1887

Abstract

A novel actinobacterial strain, designated SYSU K10005, was isolated from a soil sample collected from a karst cave in Xingyi county, Guizhou province, south-west 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 K10005 was most closely related to the type strains of the genus Nonomuraea , and shared highest sequence similarity of 98.4 % with Nonomuraea candida HMC10. DNA–DNA hybridization values between the two strains were less than 70 %. The whole-cell hydrolysates of strain SYSU K10005 contained meso-diaminopimelic acid (diagnostic diamino acid), and arabinose, madurose and rhamnose (whole-cell sugars). The major isoprenoid quinone was MK-9(H4), while the major fatty acids were iso-C16 : 0, 10-methyl C17 : 0, C17  : 1ω8c and C17 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, hydroxyl-phosphatidylethanolamine, lyso-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides, an unidentified lipid, two unidentified ninhydrin-positive phosphoglycolipids and two unidentified phospholipids. The genomic DNA G+C content of strain SYSU K10005 was 64.2 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU K10005 can be characterized to represent a novel species of the genus Nonomuraea , for which the name Nonomuraea cavernae sp. nov. is proposed. The type strain is SYSU K10005 (=KCTC 39805=CGMCC 4.7368).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002364
2017-10-06
2019-10-17
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/11/4692.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002364&mimeType=html&fmt=ahah

References

  1. Zhang Z, Wang Y, Ruan J. Reclassification of Thermomonospora and Microtetraspora. Int J Syst Bacteriol 1998; 48: 411– 422 [CrossRef]
    [Google Scholar]
  2. Nonomura H, Ohara Y. Distribution of actinomycetes in soil. XI. Some new species of the genus Actinomadura Lechevalier, et al. J Ferment Technol 1971; 49: 266: 904– 912
    [Google Scholar]
  3. Chiba S, Suzuki M, Ando K. Taxonomic re-evaluation of 'Nocardiopsis' sp K-252T (=NRRL 15532T): a proposal to transfer this strain to the genus Nonomuraea as Nonomuraea longicatena sp. nov. Int J Syst Bacteriol 1999; 49: 1623– 1630 [CrossRef]
    [Google Scholar]
  4. Quintana E, Maldonado L, Goodfellow M. Nonomuraea terrinata sp. nov., a novel soil actinomycete. Antonie van Leeuwenhoek 2003; 84: 1– 6 [CrossRef]
    [Google Scholar]
  5. Kampfer P, Kroppenstedt RM, Grűn-Wollny I. Nonomuraea kuesteri sp. nov. Int J Syst Evol Microbiol 2005; 55: 847– 851 [CrossRef]
    [Google Scholar]
  6. Lechevalier MP, Lechevalier HA. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 197: 435– 443
    [Google Scholar]
  7. Suksaard P, Mingma R, Srisuk N, Matsumoto A, Takahashi A et al. Nonomuraea purpurea sp. nov., an actinomycete isolated from mangrove sediment. Int J Syst Evol Microbiol 2016; 66: 4987– 4992 [Crossref]
    [Google Scholar]
  8. Goodfellow M, Stanton LJ, Simpson KE, Minnikin DE. Numerical and chemical classification of Actinoplanes and some related actinomycetes. J Gen Microbiol 1990; 136: 19– 36 [CrossRef]
    [Google Scholar]
  9. Kämpfer P. Genus VI. Nonomuraea. In Whitman WB, Goodfellow M, Busse HJ, Trujillo ME, Ludwig W. et al. (editors) Bergey's Manual of Systematic Bacteriologyvol. 5 The Actinobacteria, 2nd ed. New York: Springer; 2012; pp. 1844– 1861 [Crossref]
    [Google Scholar]
  10. Ml R, Meyers PR. Nonomuraea candida sp. nov., a new species from South African soil. Antonie van Leeuwenhoek 2009; 93: 133– 139
    [Google Scholar]
  11. Sripreechasak P, Phongsopitanun W, Supong K, Pittayakhajonwut P, Kudo T et al. Nonomuraea rhodomycinica sp. nov., isolated from peat swamp forest soil. Int J Syst Evol Microbiol 2017; 67: 1683– 1687 [CrossRef]
    [Google Scholar]
  12. Qin S, Zhao G-Z, Klenk H-P, Li J, Zhu W-Y et al. Nonomuraea antimicrobica sp. nov., an endophytic actinomycete isolated from a leaf of Maytenus austroyunnanensis. Int J Syst Evol Microbiol 2009; 59: 2747– 2751 [CrossRef] [PubMed]
    [Google Scholar]
  13. Li J, Zhao G-Z, Huang H-Y, Zhu W-Y, Lee J-C et al. Nonomuraea endophytica sp. nov., an endophytic actinomycete isolated from Artemisia annua L. Int J Syst Evol Microbiol 2011; 61: 757– 761 [CrossRef] [PubMed]
    [Google Scholar]
  14. Wang F, Shi JD, Huang YJ, Wu Y, Deng XM. Nonomuraea ceibae sp. nov., an actinobacterium isolated from Ceiba speciosa rhizosphere. Int J Syst Evol Microbiol 2017; 67: 1158– 1162 [CrossRef] [PubMed]
    [Google Scholar]
  15. Shen Y, Jia F, Liu C, Li J, Guo S et al. Nonomuraea zeae sp. nov., isolated from the rhizosphere of corn (Zea mays L.). Int J Syst Evol Microbiol 2016; 66: 2259– 2264 [CrossRef] [PubMed]
    [Google Scholar]
  16. Rachniyom H, Matsumoto A, Indananda C, Duangmal K, Takahashi Y et al. Nonomuraea syzygii sp. nov., an endophytic actinomycete isolated from the roots of a jambolan plum tree (Syzygium cumini L. Skeels). Int J Syst Evol Microbiol 2015; 65: 1234– 1240 [CrossRef] [PubMed]
    [Google Scholar]
  17. Wang S, Liu C, Zhang Y, Zhao J, Zhang X et al. Nonomuraea guangzhouensis sp. nov., and Nonomuraea harbinensis sp. nov., two novel actinomycetes isolated from soil. Antonie van Leeuwenhoek 2014; 105: 109– 118 [CrossRef]
    [Google Scholar]
  18. Hozzein WN, Goodfellow M. Nonomuraea aegyptia sp. nov., a novel actinomycete isolated from a sand dune. Antonie van Leeuwenhoek 2007; 92: 165– 171 [CrossRef] [PubMed]
    [Google Scholar]
  19. Zhang Y, Zhao J, Liu C, Shen Y, Jia F et al. Nonomuraea shaanxiensis sp. nov., a novel actinomycete isolated from a soil sample. Antonie van Leeuwenhoek 2014; 105: 57– 64 [CrossRef] [PubMed]
    [Google Scholar]
  20. Ming H, Yin YR, Li S, Nie GX, Yu TT et al. Thermus caliditerrae sp. nov., a novel thermophilic species isolated from a geothermal area. Int J Syst Evol Microbiol 2014; 64: 650– 656 [CrossRef] [PubMed]
    [Google Scholar]
  21. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16: 313– 340 [CrossRef]
    [Google Scholar]
  22. Waksman SA. The Actinomycetes. A Summary of Current Knowledge New York: Ronald Press; 1967
    [Google Scholar]
  23. Reasoner DJ, Geldreich EE. A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 1985; 49: 1– 7
    [Google Scholar]
  24. 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]
  25. Xu P 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 [CrossRef]
    [Google Scholar]
  26. 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]
  27. 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 Bacteriologyvol. 4 Baltimore: Williams & Willkins; 1989; pp. 2453– 2492
    [Google Scholar]
  28. Athalye M, Goodfellow M, Lacey J, White RP. Numerical classification of Actinomadura and Nocardiopsis. Int J Syst Bacteriol 1985; 35: 86– 98 [CrossRef]
    [Google Scholar]
  29. Pridham TG, Gottlieb G. The utilization of carbon compounds by some Actinomycetales as an aid for species determination. J Bacteriol 1948; 56: 107– 114
    [Google Scholar]
  30. 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]
  31. 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 [Crossref]
    [Google Scholar]
  32. Yoon SH, Sm H, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 2017; 67: 1613– 1617 [Crossref]
    [Google Scholar]
  33. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215: 403– 410 [CrossRef] [PubMed]
    [Google Scholar]
  34. Thompson J, 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 [CrossRef]
    [Google Scholar]
  35. 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]
  36. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4: 406– 425
    [Google Scholar]
  37. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20: 406– 416 [CrossRef]
    [Google Scholar]
  38. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17: 368– 376 [CrossRef]
    [Google Scholar]
  39. 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 [CrossRef]
    [Google Scholar]
  40. Kimura M. The Neutral Theory of Molecular Evolution Cambridge, UK: Cambridge University Press; 1985
    [Google Scholar]
  41. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39: 783– 791 [CrossRef] [PubMed]
    [Google Scholar]
  42. 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 [CrossRef]
    [Google Scholar]
  43. 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 [CrossRef]
    [Google Scholar]
  44. 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 [CrossRef]
    [Google Scholar]
  45. 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 [CrossRef] [PubMed]
    [Google Scholar]
  46. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36: 407– 477
    [Google Scholar]
  47. 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 [CrossRef] [PubMed]
    [Google Scholar]
  48. 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]
  49. 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 [CrossRef]
    [Google Scholar]
  50. 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 [CrossRef]
    [Google Scholar]
  51. Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 1983; 54: 31– 36 [CrossRef]
    [Google Scholar]
  52. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark: Microbial ID, Inc; 1990
    [Google Scholar]
  53. 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 [CrossRef]
    [Google Scholar]
  54. 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 [CrossRef]
    [Google Scholar]
  55. Minnikin DE, Hutchinson IG, Caldicott AB, Goodfellow M. Thin-layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromatogr A 1980; 188: 221– 233 [CrossRef]
    [Google Scholar]
  56. 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 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002364
Loading
/content/journal/ijsem/10.1099/ijsem.0.002364
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error