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Volume 67, Issue 7

sp. nov., an actinobacterium isolated from a karst cave sample, and emended description of the genus Free

Abstract

A novel actinobacterial strain, designated SYSU K10001, was isolated from a limestone sample collected from a karst cave in Xingyi county, Guizhou province, south-western China. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of the strain were aerobic and Gram-stain-positive. On the basis of 16S rRNA gene sequence analysis, strain SYSU K10001 was most closely related to the type strains of the genus , NBRC 16102 (98.8 % similarity) and NRRL B-16159 (98.6 %), and is therefore considered to represent a member of the genus DNA–DNA hybridization values between strain SYSU K10001 and related type strains of the genus were less than 70 %. In addition, -diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The whole-cell sugars were arabinose, fructose, mannose and xylose. The major isoprenoid quinone was MK-9(H), while the major fatty acids (>10 %) were iso-C and C. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, one unidentified phospholipid and one unidentified lipid. The genomic DNA G+C content of strain SYSU K10001 was 69.4 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU K10001 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is SYSU K10001 (=KCTC 39804=CGMCC 4.7367=NBRC 112394).

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Keyword(s): karst cave , Lentzea cavernae sp. nov. , limestone sample and polyphasic taxonomy
© 2017 IUMS
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2017-07-01
2024-04-19
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References

  1. Yassin AF, Rainey FA, Brzezinka H, Jahnke KD, Weissbrodt H et al. Lentzea gen. nov., a new genus of the order Actinomycetales . Int J Syst Bacteriol 1995; 45:357–363 [View Article][PubMed]
     [Google Scholar]
  2. Lee SD, Kim ES, Roe JH, Kim J, Kang SO et al. Saccharothrix violacea sp. nov., isolated from a gold mine cave, and Saccharothrix albidocapillata comb. nov. Int J Syst Evol Microbiol 2000; 50:1315–1323 [View Article][PubMed]
     [Google Scholar]
  3. Labeda DP, Hatano K, Kroppenstedt RM, Tamura T. Revival of the genus Lentzea and proposal for Lechevalieria gen. nov. Int J Syst Evol Microbiol 2001; 51:1045–1050 [View Article][PubMed]
     [Google Scholar]
  4. Labeda DP, Goodfellow M, Chun J, Zhi XY, Li WJ. Reassessment of the systematics of the suborder Pseudonocardineae: transfer of the genera within the family Actinosynnemataceae Labeda and Kroppenstedt 2000 emend. Zhi et al. 2009 into an emended family Pseudonocardiaceae Embley et al. 1989 emend. Zhi et al. 2009. Int J Syst Evol Microbiol 2011; 61:1259–1264 [View Article][PubMed]
     [Google Scholar]
  5. Labeda DP. Genus XI. Lentzea Yassin, Rainey, Brzezinka, Jahnke, Weissbrodt, Budzikiewicz, Stackebrandt and Schaal 1995, 1125VP emend. Labeda, Hatano, Kroppenstedt and Tamura 2001, 1049. In Goodfellow M, Kämpfer P, Busse H-J, Trujillo ME, Suzuki K-I. et al. (editors) Bergey’s Manual of Systematic Bacteriology, Part A, 2nd ed. vol. 5 New York: Springer; 2012 pp. 1379–1383
     [Google Scholar]
  6. Cao CL, Zhou XQ, Qin S, Tao FX, Jiang JH et al. Lentzea guizhouensis sp. nov., a novel lithophilous actinobacterium isolated from limestone from the Karst area, Guizhou, China. Antonie van Leeuwenhoek 2015; 108:1365–1372 [View Article][PubMed]
     [Google Scholar]
  7. 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]
  8. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  9. Waksman SA. The Actinomycetes. A Summary of Current Knowledge New York: Ronald Press; 1967
     [Google Scholar]
  10. Kelly KL. Inter-Society Color Council-National Bureau of Standards Color-Name Charts Illustrated with Centroid Colors Washington: US Government Printing Office; 1964
     [Google Scholar]
  11. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article][PubMed]
     [Google Scholar]
  12. 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]
  13. Williams ST, Goodfellow M, Alderson G. Genus Streptomyces Waksman and Henrici 1943, 339AL . In Williams ST, Sharpe ME, Holt JG. (editors) Bergey’s Manual of Systematic Bacteriology vol. 4 Baltimore: Williams & Willkins; 1989 pp. 2453–2492
     [Google Scholar]
  14. Athalye M, Goodfellow M, Lacey J, White RP. Numerical classification of Actinomadura and Nocardiopsis . Int J Syst Bacteriol 1985; 35:86–98 [View Article]
     [Google Scholar]
  15. Pridham TG, Gottlieb D. The utilization of carbon compounds by some actinomycetales as an aid for species determination. J Bacteriol 1948; 56:107–114[PubMed]
     [Google Scholar]
  16. Nie GX, Ming H, Li S, Zhou EM, Cheng J et al. Amycolatopsis dongchuanensis sp. nov., a novel actinobacterium isolated from dry-hot valley in Yunnan, south-west China. Int J Syst Evol Microbiol 2012; 62:2650–2656 [CrossRef]
     [Google Scholar]
  17. Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia . Int J Syst Evol Microbiol 2007; 57:1424–1428 [View Article][PubMed]
     [Google Scholar]
  18. 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]
  19. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article][PubMed]
     [Google Scholar]
  20. 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]
  21. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
     [Google Scholar]
  22. 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]
  23. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
     [Google Scholar]
  24. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  25. 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]
  26. Kimura M. The Neutral Theory of Molecular Evolution Cambridge, UK: Cambridge University Press; 1985
     [Google Scholar]
  27. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
     [Google Scholar]
  28. 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]
  29. 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]
  30. Christensen H, Angen O, Mutters R, Olsen JE, Bisgaard M. DNA-DNA hybridization determined in micro-wells using covalent attachment of DNA. Int J Syst Evol Microbiol 2000; 50:1095–1102 [View Article][PubMed]
     [Google Scholar]
  31. Li SH, Yu XY, Park DJ, Hozzein WN, Kim CJ et al. Rhodococcus soli sp. nov., an actinobacterium isolated from soil using a resuscitative technique. Antonie van Leeuwenhoek 2015; 107:357–366 [View Article][PubMed]
     [Google Scholar]
  32. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477[PubMed]
     [Google Scholar]
  33. Tang SK, Wang Y, Chen Y, Lou K, Cao LL et al. Zhihengliuella alba sp. nov., and emended description of the genus Zhihengliuella . Int J Syst Evol Microbiol 2009; 59:2025–2032 [View Article][PubMed]
     [Google Scholar]
  34. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria . J Gen Microbiol 1977; 100:221–230 [View Article][PubMed]
     [Google Scholar]
  35. 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]
  36. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded Ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
     [Google Scholar]
  37. Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 1983; 54:31–36 [View Article]
     [Google Scholar]
  38. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:16
     [Google Scholar]
  39. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
     [Google Scholar]
  40. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar Lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 1979; 47:87–95 [View Article]
     [Google Scholar]
  41. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O 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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Lentzea cavernae sp. nov., an actinobacterium isolated from a karst cave sample, and emended description of the genus Lentzea
Int J Syst Evol Microbiol 67, 2357 (2017); https://doi.org/10.1099/ijsem.0.001958
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