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Abstract

A mesophilic, aerobic, Gram-stain-positive, filamentous bacterial strain, designated ZYf1a3, was isolated from rice paddy soil in Japan. This strain grew on a solid medium with formation of substrate mycelium; endospores were produced singly along the mycelium. Formation of aerial mycelium was not observed on any of the media tested. This strain produced a characteristic saffron yellow soluble pigment. Cloned 16S rRNA gene sequences of strain ZYf1a3 yielded three different copies (similarity between the three sequences: 99.8–99.9 %). One of these sequences had one base deletion. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain ZYf1a3 belongs to an independent phylogenetic lineage of the family . The cell wall of strain ZYf1a3 contained -diaminopimelic acid, alanine and glutamic acid, but no characteristic sugars. It contained menaquinone 7 as the sole menaquinone. The major cellular fatty acids were iso-C and anteiso-C.The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidyl--methylethanolamine and unidentified aminophospholipids. The DNA G+C content was 42.5 mol%. From phylogenetic analysis based on 16S rRNA gene sequences and phenotypic characteristics, this strain is considered to represent a novel species in a new genus, for which the name gen. nov., sp. nov. is proposed. The type strain of is ZYf1a3 ( = JCM 30426 = CCUG 66446 = DSM 46876).

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2015-11-01
2019-10-14
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References

  1. Addou A. N., Schumann P., Spröer C., Bouanane-Darenfed A., Amarouche-Yala S., Hacene H., Cayol J.-L., Fardeau M.-L.. ( 2013;). Melghirimyces thermohalophilus sp. nov., a thermoactinomycete isolated from an Algerian salt lake. Int J Syst Evol Microbiol 63: 1717–1722 [CrossRef] [PubMed].
    [Google Scholar]
  2. Buck J. D.. ( 1982;). Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 44: 992–993 [PubMed].
    [Google Scholar]
  3. Buss S. N., Cole J. A., Hannett G. E., Nazarian E. J., Nazarian L., Coorevits A., Van Landschoot A., De Vos P., Schumann P., other authors. ( 2013;). Hazenella coriacea gen. nov., sp. nov., isolated from clinical specimens. Int J Syst Evol Microbiol 63: 4087–4093 [CrossRef] [PubMed].
    [Google Scholar]
  4. Christensen W. B.. ( 1946;). Urea decomposition as a means of differentiating Proteus and Paracolon cultures from each other and from Salmonella and Shigella types. J Bacteriol 52: 461–466 [PubMed].
    [Google Scholar]
  5. Claus D., Berkeley R. C. W.. ( 1986;). Genus Bacillus Cohn 1872, 174AL. . In Bergey's Manual of Systematic Bacteriology, pp. 1105–1139. Edited by Sneath P. H. A., Mair N. S., Sharpe M. E., Holt J. G..vol. 2 Baltimore: Williams & Wilkins;.
    [Google Scholar]
  6. DeLong E. F.. ( 1992;). Archaea in coastal marine environments. Proc Natl Acad Sci U S A 89: 5685–5689 [CrossRef] [PubMed].
    [Google Scholar]
  7. Felsenstein J.. ( 1985;). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791 [CrossRef].
    [Google Scholar]
  8. Hatayama K., Shoun H., Ueda Y., Nakamura A.. ( 2005;). Planifilum fimeticola gen. nov., sp. nov. and Planifilum fulgidum sp. nov., novel members of the family ‘Thermoactinomycetaceae’ isolated from compost. Int J Syst Evol Microbiol 55: 2101–2104 [CrossRef] [PubMed].
    [Google Scholar]
  9. Kawamoto I., Oka T., Nara T.. ( 1981;). Cell wall composition of Micromonospora olivoasterospora, Micromonospora sagamiensis, and related organisms. J Bacteriol 146: 527–534 [PubMed].
    [Google Scholar]
  10. Kim O.-S., Cho Y.-J., Lee K., Yoon S.-H., Kim M., Na H., Park S.-C., Jeon Y. S., Lee J.-H., other authors. ( 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 [CrossRef] [PubMed].
    [Google Scholar]
  11. 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] [PubMed].
    [Google Scholar]
  12. Lacey J., Cross T.. ( 1989;). Genus Thermoactinomyces Tsiklinsky 1899, 501AL. . In Bergey's Manual of Systematic Bacteriology, pp. 2574–2585. Edited by Williams S. T., Sharpe M. E., Holt J. G..vol. 4 Baltimore: Williams and Wilkins;.
    [Google Scholar]
  13. Li J., Zhang G.-T., Yang J., Tian X.-P., Wang F.-Z., Zhang C. S., Zhang S., Li W.-J.. ( 2012;). Marininema mesophilum gen. nov., sp. nov., a thermoactinomycete isolated from deep sea sediment, and emended description of the family Thermoactinomycetaceae. Int J Syst Evol Microbiol 62: 1383–1388 [CrossRef] [PubMed].
    [Google Scholar]
  14. Matsuo Y., Katsuta A., Matsuda S., Shizuri Y., Yokota A., Kasai H.. ( 2006;). Mechercharimyces mesophilus gen. nov., sp. nov. and Mechercharimyces asporophorigenens sp. nov., antitumour substance-producing marine bacteria, and description of Thermoactinomycetaceae fam. nov. Int J Syst Evol Microbiol 56: 2837–2842 [CrossRef] [PubMed].
    [Google Scholar]
  15. 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]
  16. Nishijima M., Araki-Sakai M., Sano H.. ( 1997;). Identification of isoprenoid quinones by frit-FAB liquid chromatography-mass spectrometry for the chemotaxonomy of microorganisms. J Microbiol Methods 28: 113–122 [CrossRef].
    [Google Scholar]
  17. Park D.-J., Dastager S. G., Lee J.-C., Yeo S.-H., Yoon J.-H., Kim C.-J.. ( 2007;). Shimazuella kribbensis gen. nov., sp. nov., a mesophilic representative of the family Thermoactinomycetaceae. Int J Syst Evol Microbiol 57: 2660–2664 [CrossRef] [PubMed].
    [Google Scholar]
  18. Reasoner D. J., Geldreich E. E.. ( 1985;). A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 49: 1–7 [PubMed].
    [Google Scholar]
  19. 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]
  20. Shirling E. B., Gottlieb D.. ( 1966;). Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16: 313–340 [CrossRef].
    [Google Scholar]
  21. 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]
  22. Tamura K., Nei M.. ( 1993;). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10: 512–526 [PubMed].
    [Google Scholar]
  23. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S.. ( 2013;). mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30: 2725–2729 [CrossRef] [PubMed].
    [Google Scholar]
  24. 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]
  25. Tsubouchi T., Shimane Y., Mori K., Usui K., Hiraki T., Tame A., Uematsu K., Maruyama T., Hatada Y.. ( 2013;). Polycladomyces abyssicola gen. nov., sp. nov., a thermophilic filamentous bacterium isolated from hemipelagic sediment. Int J Syst Evol Microbiol 63: 1972–1981 [CrossRef] [PubMed].
    [Google Scholar]
  26. von Jan M., Riegger N., Pötter G., Schumann P., Verbarg S., Spröer C., Rohde M., Lauer B., Labeda D. P., Klenk H.-P.. ( 2011;). Kroppenstedtia eburnea gen. nov., sp. nov., a thermoactinomycete isolated by environmental screening, and emended description of the family Thermoactinomycetaceae Matsuo et al. 2006 emend. Yassin et al. 2009. Int J Syst Evol Microbiol 61: 2304–2310 [CrossRef] [PubMed].
    [Google Scholar]
  27. Yassin A. F., Hupfer H., Klenk H.-P., Siering C.. ( 2009;). Desmospora activa gen. nov., sp. nov., a thermoactinomycete isolated from sputum of a patient with suspected pulmonary tuberculosis, and emended description of the family Thermoactinomycetaceae Matsuo et al. 2006. Int J Syst Evol Microbiol 59: 454–459 [CrossRef] [PubMed].
    [Google Scholar]
  28. Yoon J.-H., Kim I.-G., Shin Y.-K., Park Y.-H.. ( 2005;). Proposal of the genus Thermoactinomyces sensu stricto and three new genera, Laceyella, Thermoflavimicrobium and Seinonella, on the basis of phenotypic, phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 55: 395–400 [CrossRef] [PubMed].
    [Google Scholar]
  29. Yu T.-T., Zhang B.-H., Yao J.-C., Tang S.-K., Zhou E.-M., Yin Y.-R., Wei D.-Q., Ming H., Li W.-J.. ( 2012;). Lihuaxuella thermophila gen. nov., sp. nov., isolated from a geothermal soil sample in Tengchong, Yunnan, south-west China. Antonie van Leeuwenhoek 102: 711–718 [CrossRef] [PubMed].
    [Google Scholar]
  30. Zarparvar P., Amoozegar M. A., Nikou M. M., Schumann P., Ventosa A.. ( 2014;). Salinithrix halophila gen. nov., sp. nov., a halophilic bacterium in the family Thermoactinomycetaceae. Int J Syst Evol Microbiol 64: 4115–4119 [CrossRef] [PubMed].
    [Google Scholar]
  31. Zhou E.-M., Yu T.-T., Liu L., Ming H., Yin Y.-R., Dong L., Tseng M., Nie G.-X., Li W.-J.. ( 2014;). Geothermomicrobium terrae gen. nov., sp. nov., a novel member of the family Thermoactinomycetaceae. Int J Syst Evol Microbiol 64: 2998–3004 [CrossRef] [PubMed].
    [Google Scholar]
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