sp. nov., isolated from a compost sample Free

Abstract

An actinomycete strain, designated YU1183-22, was isolated from a compost sample collected in Nikko, Japan. The isolate formed white aerial mycelium with relatively long aerial hyphae showing chains of arthrospores. Strain YU1183-22 grew with 0–10 % (w/v) NaCl, at pH 6–11 and at 10–37 °C (optimum 30 °C). Strain YU1183-22 contained -diaminopimelic acid and no diagnostic sugars. The predominant menaquinones were MK-10(H) and MK-10(H). The polar lipids were phosphatidylcholine and phosphatidylglycerol. The major cellular fatty acids were iso-C, anteiso-C and tuberculostearic acid. The G+C content of the DNA was 72.3 mol%. Chemotaxonomic and morphological characterization clearly demonstrated that strain YU1183-22 belonged to the genus . Phylogenetic analysis using 16S rRNA gene sequences showed that the isolate was closely related to YIM 90010 (98.0 % 16S rRNA gene sequence similarity), YIM 90004 (97.9 %) and HA-9 (97.3 %). However, DNA–DNA relatedness as well as physiological and biochemical analyses showed that strain YU1183-22 could be differentiated from its closest phylogenetic relatives. It is proposed that this strain be classified as a representative of a novel species of the genus , with the name sp. nov. The type strain is YU1183-22 (=NBRC 102170 =KCTC 19666).

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2010-12-01
2024-03-28
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References

  1. Chen Y.-G., Cui X.-L., Kroppenstedt R. M., Stackebrandt E., Wen M.-L., Xu L.-H., Jiang C.-L. 2008; Nocardiopsis quinghaiensis sp. nov., isolated from saline soil in China. Int J Syst Evol Microbiol 58:699–705 [CrossRef]
    [Google Scholar]
  2. Chun J., Bae K. S., Moon E. Y., Jung S. O., Lee H. K., Kim S. J. 2000; Nocardiopsis kunsanensis sp. nov., a moderately halophilic actinomycete isolated from a saltern. Int J Syst Evol Microbiol 50:1909–1913
    [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]
    [Google Scholar]
  4. Evtushenko L. I., Taran V. V., Akimov V. N., Kroppenstedt R. M., Tiedje J. M., Stackebrandt E. 2000; Nocardiopsis tropica sp. nov., Nocardiopsis trehalosi sp. nov., nom. rev. and Nocardiopsisdassonvillei subsp. albirubida subsp. nov., comb. nov. Int J Syst Evol Microbiol 50:73–81 [CrossRef]
    [Google Scholar]
  5. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [CrossRef]
    [Google Scholar]
  6. Gerhardt P. 1981 Manual of Methods for General Bacteriology Washington, DC: American Society for Microbiology;
    [Google Scholar]
  7. Gordon R. E., Mihm J. M. 1962; Identification of Nocardia caviae (Erikson) nov. comb. Ann N Y Acad Sci 98:628–636
    [Google Scholar]
  8. 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 (Web Server Issue):W557–W559 [CrossRef]
    [Google Scholar]
  9. Hasegawa T., Takizawa M., Tanida S. 1983; A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 29:319–322 [CrossRef]
    [Google Scholar]
  10. Hatano K., Nishii T., Kasai H. 2003; Taxonomic re-evaluation of whorl-forming Streptomyces (formerly Streptoverticillium ) species by using phenotype, DNA–DNA hybridization and sequences of gyrB , and proposal of Streptomyces luteireticuli ( ex Katoh and Arai 1957) corrig. sp. nov., nom. rev.. Int J Syst Evol Microbiol 531519–1529 [CrossRef]
    [Google Scholar]
  11. 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]
  12. Hayakawa M., Iino S., Nonomura H. 1982; Heavy metal resistance and melanoid pigment production in the streptomycete flora of copper-polluted vineyard soils. Hakkokogaku Kaishi 60:1–9
    [Google Scholar]
  13. Hozzein W. N., Goodfellow M. 2008; Nocardiopsis arabia sp. nov., a halotolerant actinomycete isolated from a sand-dune soil. Int J Syst Evol Microbiol 58:2520–2524 [CrossRef]
    [Google Scholar]
  14. Isik K., Chun J., Hah Y. C., Goodfellow M. 1999; Nocardia salmonicida nom. rev., a fish pathogen. Int J Syst Bacteriol 49:833–837 [CrossRef]
    [Google Scholar]
  15. Japan Colour Research Institute 1954 Guide to Colour Standard Tokyo: Nihon Shikisai Sha Co;
    [Google Scholar]
  16. Kämpfer P., Busse H. J., Rainey F. A. 2002; Nocardiopsis compostus sp. nov., from the atmosphere of a composting facility. Int J Syst Evol Microbiol 52:621–627
    [Google Scholar]
  17. Kim J. W., Adachi H., Shin-ya K., Hayakawa Y., Seto H. 1997; Apoptolidin, a new apoptosis inducer in transformed cells from Nocardiopsis sp. J Antibiot (Tokyo 50:628–630 [CrossRef]
    [Google Scholar]
  18. Küster E., Williams S. T. 1964; Production of hydrogen sulfide by streptomycetes and methods for its detection. Appl Microbiol 12:46–52
    [Google Scholar]
  19. Kusunoki S., Ezaki T., Tamesada S., Hatanaka Y., Asano K., Hashimoto Y., Yabuuchi E. 1991; Application of calorimetric microdilution plate hybridization for rapid generic identification of 22 Mycobacterium species. J Clin Microbiol 29:1596–1603
    [Google Scholar]
  20. 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]
  21. 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]
  22. Li M.-G., Li W.-J., Xu P., Cui X.-L., Xu L.-H., Jiang C.-L. 2003; Nocardiopsis xinjiangensis sp. nov., a halophilic actinomycete isolated from a saline sample in China. Int J Syst Evol Microbiol 53:317–321 [CrossRef]
    [Google Scholar]
  23. Li W.-J., Park D.-J., Tang S.-K., Wang D., Lee J.-C., Xu L.-H., Kim C.-J., Jiang C.-L. 2004; Nocardiopsis salina sp. nov., a novel halophilic actinomycete isolated from saline soil in China. Int J Syst Evol Microbiol 54:1805–1809 [CrossRef]
    [Google Scholar]
  24. Li Y. Q., Li M. G., Li W., Zhao J. Y., Ding Z. G., Cui X. L., Wen M. L. 2007; Griseusin D, a new pyranonaphthoquinone derivative from a alkaphilic Nocardiopsis sp. J Antibiot (Tokyo 60:757–761 [CrossRef]
    [Google Scholar]
  25. Meyer J. 1976; Nocardiopsis , a new genus of the order Actinomycetales . Int J Syst Bacteriol 26:487–493 [CrossRef]
    [Google Scholar]
  26. 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 [CrossRef]
    [Google Scholar]
  27. Saito H., Miura K.-I. 1963; Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim Biophys Acta 72:619–629 [CrossRef]
    [Google Scholar]
  28. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
    [Google Scholar]
  29. Schaal K. P. 1985; Identification of clinically significant actinomycetes and related bacteria using chemical techniques. In Chemical Methods in Bacterial Systematics pp 359–381 Edited by Goodfellow M., Minnikin D. E. London: Academic Press;
    [Google Scholar]
  30. Shirling E. B., Gottlieb D. 1966; Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340 [CrossRef]
    [Google Scholar]
  31. Sierra G. 1957; A simple method for the detection of lipolytic activity of micro-organisms and some observations on the influence of the contact between cells and fatty substrates. Antonie van Leeuwenhoek 23:15–22 [CrossRef]
    [Google Scholar]
  32. Sun H. H., White C. B., Dedinas J., Cooper R., Sedlock D. M. 1991; Methylpendolmycin, an indolactam from a Nocardiopsis sp. J Nat Prod 54:1440–1443 [CrossRef]
    [Google Scholar]
  33. Takahashi K., Nei M. 2000; Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Mol Biol Evol 17:1251–1258 [CrossRef]
    [Google Scholar]
  34. Tamura T., Hatano K. 2001; Phylogenetic analysis of the genus Actinoplanes and transfer of Actinoplanes minutisporangius Ruan et al. 1986 and ‘ Actinoplanes aurantiacus ’ to Cryptosporangium minutisporangium comb. nov. and Cryptosporangium aurantiacum sp. nov.. Int J Syst Evol Microbiol 51:2119–2125 [CrossRef]
    [Google Scholar]
  35. Tamura T., Nakagaito Y., Nishii T., Hasegawa T., Stackebrandt E., Yokota A. 1994; A new genus of the order Actinomycetales , Couchioplanes gen. nov., with descriptions of Couchioplanes caeruleus (Horan and Brodsky 1986) comb. nov. and Couchioplanes caeruleus subsp. azureus subsp. nov.. Int J Syst Bacteriol 44:193–203 [CrossRef]
    [Google Scholar]
  36. 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]
    [Google Scholar]
  37. 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]
  38. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E. other authors 1987; International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464 [CrossRef]
    [Google Scholar]
  39. Williams S. T., Goodfellow M., Alderson G., Wellington E. M. H., Sneath P. H. A., Sackin M. J. 1983; Numerical classification of Streptomyces and related genera. J Gen Microbiol 129:1743–1813
    [Google Scholar]
  40. Yang R., Zhang L.-P., Guo L.-G., Shi N., Lu Z., Zhang X. 2008; Nocardiopsis valliformis sp. nov., an alkaliphilic actinomycete isolated from alkali lake soil in China. Int J Syst Evol Microbiol 58:1542–1546 [CrossRef]
    [Google Scholar]
  41. Yassin A. F., Rainey F. A., Burghardt J., Gierth D., Ungerechts J., Lux I., Seifert P., Bal C., Schaal K. P. 1997; Description of Nocardiopsis synnemataformans sp. nov., elevation of Nocardiopsis alba subsp. prasina to Nocardiopsis prasina comb. nov., and designation of Nocardiopsis antarctica and Nocardiopsis alborubida as later subjective synonyms of Nocardiopsis dassonvillei . Int J Syst Bacteriol 47:983–988 [CrossRef]
    [Google Scholar]
  42. Zhang X., Zhang L.-P., Yang R., Shi N., Lu Z., Chen W. X., Jiang C.-L., Xu L.-H. 2008; Nocardiopsis ganjiahuensis sp. nov., isolated from a soil from Ganjiahu, China. Int J Syst Evol Microbiol 58:195–199 [CrossRef]
    [Google Scholar]
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