Antonie van Leeuwenhoek

, Volume 111, Issue 6, pp 891–896 | Cite as

Streptomyces ginkgonis sp. nov., an endophyte from Ginkgo biloba

  • Xia Yan
  • Yanfang Li
  • Nana Wang
  • Yue Chen
  • Li-li Huang
Original Paper


A novel endophytic actinomycete strain, designated KM-1-2T, was isolated from seeds of Ginkgo biloba at Yangling, China. A polyphasic approach was used to study the taxonomy of strain KM-1-2T and it was found to show a range of phylogenetic and chemotaxonomic properties consistent with those of members of the genus Streptomyces. The diamino acid of the cell wall peptidoglycan was identified as LL-diaminopimelic acid. No diagnostic sugars were detected in whole cell hydrolysates. The predominant menaquinones were identified as MK-9(H6) and MK-9(H8). The diagnostic phospholipids were found to be phosphatidylethanolamine and phosphatidylcholine. The DNA G + C content of the novel strain was determined to be 72.9 mol%. The predominant cellular fatty acids (> 10.0 %) were identified as iso-C14 : 0, iso-C16 : 0, C16 : 0 and C17 : 0 cyclo. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain is closely related to Streptomyces carpaticus JCM 6915T (99.3%), Streptomyces harbinensis DSM 42076T (98.9%) and Streptomyces cheonanensis JCM 14549T (98.5%). DNA-DNA hybridizations with these three close relatives gave similarity values of 39.1 ± 1.9, 35.8 ± 2.3, and 47.4 ± 2.7%, respectively, which indicated that strain KM-1-2T represents a novel species of the genus Streptomyces. This is consistent with the morphological, physiological and chemotaxonomic data. Cumulatively, these data suggest that strain KM-1-2T represents a novel Streptomyces species, for which the name Streptomyces ginkgonis sp. nov. is proposed, with the type strain KM-1-2T (= CCTCC AA2016004T = KCTC 39801T).


Endophyte Streptomyces ginkgonis sp. nov. Ginkgo biloba Polyphasic approach 



This work was supported by Foundation Research Project of Shaanxi Province (No. 2017JZ006); National Natural Science Foundation of China (No. 31101476); Science and Technology Program of Yangling Demonstration Zone (No. 2014NY-41).

Compliance with ethical standards

Conflict of interest

Authors do not claim any conflict of interest.


  1. Cao LX, Qiu ZQ, You JL, Tan HM, Zhou S (2004) Isolation and characterization of endophytic Streptomyces antagonists of Fusarium wilt pathogen from surface sterilized banana roots. FEMS Microbiol Lett 247:147–152CrossRefGoogle Scholar
  2. Collins MD (1985) Isoprenoid quinone analysis in classification and identification. In: Goodfellow M, Minnikin DE (eds) Chemical methods in bacterial systematics. Academic Press, London, pp 267–287Google Scholar
  3. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefPubMedGoogle Scholar
  4. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416CrossRefGoogle Scholar
  5. Hain T, Ward-Rainey N, Kroppenstedt RM, Stackebrandt E, Rainey FA (1997) Discrimination of Streptomyces albidoflavus strains based on the size and number of 16S-23S ribosomal DNA intergenic spacers. Int J Syst Bacteriol 47:202–206CrossRefPubMedGoogle Scholar
  6. Haritha R, Sivakumar K, Swathi A et al (2012) Characterization of marine Streptomyces carpaticus and optimization of conditions for production of extracellular protease. Appl Environ Microbiol 78:4826–4834CrossRefGoogle Scholar
  7. Hwang KS, Kim HU, Charusanti P, Palsson BØ, Sang YL (2014) Systems biology and biotechnology of Streptomyces, species for the production of secondary metabolites. Biotechnol Adv 32:255–268CrossRefPubMedGoogle Scholar
  8. Kämpfer P, Kroppenstedt RM (1996) Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42:989–1005CrossRefGoogle Scholar
  9. Kelly KL (1964) Inter-Society Color Council-National Bureau of Standards color name charts illustrated with centroid colors. US Government Printing Office, WashingtonGoogle Scholar
  10. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120CrossRefPubMedGoogle Scholar
  11. Kirkpatrick M, Dugatkin LA (2015) Antimicrobial and antioxidant activities of a new benzamide from endophytic Streptomyces sp. YIM 67086. Nat Prod Res 29:331–335CrossRefGoogle Scholar
  12. Kumar S, Stecher G, Tamura K (2016) Mega7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870CrossRefPubMedGoogle Scholar
  13. Labeda DP, Goodfellow M, Brown R, Ward AC, Lanoot B, Vanncanneyt M et al (2012) Phylogenetic study of the species within the family streptomycetaceae. Antonie Van Leeuwenhoek 101:73–104CrossRefPubMedGoogle Scholar
  14. Lechevalier HA, Lechevalier MP (1980) The chemotaxonomy of actinomycetes. In: Dietz A, Thayer DW (eds) Actinomycete taxonomy. (Special Publication 6). Society of Industrial Biology, Arlington, pp 277–284Google Scholar
  15. Lechevalier HA, Lechevalier MP, Gerber NN (1970) Chemical composition as a criterion in the classification of actinomycetes. Int J Syst Evol Microbiol 20(4):435–443Google Scholar
  16. Lechevalier MP, Stern AE, Lechevalier HA (1981) Phospholipids in the taxonomy of actinomycetes. Zentralbl. Bakteriol. Parasitenkd. Infektionskr. Hyg. Abt. 1(Suppl. 11):111–116Google Scholar
  17. Liu M, Abdel-Mageed WM, Ren B et al (2014) Endophytic Streptomyces sp. Y3111 from traditional Chinese medicine produced antitubercular pluramycins. Appl Microbiol Biotechnol 98:1077–1085CrossRefPubMedGoogle Scholar
  18. Loria R, Bukhalid RA, Fry BA, King RR (1997) Plant pathogenecity in the genus Streptomyces. Plant Dis 81:836–846CrossRefGoogle Scholar
  19. Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167CrossRefGoogle Scholar
  20. Passari AK, Mishra VK, Gupta VK et al (2016) Distribution and identification of endophytic Streptomyces species from Schima wallichii as potential biocontrol agents against fungal plant pathogens. Pol Soc Microbiol 65:319–329CrossRefGoogle Scholar
  21. Pridham TG, Gottlieb D (1948) The utilization of carbon compounds by some actinomycetales as an aid for species determination. J Bacteriol 56:107PubMedPubMedCentralGoogle Scholar
  22. Rainey FA, Ward-Rainey N, Kroppenstedt RM, Stackebrandt E (1996) The genus Nocardiopsis represents a phylogenetically coherent taxon and a distinct actinomycete lineage: proposal of Nocardiopsaceae fam. nov. Int J Syst Bacteriol 46:1088–1092CrossRefPubMedGoogle Scholar
  23. Rong X, Guo Y, Huang Y (2009) Proposal to reclassify the Streptomyces albidoflavus clade on the basis of multilocus sequence analysis and DNA-DNA hybridization, and taxonomic elucidation of Streptomyces griseus subsp. solvifaciens. Syst Appl Microbiol 32:314–322CrossRefPubMedGoogle Scholar
  24. Rosselló-Móra R, Trujillo ME, Sutcliffe IC (2017) Introducing a digital protologue: a timely move towards a database-driven systematics of archaea and bacteria. Syst Appl Microbiol 110:455–456Google Scholar
  25. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  26. Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340CrossRefGoogle Scholar
  27. Stackebrandt E, Rainey FA, Wardrainey NL (1997) Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 47:479–491CrossRefGoogle Scholar
  28. Stone JK, Bacon CW, White JF (2000) An overview of endophytic microbes: endophytism defined. Microb Endophytes 3:29–33Google Scholar
  29. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882CrossRefPubMedPubMedCentralGoogle Scholar
  30. Van de Peer PY, de Wachter R (1994) TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci 10:569–570PubMedGoogle Scholar
  31. Waksman SA, Henrici AT (1943) The nomenclature and classification of the actinomycetes. J Bacteriol 46:337–341PubMedPubMedCentralGoogle Scholar
  32. Xiao J, Wang Y, Luo Y, Xie SJ, Ruan JS, Xu J (2009) Streptomyces avicenniae sp. nov., a novel actinomycete isolated from the rhizosphere of the mangrove plant Avicennia mariana. Int J Syst Evol Microbiol 59:2624–2628CrossRefPubMedGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2017

Authors and Affiliations

  • Xia Yan
    • 1
    • 3
  • Yanfang Li
    • 1
    • 3
  • Nana Wang
    • 1
    • 3
  • Yue Chen
    • 1
    • 3
  • Li-li Huang
    • 1
    • 2
  1. 1.State Key Laboratory of Crop Stress Biology in Arid AreasNorthwest A&F UniversityYanglingChina
  2. 2.College of Plant ProtectionNorthwest A&F UniversityYanglingChina
  3. 3.College of Life SciencesNorthwest A&F UniversityYanglingChina

Personalised recommendations