Skip to main content
SpringerLink
Log in

Genetic Identification and Antimicrobial Activity of Streptomyces sp. Strain Je 1–6 Isolated from Rhizosphere Soil of Juniperus excelsa Bieb

  • Published:
Cytology and Genetics Aims and scope Submit manuscript

Abstract

Actinobacteria isolated from poorly explored biotopes are of interest as producers of biologically active compounds. A report is given about the producer of lydicamycin Je 1–6 isolated from the rhizosphere soil of J. excelsa Bieb. collected from the Crimean Peninsula, Ukraine, that demonstrated its antagonistic activity against gram-positive bacteria. Based on the 16S rRNA gene sequence analysis, the strain Je 1–6 was affiliated to the Streptomyces genus. The crude extract from the biomass of this strain showed its activity against gram-positive bacteria, including polyresistant clinical isolates of Staphylococcus sp. The dereplication analysis of the extract of the strain Je 1–6 revealed lydicamycin and its congeners: 30-demethyllydicamycin, 30-demethyl-8-deoxylydicamycin, and 8-deoxylydicamycin. MLSA analysis based on the 16S rRNA gene and five housekeeping genes atpD, gyrB, rpoB, recA, and trpB of the strain Je 1–6 showed a high level of homology with Streptomyces sp. ID38640.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1.
Fig. 2.
Fig. 3.
Fig. 4.

Similar content being viewed by others

REFERENCES

  1. Ahmad, M.S., El-Gendy, A.O., Ahmed, R.R., et al., Exploring the antimicrobial and antitumor potentials of Streptomyces sp. AGM12-1 isolated from Egyptian soil, Front. Microbiol., 2017, vol. 8, p. 438. https://doi.org/10.3389/fmicb.2017.00438

    Article  PubMed  PubMed Central  Google Scholar 

  2. Aminov, R., History of antimicrobial drug discovery: major classes and health impact, Biochem. Pharmacol., 2017, vol. 133, pp. 4–19. https://doi.org/10.1016/j.bcp.2016.10.001

    Article  CAS  PubMed  Google Scholar 

  3. Bauer, A.W., Kirby, W.M., Sherris, J.C., et al., Antibiotic susceptibility testing by a standardized single disk method, Am. J. Clin. Pathol., 1996, vol. 45, pp. 493–496.

    Article  Google Scholar 

  4. Bilyk, O., Sekurova, O.N., Zotchev, S.B., et al., Cloning and heterologous expression of the grecocycline bio-synthetic gene cluster, PLoS One, 2016, vol. 11, no. 7. e0158682. https://doi.org/10.1371/journal.pone.0158682

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Buckingham, J., Dictionary of Natural Products, London: CRC Press/Taylor and Francis Group, 1993.

    Google Scholar 

  6. Edgar, R.C., MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res., 2004, vol. 32, pp. 1792–1797. https://doi.org/10.1093/nar/gkh340

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Felsenstein, J., Evolutionary trees from DNA sequences: a maximum likelihood approach, J. Mol. Evol., 1981, vol. 17, pp. 368–376.

    Article  CAS  PubMed  Google Scholar 

  8. Felsenstein, J., Confidence limits on phylogenies: an approach using the bootstrap, Evolution, 1985, vol. 39, pp. 783–791.

    Article  PubMed  Google Scholar 

  9. Furumai, T., Eto, K., Sasaki, T., et al., TPU-0037-A, B, C and D, novel lydicamycin congeners with anti-MRSA activity from Streptomyces platensis TP-A0598, J. Antibiot., 2002, vol. 55, no. 10, pp. 873–880. https://doi.org/10.7164/an-tibiotics.55.873

    Article  CAS  Google Scholar 

  10. Genilloud, O., Actinomycetes: still a source of novel antibiotics, Nat. Prod. Rep., 2017, vol. 34, pp. 1203–1232. https://doi.org/10.1039/c7np00026j

    Article  CAS  PubMed  Google Scholar 

  11. Goodfellow, M. and Williams, S., Ecology of actinomycetes, Ann. Rev. Microbiol., 1983, vol. 37, pp. 189–216.

    Article  CAS  Google Scholar 

  12. Guo, Y., Zheng, W., Rong, X., et al., A multilocus phylogeny of the Streptomyces griseus 16S rRNA gene clade: use of multilocus sequence analysis for streptomycete systematics, Int. J. Syst. Evol. Microbiol., 2008, vol. 58, pp. 149–159. https://doi.org/10.1099/ijs.0.65224-0

    Article  CAS  PubMed  Google Scholar 

  13. Hayakawa, Y., Kanamaru, N., Shimazu, A., et al., Lydicamycin, a new antibiotic of a novel skeletal type. I. Taxonomy, fermentation, isolation and biological activity, J. Antibiot., 1991, vol. 44, no. 3, pp. 282–287.

    Article  CAS  Google Scholar 

  14. Khamna, S., Yokota, A., and Lumyong, S., Actinomycetes isolated from medicinal plant rhizosphere soils: diversity and screening of antifungal compounds, indole-3-acetic acid and siderophore production, World J. Microbiol. Biotechnol., 2009, vol. 25, pp. 649–655. https://doi.org/10.1007/s11274-008-9933-x

    Article  CAS  Google Scholar 

  15. Kieser, B., Buttner, M., Charter, K., and Hopwood, B., Practical Streptomyces Genetics, Norwich: John Innes Foundation, 2000.

    Google Scholar 

  16. Kimura, M., A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, J. Mol. Evol., 1980, vol. 16, pp. 111–120.

    Article  CAS  PubMed  Google Scholar 

  17. Komaki, H., Hosoyama, A., Igarashi, Y., et al., Streptomyces lydicamycinicus sp. nov. and its secondary metabolite biosynthetic gene clusters for polyketide and nonribosomal peptide compounds, Microorganisms, 2020, vol. 8, no. 3, p. 370. https://doi.org/10.3390/microorganisms8030370

    Article  CAS  PubMed Central  Google Scholar 

  18. Kostyanev, T. and Can, F., The global crisis of antimicrobial resistance, in Antimicrobial Stewardship, 1st ed., Pulcini, C., Ergonul, O., Can, F., and Beovic, B., Eds., Cambridge: Academic Press, 2017, pp. 3–12.

    Google Scholar 

  19. Kumar, S., Stecher, G., Li, M., et al., MEGA X: molecular evolutionary genetics analysis across computing platforms, Mol. Biol. Evol., 2018, vol. 35, no. 6, pp. 1547–1549. https://doi.org/10.1093/molbev/msy096

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Labeda, D.P., Doroghazi, J.R., Ju, K.S., et al., Taxonomic evaluation of Streptomyces albus and related species using multilocus sequence analysis and proposals to emend the description of Streptomyces albus and describe Streptomyces pathocidini sp. nov., Int. J. Syst. Evol. Microbiol., 2014, vol. 64, pp. 894–900. https://doi.org/10.1099/ijs.0.058107-0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Liu, D., Yan, R., Fu, Y., et al., Antifungal, plant growth-promoting, and genomic properties of an endophytic actinobacterium Streptomyces sp. NEAU-S7GS2, Front. Microbiol., 2019, vol. 10, p. 2077. https://doi.org/10.3389/fmicb.2019.02077

    Article  PubMed  PubMed Central  Google Scholar 

  22. Maciejewska, M., Pessi, I.S., Arguelles-Arias, A., et al., Streptomyces lunaelactis sp. nov., a novel ferroverdin A-producing Streptomyces species isolated from a moonmilk speleothem, Antonie van Leeuwenhoek, 2015, vol. 107, pp. 519–531. https://doi.org/10.1007/s10482-014-0348-4

    Article  CAS  PubMed  Google Scholar 

  23. Raju, R., Gromyko, O., Fedorenko, V., et al., Juniperolide A: a new polyketide isolated from a terrestrial actinomycete, Streptomyces sp., Org. Lett., 2012a, vol. 14, no. 23, pp. 5860–5863. https://doi.org/10.1021/ol302766z

    Article  CAS  PubMed  Google Scholar 

  24. Raju, R., Gromyko, O., Fedorenko, V., et al., Leopolic acid A, isolated from a terrestrial actinomycete, Streptomyces sp., Tetrahedron Lett., 2012b, vol. 53, pp. 6300–6301. https://doi.org/10.1016/j.tetlet.2012.09.046

    Article  CAS  Google Scholar 

  25. Rebets, Y., Ostash, B., Luzhetskyy, A., et al., Production of landomycins in Streptomyces globisporus 1912 and S. cyanogenus S136 is regulated by genes encoding putative transcriptional activators, FEMS Microbiol. Lett., 2003, vol. 222, pp. 149–153. https://doi.org/10.1016/S0378-1097(03)00258-1

    Article  CAS  PubMed  Google Scholar 

  26. Rong, X. and Huang, Y., Taxonomic evaluation of the Streptomyces hygroscopicus clade using multilocus sequence analysis and DNA–DNA hybridization, validating the MLSA scheme for systematics of the whole genus, Syst. Appl. Microbiol., 2012, vol. 35, no. 1, pp. 7–18. https://doi.org/10.1016/j.syapm.2011.10.004

    Article  CAS  PubMed  Google Scholar 

  27. Running, W., Computer software reviews, Chapman and Hall Dictionary of Natural Products on CD-ROM, J. Chem. Inf. Model., 1993, vol. 33, pp. 934–935.

    Article  Google Scholar 

  28. Saitou, N. and Nei, M., The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol. Biol. Evol., 1987, vol. 4, pp. 406–425.

    CAS  PubMed  Google Scholar 

  29. Sosio, M., Gaspari, E., Iorio, M., et al., Analysis of the Pseudouridimycin biosynthetic pathway provides insights into the formation of C-nucleoside antibiotics, Cell Chem. Biol., 2018, vol. 25, pp. 540–549. https://doi.org/10.1016/j.chembiol.2018.02.008

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Ventola, C.L., The antibiotic resistance crisis, part 1: causes and threats, P&T, 2015, vol. 40, no. 4, pp. 277–283.

    Google Scholar 

  31. Viaene, T., Langendries, S., Beirinckx, S., et al., Streptomyces as a plant’s best friend?, FEMS Microbiol. Ecol., 2016, vol. 92, no. 8. fiw119. https://doi.org/10.1093/femsec/fiw119

    Article  CAS  PubMed  Google Scholar 

  32. Wang, Q., Garrity, G.M., Tiedje, J.M., et al., Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy, Appl. Environ. Microbiol., 2016, vol. 73, pp. 5261–5267. https://doi.org/10.1128/AEM.00062-07

    Article  CAS  Google Scholar 

Download references

Funding

This study was supported by the grant H/309-2003 of the Ministry of Education and Science of Ukraine (V. Fedorenko, O. Gromyko), the state budget project of the Ministry of Health of Ukraine (O. Korniychuk, I. Tymchuk), and partially supported by the individual grant FEMS-GO- 2017-001 for S. Tistechok.

Author information

Authors and Affiliations

  1. Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79000, Lviv, Ukraine

    S. I. Tistechok, V. O. Fedorenko & O. M. Gromyko

  2. Department of Microbiology, Danylo Halytsky Lviv National Medical University, 79010, Lviv, Ukraine

    I. V. Tymchuk & O. P. Korniychuk

  3. Department of Pharmaceutical Biotechnology, Saarland University, 66123, Saarbrucken, Germany

    A. M. Luzhetskyy

  4. Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrucken, Germany

    A. M. Luzhetskyy

Authors
  1. S. I. Tistechok
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. I. V. Tymchuk
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. O. P. Korniychuk
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. V. O. Fedorenko
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. A. M. Luzhetskyy
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. O. M. Gromyko
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to O. M. Gromyko.

Ethics declarations

The authors declare that they have no conflict of interests. This article does not contain any studies involving animals or human participants performed by any of the authors.

Additional information

Translated by V. Mittova

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Tistechok, S.I., Tymchuk, I.V., Korniychuk, O.P. et al. Genetic Identification and Antimicrobial Activity of Streptomyces sp. Strain Je 1–6 Isolated from Rhizosphere Soil of Juniperus excelsa Bieb. Cytol. Genet. 55, 28–35 (2021). https://doi.org/10.3103/S0095452721010138

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.3103/S0095452721010138

Keywords:

Search

Navigation