1887

Abstract

A Gram-stain-positive, non-motile, creamy-white and rod-coccus shaped actinobacterium, designated strain Ktm-20, capable of degrading petroleum oil was isolated from oil-contaminated soil. Strain Ktm-20 was able to grow at 15–37 °C, at pH 5.5–10.0 and at 0.0–2.0 % (w/v) NaCl concentration. This strain was taxonomically characterized by a polyphasic approach. The 16S rRNA gene sequence analysis showed that strain Ktm-20 belonged to the genus and is closely related to DSM 44892, UC12, NBRC 100605, CFH S0262 and MBRL 353T (98.8, 98.7, 98.5, 98.4 and 98.3 % gene sequence similarity, respectively). The only respiratory quinone was MK-8(H2); the major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside; and the predominant fatty acids were C, summed feature 3 (Cω7 and/or Cω6) and Cω9. The cell-wall peptidoglycan contained meso-diaminopimelic acid; and galactose, glucose, arabinose and ribose were detected as diagnostic sugars from whole-cell hydrolysates. Mycolic acids were detected. The DNA G+C content was 70.9 mol%. The DNA–DNA relatedness values between strain Ktm-20 and closely related species of the genus were between 38.3–25.3 %, which falls below the threshold value of 70 % for the strain to be considered as novel. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbours. Thus, strain Ktm-20 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is Ktm-20 (=KEMB 9005-695=KACC 19390=JCM 32206).

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2018-05-01
2024-12-05
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References

  1. Zopf W. Über ausscheidung von fettfarbstoffen (Lipochromen) seitens gewisser spaltpilze. Ber Dtsch Bot Ges 1891; 9:22–28
    [Google Scholar]
  2. Tsukamura M. A further numerical taxonomic study of the Rhodochrous group. Jpn J Microbiol 1974; 18:37–44 [View Article][PubMed]
    [Google Scholar]
  3. Guo QQ, Ming H, Meng XL, Duan YY, Gao R et al. Rhodococcus agglutinans sp. nov., an actinobacterium isolated from a soil sample. Antonie van Leeuwenhoek 2015; 107:1271–1280 [View Article][PubMed]
    [Google Scholar]
  4. Nguyen TM, Kim J. Rhodococcus pedocola sp. nov. and Rhodococcus humicola sp. nov., two antibiotic-producing actinomycetes isolated from soil. Int J Syst Evol Microbiol 2016; 66:2362–2369 [View Article][PubMed]
    [Google Scholar]
  5. Yassin AF. Rhodococcus triatomae sp. nov., isolated from a blood-sucking bug. Int J Syst Evol Microbiol 2005; 55:1575–1579 [View Article][PubMed]
    [Google Scholar]
  6. Goodfellow M, Chun J, Stackebrandt E, Kroppenstedt RM. Transfer of Tsukamurella wratislaviensis Goodfellow et al. 1995 to the genus Rhodococcus as Rhodococcus wratislaviensis comb. nov. Int J Syst Evol Microbiol 2002; 52:749–755 [View Article][PubMed]
    [Google Scholar]
  7. Nimaichand S, Sanasam S, Zheng LQ, Zhu WY, Yang LL et al. Rhodococcus canchipurensis sp. nov., an actinomycete isolated from a limestone deposit site. Int J Syst Evol Microbiol 2013; 63:114–118 [View Article][PubMed]
    [Google Scholar]
  8. Klatte S, Kroppenstedt RM, Rainey FA. Rhodococcus opacus sp. nov., an unusual nutritionally versatile Rhodococcus species. Syst Appl Microbiol 1994; 17:355–360 [View Article]
    [Google Scholar]
  9. Kämpfer P, Dott W, Martin K, Glaeser SP. Rhodococcus defluvii sp. nov., isolated from wastewater of a bioreactor and formal proposal to reclassify [Corynebacterium hoagii] and Rhodococcus equi as Rhodococcus hoagii comb. nov. Int J Syst Evol Microbiol 2014; 64:755–761 [View Article][PubMed]
    [Google Scholar]
  10. Ko KS, Kim Y, Seong CN, Lee SD. Rhodococcus antrifimi sp. nov., isolated from dried bat dung of a cave. Int J Syst Evol Microbiol 2015; 65:4043–4048 [View Article][PubMed]
    [Google Scholar]
  11. Larkin MJ, Kulakov LA, Allen CC. Biodegradation and Rhodococcus–masters of catabolic versatility. Curr Opin Biotechnol 2005; 16:282–290 [View Article][PubMed]
    [Google Scholar]
  12. Pham VH, Kim J. Cultivation of unculturable soil bacteria. Trends Biotechnol 2012; 30:475–484 [View Article][PubMed]
    [Google Scholar]
  13. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961; 3:208–218 [View Article]
    [Google Scholar]
  14. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74:2461–2470 [View Article][PubMed]
    [Google Scholar]
  15. 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 (in press) [View Article][PubMed]
    [Google Scholar]
  16. 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]
  17. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41:95–98
    [Google Scholar]
  18. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  19. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
    [Google Scholar]
  20. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  21. 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]
  22. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article][PubMed]
    [Google Scholar]
  23. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  24. Yarza P, Richter M, Peplies J, Euzeby J, Amann R et al. The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008; 31:241–250 [View Article][PubMed]
    [Google Scholar]
  25. Beveridge TJ, Lawrence JR, Murray RGE. Sampling and staining for light microscopy. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM et al. (editors) Methods for General and Molecular Microbiology Washington, DC: American Society for Microbiology; 2007 pp. 19–33
    [Google Scholar]
  26. Breznak JA, Costilow RN. Physicochemical factors in growth. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: American Society for Microbiology; 2007 pp. 309–329
    [Google Scholar]
  27. Hemraj V, Diksha S, Avneet G. A review on commonly used biochemical test for bacteria. Innovare J Life Sci 2013; 1:1–7
    [Google Scholar]
  28. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC, USA: American Society for Microbiology; 1994 pp. 607–654
    [Google Scholar]
  29. Chaudhary DK, Kim J. Sphingomonas olei sp. nov., with the ability to degrade aliphatic hydrocarbons, isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2017; 67:2731–2738 [View Article][PubMed]
    [Google Scholar]
  30. 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]
  31. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [View Article]
    [Google Scholar]
  32. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316–354[PubMed]
    [Google Scholar]
  33. Komagata K, Suzuki K. Lipids and cell wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–203 [Crossref]
    [Google Scholar]
  34. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  35. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231[PubMed]
    [Google Scholar]
  36. 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]
  37. 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]
  38. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
    [Google Scholar]
  39. 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]
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