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Abstract

An endophytic actinobacterium, strain WES2, was isolated from the stem of a jasmine rice plant collected from a paddy field in Thung Gura Rong Hai, Roi Et province, Thailand. As a result of a polyphasic study, this strain was identified as representing a novel member of the genus . This strain was a Gram-stain-positive, aerobic actinobacterium with well-developed substrate mycelia and forming chains of looped spores. The closest phylogenetic relations, which shared the highest 16S rRNA gene sequence similarity, were JCM 4799 and NRRL-ISP 5487 at 99.1 and 99.0 %, respectively. Chemotaxonomic data, including major fatty acids, cell wall components and major menaquinones, confirmed the affiliation of WES2 to the genus The data from the phylogenetic analysis, including physiological and biochemical studies and DNA–DNA hybridization, revealed the genotypic and phenotypic differentiation of WES2 from the most closely related species with validly published names. The name proposed for the novel species is sp. nov. The type strain is WES2 (=DSM 101729=NRRL B-65344).

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2017-11-01
2024-12-14
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References

  1. Kämpfer P. Streptomyces Waksman and Henrici 1943, 339AL emend. Witt and Stackebrandt 1990, 370 emend. Wellington, Stackebrandt, Sanders, Wolstrup and Jorgensen 1992, 159. In Whitman WB, Goodfellow M, Kämpfer P, Busse HJ, Trujillo ME et al. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed. vol. 4 New York: Springer; 2012 pp. 1455–1804 [Crossref]
    [Google Scholar]
  2. Lechevalier MP, de Bievre C, Lechevalier H. Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 1977; 5:249–260 [View Article]
    [Google Scholar]
  3. Liu N, Wang H, Liu M, Gu Q, Zheng W et al. Streptomyces alni sp. nov., a daidzein-producing endophyte isolated from a root of Alnus nepalensis D. Don. Int J Syst Evol Microbiol 2009; 59:254–258 [View Article][PubMed]
    [Google Scholar]
  4. Bian GK, Qin S, Yuan B, Zhang YJ, Xing K et al. Streptomyces phytohabitans sp. nov., a novel endophytic actinomycete isolated from medicinal plant Curcuma phaeocaulis . Antonie van Leeuwenhoek 2012; 102:289–296 [View Article][PubMed]
    [Google Scholar]
  5. Li J, Zhao GZ, Zhu WY, Huang HY, Xu LH et al. Streptomyces endophyticus sp. nov., an endophytic actinomycete isolated from Artemisia annua L. Int J Syst Evol Microbiol 2013; 63:224–229 [View Article][PubMed]
    [Google Scholar]
  6. Qin S, Bian GK, Tamura T, Zhang YJ, Zhang WD et al. Streptomyces halophytocola sp. nov., an endophytic actinomycete isolated from the surface-sterilized stems of a coastal halophyte Tamarix chinensis Lour. Int J Syst Evol Microbiol 2013; 63:2770–2775 [View Article][PubMed]
    [Google Scholar]
  7. Sarmin NI, Tan GY, Franco CM, Edrada-Ebel R, Latip J et al. Streptomyces kebangsaanensis sp. nov., an endophytic actinomycete isolated from an ethnomedicinal plant, which produces phenazine-1-carboxylic acid. Int J Syst Evol Microbiol 2013; 63:3733–3738 [View Article][PubMed]
    [Google Scholar]
  8. Mingma R, Duangmal K, Thamchaipenet A, Trakulnaleamsai S, Matsumoto A et al. Streptomyces oryzae sp. nov., an endophytic actinomycete isolated from stems of rice plant. J Antibiot 2015; 68:368–372 [View Article][PubMed]
    [Google Scholar]
  9. Li C, Jin P, Liu C, Ma Z, Zhao J et al. Streptomyces bryophytorum sp. nov., an endophytic actinomycete isolated from moss (Bryophyta). Antonie van Leeuwenhoek 2016; 109:1209–1215 [View Article][PubMed]
    [Google Scholar]
  10. Wang HF, Li QL, Xiao M, Zhang YG, Zhou XK et al. Streptomyces capparidis sp. nov., a novel endophytic actinobacterium isolated from fruits of Capparis spinosa L. Int J Syst Evol Microbiol 2017; 67:133–137 [View Article][PubMed]
    [Google Scholar]
  11. Guo SY, Liu CX, Liu SH, Guan XJ, Guo LF et al. Streptomyces polygonati sp. nov., an endophytic actinomycete isolated from a root of Polygonatum odoratum (Mill.). Int J Syst Evol Microbiol 2016; 66:1488–1493 [Crossref]
    [Google Scholar]
  12. Coombs JT, Franco CM. Isolation and identification of actinobacteria from surface-sterilized wheat roots. Appl Environ Microbiol 2003; 69:5603–5608 [View Article][PubMed]
    [Google Scholar]
  13. Hayakawa M, Nonomura H. Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. J Ferment Technol 1987; 65:501–509 [View Article]
    [Google Scholar]
  14. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
    [Google Scholar]
  15. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article][PubMed]
    [Google Scholar]
  16. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  17. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425[PubMed]
    [Google Scholar]
  18. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526[PubMed]
    [Google Scholar]
  19. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  20. Ezaki T, Hashimoto Y, Yabuuchi E. 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 1989; 39:224–229 [View Article]
    [Google Scholar]
  21. Kusunoki S, Ezaki T, Tamesada M, Hatanaka Y, Asano K et al. Application of colorimetric microdilution plate hybridization for rapid genetic identification of 22 Mycobacterium species. J Clin Microbiol 1991; 29:1596–1603[PubMed]
    [Google Scholar]
  22. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
    [Google Scholar]
  23. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989; 39:159–167 [View Article]
    [Google Scholar]
  24. Bousfield IJ, Keddie RM, Dando TR, Shaw S. Simple rapid methods of cell wall analysis as an aid in the identification of aerobic coryneform bacteria. Chemical method in bacterial systematics. Technical Series 1985; 20:221–236
    [Google Scholar]
  25. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
    [Google Scholar]
  26. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
    [Google Scholar]
  27. Komagata K, Suzuki K. Lipid and cell wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207 [Crossref]
    [Google Scholar]
  28. Kaewkla O, Franco CMM. Actinopolymorpha pittospori sp. nov., an endophytic actinobacterium isolated from surface-sterilized leaves of an Australian native apricot tree. Int J Syst Evol Microbiol 2011; 62:2616–2620 [Crossref]
    [Google Scholar]
  29. Sasser M. identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, Technical Note 101. 2001
    [Google Scholar]
  30. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  31. Atlas RM. In Parks LC. (editor) Handbook of Microbiological Media Boca Raton: CRC Press; 1994
    [Google Scholar]
  32. Kornerup J, Wanscher H. In Pavey D. (editor) Methuen Handbook of Colour, 3rd ed. Fakenham, Norfolk: Cox & Wyman Ltd; 1978
    [Google Scholar]
  33. Gordon RE, Barnett DA, Handerhan JE, Pang CH-N. Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
    [Google Scholar]
  34. Kurup PV, Schmitt JA. Numerical taxonomy of Nocardia . Can J Microbiol 1973; 19:1035–1048 [View Article][PubMed]
    [Google Scholar]
  35. Williston EH, Zia-Walrath P, Youmans GP. Plate methods for testing antibiotic activity of actinomycetes against virulent human type tubercle bacilli. J Bacteriol 1947; 54:563–568[PubMed]
    [Google Scholar]
  36. Kampapongsa D, Kaewkla O. Biodiversity of endophytic actinobacteria from jasmine rice (Oryza sativa L. KDML 105) grown in Roi-Et Province, Thailand and their antimicrobial activity against rice pathogens. Ann Microbiol 2016; 66:587–595 [View Article]
    [Google Scholar]
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