1887

Abstract

A novel actinobacterial strain, designated SYSU K10008, was isolated from a soil sample collected from a karst cave in Xingyi County, Guizhou Province, south-western PR China. The taxonomic position of the strain was investigated by using a polyphasic approach. Cells of the strain were aerobic, Gram-stain-positive and non-motile. On the basis of 16S rRNA gene sequence similarities and the results of phylogenetic analysis, strain SYSU K10008 was most closely related to CGMCC 4.1671, and shared the highest sequence identity of 98.3 % based on the NCBI database. In addition, -diaminopimelic acid was the diagnostic diamino acid in cell-wall peptidoglycan. The whole-cell sugars were glucose and rhamnose. The major isoprenoid quinone was MK-9(H), while the major fatty acids (>10 %) were C, iso-C, anteiso-C and summed feature 3 (C 7/C 6). The polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and one unidentified lipid. The genomic DNA G+C content of strain SYSU K10008 was 70.5 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU K10008 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is SYSU K10008 (=KCTC 39850=DSM 104115).

Funding
This study was supported by the:
  • Natural Science Foundation of Guangdong Province (Award 2016A030312003)
    • Principle Award Recipient: Wen-Jun Li
  • National Natural Science Foundation of China (Award 31600015)
    • Principle Award Recipient: Bao-Zhu Fang
  • National Key R&D Program of China (Award 2017YFD0200503)
    • Principle Award Recipient: Wen-Jun Li
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2020-02-03
2024-12-14
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References

  1. Waksman SA, Henrici AT. The nomenclature and classification of the actinomycetes. J Bacteriol 1943; 46:337–341
    [Google Scholar]
  2. 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]
  3. Kämpfer P. Genus I. Streptomyces Waksman and Henrici 1943, 339ALemend. Witt and Stackebrandt 1990, 370 emend. Welling-ton, Stackebrandt, Sanders, Wolstrup and Jorgensen 1992, 159. In Kämpfer P, Busse HJ, Trujillo ME, Suzuki KI. (editors) Bergey’s Manual of Systematic Bacteriology 5, 2nd ed. New York: Springer; 2012 pp 1455–1767
    [Google Scholar]
  4. Omura S, Takahashi Y, Iwai Y, TANAKA H. Kitasatosporia, a new genus of the order Actinomycetales . J Antibiot 1982; 35:1013–1019 [View Article]
    [Google Scholar]
  5. Kim SB, Lonsdale J, Seong CN, Goodfellow M. Streptacidiphilus gen. nov., acidophilic actinomycetes with wall chemotype I and emendation of the family Streptomycetaceae (Waksman and Henrici (1943) al) emend. Rainey, et al. 1997. Antonie Van Leeuwenhoek 2003; 83:107–116 [View Article]
    [Google Scholar]
  6. Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T et al. Genome-based taxonomic classification of the phylum Actinobacteria . Front Microbiol 2007; 2018:9
    [Google Scholar]
  7. Huang M-J, Rao MPN, Salam N, Xiao M, Huang H-Q et al. Allostreptomyces psammosilenae gen. nov., sp. nov., an endophytic actinobacterium isolated from the roots of Psammosilene tunicoides and emended description of the family Streptomycetaceae [Waksman and Henrici (1943)AL] emend. Rainey et al. 1997, emend. Kim et al. 2003, emend. Zhi et al. 2009. Int J Syst Evol Microbiol 2017; 67:288–293 [View Article]
    [Google Scholar]
  8. Currie CR, Scott JA, Summerbell RC, Malloch D. Fungus-growing ants use antibiotic-producing bacteria to control garden parasites. Nature 1999; 398:701–704 [View Article]
    [Google Scholar]
  9. Mingma R, Duangmal K, Thamchaipenet A, Trakulnaleamsai S, Matsumoto A et al. Streptomyces oryzae sp. nov., an endophytic actinomycete isolated from stems of rice plant. J Antibiot 2015; 68:368–372 [View Article]
    [Google Scholar]
  10. LH X, Tian YQ, Zhang YF, Zhao LX, Jiang CL et al. Streptomyces thermogriseus, a new species of the genus Streptomyces from soil, lake and hot-spring. Int J Syst Bacteriol 1998; 48:1089–1093
    [Google Scholar]
  11. Silva FSP, Souza DT, Zucchi TD, Pansa CC, de Figueiredo Vasconcellos RL et al. Streptomyces atlanticus sp. nov., a novel actinomycete isolated from marine sponge Aplysina fulva (Pallas, 1766). Antonie Van Leeuwenhoek 2016; 109:1467–1474 [View Article]
    [Google Scholar]
  12. Phongsopitanun W, Kudo T, Ohkuma M, Pittayakhajonwut P, Suwanborirux K et al. Streptomyces verrucosisporus sp. nov., isolated from marine sediments. Int J Syst Evol Microbiol 2016; 66:3607–3613 [View Article]
    [Google Scholar]
  13. Bérdy J. Bioactive microbial metabolites. J Antibiot 2005; 58:1–26 [View Article]
    [Google Scholar]
  14. Bérdy J. Thoughts and facts about antibiotics: where we are now and where we are heading. J Antibiot 2012; 65:385–395 [View Article]
    [Google Scholar]
  15. Bekiesch P, Basitta P, Apel AK. ChemInform Abstract: challenges in the heterologous production of antibiotics in Streptomyces . ChemInform 2016; 47:594–601 [View Article]
    [Google Scholar]
  16. 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]
  17. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  18. Waksman SA. The actinomycetes. A summary of current knowledge New York: Ronald Press; 1967
    [Google Scholar]
  19. 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]
  20. 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]
  21. 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]
  22. Gordon RE, Barnett DA, Handerhan JE, Pang CHN. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
    [Google Scholar]
  23. 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 4 Baltimore: Williams & Willkins; 1989 pp 2453–2492
    [Google Scholar]
  24. 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]
  25. 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]
  26. 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
    [Google Scholar]
  27. WJ L, 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
    [Google Scholar]
  28. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article]
    [Google Scholar]
  29. 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]
  30. 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]
    [Google Scholar]
  31. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425
    [Google Scholar]
  32. 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]
  33. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
    [Google Scholar]
  34. 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]
  35. Kimura M. The Neutral Theory of Molecular Evolution Cambridge University Press; 1985
    [Google Scholar]
  36. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [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. 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]
  39. SH L, XY Y, 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
    [Google Scholar]
  40. Harrison P, Strulo B. SPADES - a process algebra for discrete event simulation. Journal of Logic and Computation 2000; 10:3–42 [View Article]
    [Google Scholar]
  41. Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article]
    [Google Scholar]
  42. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 2017; 110:1281–1286 [View Article]
    [Google Scholar]
  43. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477
    [Google Scholar]
  44. Tang S-K, Wang Y, Chen Y, Lou K, Cao L-L et al. Zhihengliuella alba sp. nov., and emended description of the genus Zhihengliuella . Int J Syst Evol Microbiol 2009; 59:2025–2032 [View Article]
    [Google Scholar]
  45. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria . J Gen Microbiol 1977; 100:221–230 [View Article]
    [Google Scholar]
  46. 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 Appl Bacteriol 1984; 2:233–241 [View Article]
    [Google Scholar]
  47. 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]
  48. 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]
  49. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark: Microbial ID, Inc; 1990
    [Google Scholar]
  50. 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]
  51. 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]
  52. 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]
  53. 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]
  54. Goris J, Klappenbach JA, Vandamme P, Coenye T, Konstantinidis KT et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article]
    [Google Scholar]
  55. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article]
    [Google Scholar]
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