sp. nov., a novel actinobacterium isolated from a karst cave sample Free

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 , and shared highest sequence similarity of 98.4 % with HMC10. DNA–DNA hybridization values between the two strains were less than 70 %. The whole-cell hydrolysates of strain SYSU K10005 contained -diaminopimelic acid (diagnostic diamino acid), and arabinose, madurose and rhamnose (whole-cell sugars). The major isoprenoid quinone was MK-9(H), while the major fatty acids were iso-C, 10-methyl C, C ω8 and C. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, hydroxyl-phosphatidylethanolamine, -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 , for which the name sp. nov. is proposed. The type strain is SYSU K10005 (=KCTC 39805=CGMCC 4.7368).

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2017-11-01
2024-03-29
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References

  1. Zhang Z, Wang Y, Ruan J. Reclassification of Thermomonospora and Microtetraspora . Int J Syst Bacteriol 1998; 48:411–422 [View Article]
    [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 [View Article]
    [Google Scholar]
  4. Quintana E, Maldonado L, Goodfellow M. Nonomuraea terrinata sp. nov., a novel soil actinomycete. Antonie van Leeuwenhoek 2003; 84:1–6 [View Article]
    [Google Scholar]
  5. Kampfer P, Kroppenstedt RM, Grűn-Wollny I. Nonomuraea kuesteri sp. nov. Int J Syst Evol Microbiol 2005; 55:847–851 [View Article]
    [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 [View Article]
    [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 Bacteriology vol. 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 [View Article]
    [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 [View Article][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 [View Article][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 [View Article][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 [View Article][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 [View Article][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 [View Article]
    [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 [View Article][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 [View Article][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 [View Article][PubMed]
    [Google Scholar]
  21. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [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 [View Article]
    [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 [View Article]
    [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 Bacteriology vol. 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 [View Article]
    [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 [View Article][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 [View Article]
    [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 [View Article][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 [View Article]
    [Google Scholar]
  38. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
    [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 [View Article]
    [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 [View Article][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 [View Article]
    [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 [View Article]
    [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 [View Article]
    [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 [View Article][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 [View Article][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 [View Article][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 [View Article]
    [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 [View Article]
    [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 [View Article]
    [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 [View Article]
    [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 [View Article]
    [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 [View Article]
    [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 [View Article]
    [Google Scholar]
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