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Abstract

A novel endophytic actinomycete, designated strain RS15-1S, was isolated from surface-sterilized stems of Oryza sativa L. collected from Sisaket province, Thailand. The colony of strain was strong orange, catalase-positive and oxidase-negative. Growth occurred at a temperature range of 17–37 °C, at pH 4.0–9.0 and in the presence of 0–13 % (w/v) NaCl. Phylogenetic analyses based on the 16S rRNA sequences showed that strain RS15-1S belonged to the genus Gordonia and was closely related to Gordonia polyisoprenivorans DSM 44302 (98.8 %) and Gordonia rhizosphera DSM 44383 (98.4 %). The major cellular fatty acids were C16 : 0, C18 : 0 10-methyl (tbsa), C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω9c. The menaquinones were MK-9(H2) and MK-8(H2). Strain RS15-1S contained meso-diaminopimelic acid, arabinose, galactose, mannose and ribose in whole-cell hydrolysates. The polar lipids of the strain were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannosides, an unidentified polar lipid and two unidentified phospholipids. The DNA G+C content was 66.3 mol%. In silico DNA–DNA hybridization of strain RS15-1S showed 48.3 and 20.5 % relatedness to its closest neighbours, Gordonia polyisoprenivorans DSM 44302 and Gordonia rhizosphera DSM 44383, respectively. Based on data of genotypic, phenotypic, phylogenetic and chemotaxonomic analysis, strain RS15-1S represents a novel species of the genus Gordonia , for which the name Gordonia oryzae sp. nov. is proposed. The type strain is RS15-1S (=TBRC 8485=NBRC 113446).

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2019-04-01
2019-08-22
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References

  1. Tsukamura M. Proposal of a new genus, Gordona, for slightly acid-fast organisms occurring in sputa of patients with pulmonary disease and in soil. J Gen Microbiol 1971;68:15–26 [CrossRef][PubMed]
    [Google Scholar]
  2. Parte AC. LPSN - list of prokaryotic names with standing in nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018;68:1825–1829 [CrossRef][PubMed]
    [Google Scholar]
  3. Goodfellow M, Kumar Y, Maldonado LA. Genus Gordonia. In Kämpfer P, Busse H-J, Trujillo ME, Suzuki K-I. (editors) Bergey’s Manual of Systematic Bacteriology, Second ed. New York: Springer; 2012; pp.419–435
    [Google Scholar]
  4. Takeuchi M, Hatano K. Gordonia rhizosphera sp. nov. isolated from the mangrove rhizosphere. Int J Syst Bacteriol 1998;48:907–912 [CrossRef][PubMed]
    [Google Scholar]
  5. Linos A, Steinbüchel A, Spröer C, Kroppenstedt RM. Gordonia polyisoprenivorans sp. nov., a rubber-degrading actinomycete isolated from an automobile tyre. Int J Syst Bacteriol 1999;49:1785–1791 [CrossRef][PubMed]
    [Google Scholar]
  6. Kämpfer P, Young CC, Chu JN, Frischmann A, Busse HJ et al. Gordonia humi sp. nov., isolated from soil. Int J Syst Evol Microbiol 2011;61:65–70 [CrossRef][PubMed]
    [Google Scholar]
  7. Li SH, Jin Y, Cheng J, Park DJ, Kim CJ et al. Gordonia jinhuaensis sp. nov., a novel actinobacterium, isolated from a VBNC (viable but non-culturable) state in pharmaceutical wastewater. Antonie van Leeuwenhoek 2014;106:347–356 [CrossRef][PubMed]
    [Google Scholar]
  8. Kang YQ, Ming H, Gonoi T, Chen Y, Cao Y et al. Gordonia iterans sp. nov., isolated from a patient with pneumonia. Int J Syst Evol Microbiol 2014;64:3520–3525 [CrossRef][PubMed]
    [Google Scholar]
  9. Tsang CC, Xiong L, Poon RW, Chen JH, Leung KW et al. Gordonia hongkongensis sp. nov., isolated from blood culture and peritoneal dialysis effluent of patients in Hong Kong. Int J Syst Evol Microbiol 2016;66:3942–3950 [CrossRef][PubMed]
    [Google Scholar]
  10. de Menezes CB, Afonso RS, de Souza WR, Parma M, de Melo IS et al. Gordonia didemni sp. nov. an actinomycete isolated from the marine ascidium Didemnum sp. Antonie van Leeuwenhoek 2016;109:297–303 [CrossRef][PubMed]
    [Google Scholar]
  11. Jin D, Kong X, Jia M, Yu X, Wang X et al. Gordonia phthalatica sp. nov., a di-n-butyl phthalate-degrading bacterium isolated from activated sludge. Int J Syst Evol Microbiol 2017;67:5128–5133 [CrossRef][PubMed]
    [Google Scholar]
  12. Himaman W, Thamchaipenet A, Pathom-aree W, Duangmal K. Actinomycetes from eucalyptus and their biological activities for controlling eucalyptus leaf and shoot blight. Microbiol Res 2016;188-189:42–52 [CrossRef][PubMed]
    [Google Scholar]
  13. Kuester E, Williams ST. Selection of media for isolation of streptomycetes. Nature 1964;202:928–929 [CrossRef][PubMed]
    [Google Scholar]
  14. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966;16:313–340 [CrossRef]
    [Google Scholar]
  15. Wellington E. Preservation of actinomycete inoculum in frozen glycerol. Microbios Lett 1979;6:151–157
    [Google Scholar]
  16. Kieser T, Foundation JI, Bibb MJ, Buttner MJ, Chater KF et al. Practical Streptomyces Genetics John Innes Foundation; 2000
    [Google Scholar]
  17. Kataoka M, Ueda K, Kudo T, Seki T, Yoshida T. Application of the variable region in 16S rDNA to create an index for rapid species identification in the genus Streptomyces. FEMS Microbiol Lett 1997;151:249–255 [CrossRef][PubMed]
    [Google Scholar]
  18. Mingma R, Pathom-aree W, Trakulnaleamsai S, Thamchaipenet A, Duangmal K. Isolation of rhizospheric and roots endophytic actinomycetes from Leguminosae plant and their activities to inhibit soybean pathogen, Xanthomonas campestris pv. glycine. World J Microbiol Biotechnol 2014;30:271–280 [CrossRef][PubMed]
    [Google Scholar]
  19. Chun J. Computer Assisted Classification and Identification of Actinomycetes UK: University of Newcastle; 1995; pp.165
    [Google Scholar]
  20. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017;67:1613–1617 [CrossRef][PubMed]
    [Google Scholar]
  21. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  22. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971;20:406–416 [CrossRef]
    [Google Scholar]
  23. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  24. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  25. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  26. Tarlachkov SV, Starodumova IP. TaxonDC: Calculating the similarity value of the 16S rRNA gene sequences of prokaryotes or ITS regions of fungi. J Bioinform Genom 2017;3:
    [Google Scholar]
  27. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012;19:455–477 [CrossRef][PubMed]
    [Google Scholar]
  28. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013;29:1072–1075 [CrossRef][PubMed]
    [Google Scholar]
  29. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016;66:1100–1103 [CrossRef][PubMed]
    [Google Scholar]
  30. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013;14:60–14 [CrossRef][PubMed]
    [Google Scholar]
  31. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018;68:461–466 [CrossRef][PubMed]
    [Google Scholar]
  32. 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 [CrossRef]
    [Google Scholar]
  33. Mundie DA. The NBS/ISCC Color System/David A Mundie Pittsburgh, PA: Polymath Systems; 1995; pp.535.6
    [Google Scholar]
  34. Williams ST, Goodfellow M, Alderson G, Wellington EM, Sneath PH et al. Numerical classification of Streptomyces and related genera. J Gen Microbiol 1983;129:1743–1813 [CrossRef][PubMed]
    [Google Scholar]
  35. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977;27:104–117 [CrossRef]
    [Google Scholar]
  36. Becker B, Lechevalier MP, Lechevalier HA. Chemical composition of cell-wall preparations from strains of various form-genera of aerobic actinomycetes. Appl Microbiol 1965;13:236–243[PubMed]
    [Google Scholar]
  37. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983;29:319–322 [CrossRef]
    [Google Scholar]
  38. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974;28:226–231[PubMed]
    [Google Scholar]
  39. Tomiyasu I. Mycolic acid composition and thermally adaptative changes in Nocardia asteroides. J Bacteriol 1982;151:828–837[PubMed]
    [Google Scholar]
  40. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977;100:221–230 [CrossRef][PubMed]
    [Google Scholar]
  41. Uchida K, Kudo T, Suzuki KI, Nakase T. 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 1999;45:49–56 [CrossRef][PubMed]
    [Google Scholar]
  42. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids Newark, DE: MIDI; 1990
    [Google Scholar]
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