1887

Abstract

A novel actinobacterial strain, designated YIM A1135, was isolated from a soil 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, Gram-stain-positive and partially acid-alcohol-fast. Strain YIM A1135 shared 98.3 % 16S rRNA gene sequence similarity with Nocardia jejuensis NBRC 103114 and 97.6 % with Nocardia alba YIM 30243. DNA–DNA hybridization values between strain YIM A1135 and related type strains of the genus Nocardia were less than 70 %. In addition, meso-diaminopimelic acid was the diagnostic diamino acid in cell-wall peptidoglycan. The whole-cell sugars were fructose, mannose, galactose and glucose. The major isoprenoid quinone was MK-8(H4, ω-cycl), while the major fatty acids (>10 %) were C16 : 0, C18 : 1ω9c, C18 : 0 10-methyl and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. Mycolic acids were present. The genomic DNA G+C content of strain YIM A1135 was 66.7 mol%. Based on the results of the molecular studies supported by its morphological, physiological, chemotaxnomic and other differential phenotypic characteristics, strain YIM A1135 is considered to represent a novel species within the genus Nocardia , for which the name Nocardia cavernae sp. nov. is proposed. The type strain is YIM A1135 (=KCTC 39595=CCTCC AA 2017030).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002072
2017-08-30
2019-10-13
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/8/2998.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002072&mimeType=html&fmt=ahah

References

  1. Trevisan V. I Generi E Le Specie delle Batteriacee Milan: Zanaboni & Gabuzzi; 1889
    [Google Scholar]
  2. Stackebrandt E, Rainey FA, Ward-Rainey NL. Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 1997;47:479–491 [CrossRef]
    [Google Scholar]
  3. Zhi XY, Li WJ, Stackebrandt E. An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 2009;59:589–608 [CrossRef][PubMed]
    [Google Scholar]
  4. Goodfellow M, Lechevalier MP. Genus Nocardia Trevisan 1889, 9AL. In Sneath PHA, MAIR NS, Sharpe ME, Holt JG. (editors) Bergey's Manual of Systematic Bacteriologyvol. 2 Baltimore: The Williams & Wilkins Co; 1986; pp.1459–1471
    [Google Scholar]
  5. Gordon RE, Mihm JM. A comparative study of some strains received as nocardiae. J Bacteriol 1957;73:15–27[PubMed]
    [Google Scholar]
  6. Gordon RE, Mihm JM. The type species of the genus Nocardia. J Gen Microbiol 1962;27:1–10 [CrossRef][PubMed]
    [Google Scholar]
  7. Goodfellow M. Family IV. Nocardiaceae (Castellani & Chalmers 1919) emend. Zhi, Li and Stackebrandt 2009. In Goodfellow M, Kämpfer P, Busse H-J, Trujillo ME, Suzuki K. et al. (editors) Bergey’s Manual of Systematic Bacteriology, the Actinobacteria, Part B, 2nd ed.vol. 5 New York: Springer; 2012; pp.376–496[CrossRef]
    [Google Scholar]
  8. Brown-Elliott BA, Brown JM, Conville PS, Wallace RJ. Clinical and laboratory features of the Nocardia spp. based on current molecular taxonomy. Clin Microbiol Rev 2006;19:259–282 [CrossRef][PubMed]
    [Google Scholar]
  9. Ezeoke I, Klenk HP, Pötter G, Schumann P, Moser BD et al. Nocardia amikacinitolerans sp. nov., an amikacin-resistant human pathogen. Int J Syst Evol Microbiol 2013;63:1056–1061 [CrossRef][PubMed]
    [Google Scholar]
  10. 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 [CrossRef]
    [Google Scholar]
  11. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966;16:313–340 [CrossRef]
    [Google Scholar]
  12. Berd D. Laboratory identification of clinically important aerobic actinomycetes. Appl Microbiol 1973;25:665–681[PubMed]
    [Google Scholar]
  13. Waksman SA. The Actinomycetes. a Summary of Current Knowledge New York: Ronald Press; 1967
    [Google Scholar]
  14. Atlas RM. In Parks LC. (editor) Handbook of Microbiological Media Boca Raton, FL: CRC Press; 1993
    [Google Scholar]
  15. 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]
  16. 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 [CrossRef][PubMed]
    [Google Scholar]
  17. 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]
  18. 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 and Willkins; 1989; pp.2453–2492
    [Google Scholar]
  19. 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]
  20. 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]
  21. 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]
  22. 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][PubMed]
    [Google Scholar]
  23. 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]
  24. 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]
  25. 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 [CrossRef][PubMed]
    [Google Scholar]
  26. 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]
  27. 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]
  28. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971;20:406–416 [CrossRef]
    [Google Scholar]
  29. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  30. 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][PubMed]
    [Google Scholar]
  31. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1985
    [Google Scholar]
  32. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  33. 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]
  34. 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]
  35. 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][PubMed]
    [Google Scholar]
  36. 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]
  37. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972;36:407–477[PubMed]
    [Google Scholar]
  38. 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]
  39. 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]
  40. 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]
  41. 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]
  42. Tamaoka J. Analysis of bacterial menaquinone mixtures by reverse-phase high-performance liquid chromatography. Methods Enzymol 1986;123:31–36[PubMed]
    [Google Scholar]
  43. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark: Microbial ID, Inc; 1990
    [Google Scholar]
  44. 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]
  45. 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]
  46. 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]
  47. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. Report of the ad hoc committee on the reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987;37:463–464[CrossRef]
    [Google Scholar]
  48. Lee SD. Nocardia jejuensis sp. nov., a novel actinomycete isolated from a natural cave on Jeju Island, Republic of Korea. Int J Syst Evol Microbiol 2006;56:559–562 [CrossRef][PubMed]
    [Google Scholar]
  49. Li WJ, Jiang Y, Kroppenstedt RM, Xu LH, Jiang CL et al. Nocardia alba sp. nov., a novel actinomycete strain isolated from soil in China. Sys Appl Microbiol 2004;27:308–312[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002072
Loading
/content/journal/ijsem/10.1099/ijsem.0.002072
Loading

Data & Media loading...

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