppenstedt, R. M.(1985). Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Chemical Methods in Bacterial Systematics (Society for Applied Bacteriology Technical Series vol. 20), pp. 173–199. Edited by M. Goodfellow & D. E. Minnikin. New York: Academic Press.
  21. Kumar, S., Tamura, K. & Nei, M.(2004).mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150–163.[CrossRef] [Google Scholar]
  22. Labeda, D. P.(2001).Crossiella gen. nov., a new genus related to Streptoalloteichus. Int J Syst Evol Microbiol 51, 1575–1579. [Google Scholar]
  23. Labeda, D. P. & Kroppenstedt, R. M.(2006).Goodfellowia gen. nov., a new genus of the Pseudonocardineae related to Actinoalloteichus, containing Goodfellowia coeruleoviolacea gen. nov., comb. nov. Int J Syst Evol Microbiol 56, 1203–1207.[CrossRef] [Google Scholar]
  24. Lacey, J. & Goodfellow, M.(1975). A novel actinomycete from sugar-cane bagasse, Saccharopolyspora hirsuta gen. et sp. nov. J Gen Microbiol 88, 75–85.[CrossRef] [Google Scholar]
  25. 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]
  26. 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]
  27. 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.[CrossRef] [Google Scholar]
  28. Marmur, J.(1961). A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3, 208–218.[CrossRef] [Google Scholar]
  29. Mertz, F. P. & Yao, R. C.(1988).Kibdelosporangium philippinense sp. nov. isolated from soil. Int J Syst Bacteriol 38, 282–286.[CrossRef] [Google Scholar]
  30. 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 isoprenoid quinones and polar lipids. J Microbiol Methods 2, 233–241.[CrossRef] [Google Scholar]
  31. Nonomura, H. & Ohara, Y.(1971). Distribution of actinomycetes in soil. X. New genus and species of monosporic actinomycetes. J Ferment Technol 49, 895–903. [Google Scholar]
  32. Pearson, W. R.(1990). Rapid and sensitive sequence comparison with fastp and fasta. Methods Enzymol 183, 63–98. [Google Scholar]
  33. 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.[CrossRef] [Google Scholar]
  34. Saitou, N. & Nei, M.(1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425. [Google Scholar]
  35. Sasser, M.(1990). Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 20, 16 [Google Scholar]
  36. Shearer, M. C., Colman, P. M., Ferrin, R. M., Nisbet, L. J. & Nash, C. H.(1986). New genus of the Actinomycetales: Kibdelosporangium aridum gen. nov., sp. nov. Int J Syst Bacteriol 36, 47–54.[CrossRef] [Google Scholar]
  37. Shirling, E. B. & Gottlieb, D.(1966). Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16, 313–340.[CrossRef] [Google Scholar]
  38. Society for American Bacteriologists(1957).Manual of Microbiological Methods. New York: McGraw-Hill.
  39. Stackebrandt, E., Kroppenstedt, R. M., Jahnke, K. D., Kemmerling, C. & Gürtler, H.(1994). Transfer of Streptosporangium viridogriseum (Okuda et al. 1966), Streptosporangium viridogriseum subsp. kofuense (Nonomura and Ohara 1969), and Streptosporangium albidum (Furumai et al. 1968) to Kutzneria gen. nov. as Kutzneria viridogrisea comb. nov., Kutzneria kofuensis comb. nov., and Kutzneria albida comb. nov., respectively, and emendation of the genus Streptosporangium. Int J Syst Bacteriol 44, 265–269.[CrossRef] [Google Scholar]
  40. 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]
  41. Staneck, J. L. & Roberts, G. D.(1974). Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28, 226–231. [Google Scholar]
  42. Tamaoka, J. & Komagata, K.(1984). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25, 125–128.[CrossRef] [Google Scholar]
  43. Tamura, T., Liu, Z. H., Zhang, Y. M. & Hatano, K.(2000).Actinoalloteichus cyanogriseus gen. nov., sp. nov. Int J Syst Evol Microbiol 50, 1435–1440.[CrossRef] [Google Scholar]
  44. Tatusova, T. A. & Madden, T. L.(1999).blast 2 sequences – a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 174, 247–250.[CrossRef] [Google Scholar]
  45. 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] [Google Scholar]
  46. Tomita, K., Nakakita, Y., Hoshino, Y., Numata, K. & Kawaguchi, H.(1987). New genus of the Actinomycetales: Streptoalloteichus hindustanus gen. nov., nom. rev.; sp. nov., nom. rev. Int J Syst Bacteriol 37, 211–213.[CrossRef] [Google Scholar]
  47. Tomita, K., Hoshino, Y. & Miyaki, T.(1993).Kibdelosporangium albatum sp. nov., producer of the antiviral antibiotics cycloviravins. Int J Syst Bacteriol 43, 297–301.[CrossRef] [Google Scholar]
  48. Wang, Y., Zhang, Z. & Ruan, J. S.(1996). A proposal to transfer Microbispora bispora (Lechevalier 1965) to a new genus, Thermobispora gen. nov., as Thermobispora bispora comb. nov. Int J Syst Bacteriol 46, 933–938.[CrossRef] [Google Scholar]
  49. Xu, P., Li, W. J., Xu, L. H. & Jiang, C. L.(2003). A microwave based method for genomic DNA extraction from actinomycetes. Microbiology (Beijing) 30, 82–84. [Google Scholar]
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