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Abstract

Three novel Gram-stain-positive bacteria, designated IY07-20, IY07-56 and IY07-113, were isolated from soil samples from Iriomote Island, Okinawa, Japan, and their taxonomic positions were investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the three isolates were closely related to the members of the genus , with similarity range of 95.6–98.7 %. The isolates contained -2,4-diaminobutylic acid, -alanine, -glutamic acid and glycine in their peptidoglycans. The predominant menaquinone was MK-12 and the major fatty acids were anteiso-C and anteiso-C. The DNA G+C contents were 70.9–72.9 mol%. The chemotaxonomic characteristics of the isolates matched those described for members of the genus The results of phylogenetic analysis and DNA–DNA hybridization, along with differences in phenotypic characteristics between strains IY07-20, IY07-56 and IY07-113 and the species of the genus with validly published names, indicate that the three isolates merit classification as representatives of two novel species of the genus , for which the names sp. nov. and sp. nov. are proposed; the type strains are IY07-20 ( = NBRC 106452 = DSM 26155) and IY07-56 ( = NBRC 106454 = DSM 26153), respectively.

Funding
This study was supported by the:
  • Institute for Fermentation, Osaka (IFO)
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2014-03-01
2024-04-26
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References

  1. Akimov V. N., Evtushenko L. I. ( 2012 ). Genus IV. Agromyces . . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 5, pp. 862876. Edited by Goodfellow M., Kämpfer P., Busse H. J., Trujillo M. E., Suzuki K., Ludwig W., Whitman W. B. . New York:: Springer;.
    [Google Scholar]
  2. Chen J., Chen H. M., Zhang Y. Q., Wei Y. Z., Li Q. P., Liu H. Y., Su J., Zhang Y. Q., Yu L. Y. ( 2011 ). Agromyces flavus sp. nov., an actinomycete isolated from soil. . Int J Syst Evol Microbiol 61, 17051709. [View Article] [PubMed]
    [Google Scholar]
  3. 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, 224229. [View Article]
    [Google Scholar]
  4. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [View Article] [PubMed]
    [Google Scholar]
  5. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [View Article]
    [Google Scholar]
  6. Fitch W. M. ( 1971 ). Toward defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20, 406416. [View Article]
    [Google Scholar]
  7. Gledhill W. E., Casida L. E. ( 1969 ). Predominant catalase-negative soil bacteria. III. Agromyces, gen. n., microorganisms intermediary to Actinomyces and Nocardia . . Appl Microbiol 18, 340349. [PubMed]
    [Google Scholar]
  8. Hamada M., Iino T., Iwami T., Harayama S., Tamura T., Suzuki K. ( 2010 ). Mobilicoccus pelagius gen. nov., sp. nov. and Piscicoccus intestinalis gen. nov., sp. nov., two new members of the family Dermatophilaceae, and reclassification of Dermatophilus chelonae (Masters et al. 1995) as Austwickia chelonae gen. nov., comb. nov.. J Gen Appl Microbiol 56, 427436. [View Article] [PubMed]
    [Google Scholar]
  9. Hamada M., Yamamura H., Komukai C., Tamura T., Suzuki K., Hayakawa M. ( 2012 ). Luteimicrobium album sp. nov., a novel actinobacterium isolated from a lichen collected in Japan, and emended description of the genus Luteimicrobium . . J Antibiot (Tokyo) 65, 427431. [View Article] [PubMed]
    [Google Scholar]
  10. Hayakawa M., Nonomura H. ( 1987 ). Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. . J Ferment Technol 65, 501509. [View Article]
    [Google Scholar]
  11. Hayakawa M., Nonomura H. ( 1989 ). A new method for the intensive isolation of actinomycetes from soil. . Actinomycetologica 3, 95104. [View Article]
    [Google Scholar]
  12. Jurado V., Groth I., Gonzalez J. M., Laiz L., Schuetze B., Saiz-Jimenez C. ( 2005 ). Agromyces italicus sp. nov., Agromyces humatus sp. nov. and Agromyces lapidis sp. nov., isolated from Roman catacombs. . Int J Syst Evol Microbiol 55, 871875. [View Article] [PubMed]
    [Google Scholar]
  13. 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, 716721. [View Article] [PubMed]
    [Google Scholar]
  14. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425. [PubMed]
    [Google Scholar]
  15. Sasaki J., Chijimatsu M., Suzuki K. ( 1998 ). Taxonomic significance of 2,4-diaminobutyric acid isomers in the cell wall peptidoglycan of actinomycetes and reclassification of Clavibacter toxicus as Rathayibacter toxicus comb. nov.. Int J Syst Bacteriol 48, 403410. [View Article] [PubMed]
    [Google Scholar]
  16. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. . Newark, DE:: MIDI Inc;.
    [Google Scholar]
  17. Schleifer K. H., Kandler O. ( 1972 ). Peptidoglycan types of bacterial cell walls and their taxonomic implications. . Bacteriol Rev 36, 407477. [PubMed]
    [Google Scholar]
  18. Tamaoka J., Komagata K. ( 1984 ). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. . FEMS Microbiol Lett 25, 125128. [View Article]
    [Google Scholar]
  19. 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, 27312739. [View Article] [PubMed]
    [Google Scholar]
  20. 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, 48764882. [View Article] [PubMed]
    [Google Scholar]
  21. Uchida K., Kudo T., Suzuki K. I., Nakase T. ( 1999 ). A new rapid method of glycolate test by diethyl ether extraction, which is applicable to a small amount of bacterial cells of less than one milligram. . J Gen Appl Microbiol 45, 4956. [View Article] [PubMed]
    [Google Scholar]
  22. Zgurskaya H. I., Evtushenko L. I., Akimov V. N., Voyevoda H. V., Dobrovolskaya T. G., Lysak L. V., Kalakoutskii L. V. ( 1992 ). Emended description of the genus Agromyces and description of Agromyces cerinus subsp. cerinus sp. nov., subsp. nov., Agromyces cerinus subsp. nitratus sp. nov., subsp. nov., Agromyces fucosus subsp. fucosus sp. nov., subsp. nov., and Agromyces fucosus subsp. hippuratus sp. nov., subsp. nov.. Int J Syst Bacteriol 42, 635641. [View Article]
    [Google Scholar]
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