SpringerLink
Log in

Combining Metabolomics and Metagenomics to Analyze the Biosynthetic Potential of Culturable Endophytic Fungi Isolated from Salvia miltiorrhiza

  • Published:
Applied Biochemistry and Microbiology Aims and scope Submit manuscript

Abstract

Plant endophytic fungi are reservoirs of novel bioactive natural products, which may be used directly or indirectly to treat numerous diseases. However, it is difficult to rapidly obtain the natural products of interest from enormous endogenic fungi by conventional chemical extraction and separation methods when the overall biosynthetic potential is unknown. There is a lack of systematic studies on the biosynthetic and metabolic potential of endophytic fungi of Salvia miltiorrhiza. Therefore, untargeted metabolomics and metagenomic binning technology were used in this study to analyze the biosynthetic potential of endophytic fungi isolated from S. miltiorrhiza, including 47 species and 166 strains of 24 genera. Metabolomics analysis showed that 3016 metabolites were annotated, involving multiple primary and secondary metabolic pathways. A total of 12 genera and 443 KEGG pathways were annotated in the metagenomic, involving the biosynthesis of amino acids, saccharides, lipids, terpenoids, alkaloids, and polyketides. At the genus level, the biosynthesis and differences of amino acids, saccharides, alkaloids, terpenoids, phenolic acids and polyketides by endophytic fungi of S. miltiorrhiza were revealed. It provides a basis for quickly searching specific active substances from the endophytic fungi of S. miltiorrhiza and enhancing host plant productivity.

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

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price includes VAT (Germany)

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1.
Fig. 2.
Fig. 3.
Fig. 4.
Fig. 5.
Fig. 6.

Similar content being viewed by others

REFERENCES

  1. Petrini, O., Microbial Ecology of Leaves, Andrews, J.H. and Hirano, S.S., Eds., New York: Springer, 1991, pp. 179–197. https://doi.org/10.1007/978-1-4612-3168-4_9

  2. Van Santen, J.A., Poynton, E.F., Iskakova, D., McMann, E., Alsup, T.A., Clark, T.N.,et al., Nucleic Acids Res., 2022, vol. 50, no. D1, pp. D1317–D1323. https://doi.org/10.1093/nar/gkab941

    Article  CAS  PubMed  Google Scholar 

  3. Natural Products and Cancer Drug Discovery, Badria, F.A., Ed., Intech Open, 2017. https://doi.org/10.5772/67797

  4. Su, C.Y., Ming, Q.L., Rahman, K., Han, T., and Qin, L.P., Chin. J. Nat. Med., 2015, vol. 13, no. 3, pp. 163–182. https://doi.org/10.1016/S1875-5364(15)30002-9

    Article  CAS  PubMed  Google Scholar 

  5. Li, X.Q., Zhai, X., Shu, Z.H., Dong, R.F., Ming, Q.L., Qin, L.P., et al., Curr. Microbiol., 2016, vol. 73, no. 1, pp. 31–37. https://doi.org/10.1007/s00284-016-1023-y

    Article  CAS  PubMed  Google Scholar 

  6. Ming, Q.L., Han, T., Li, W.C., Zhang, Q.Y., Zhang, H., Zheng, C.J., et al., Phytomedicine, 2012, vol. 19, nos. 3–4, pp. 330–333. https://doi.org/10.1016/j.phymed.2011.09.076

    Article  CAS  PubMed  Google Scholar 

  7. Kanehisa, M., Protein Sci., 2019, vol. 28, no. 11, pp. 1947–1951. https://doi.org/10.1002/pro.3715

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Chen, T., Zhang, H., Liu, Y., Liu, Y.X., and Huang, L., J. Genet. Genomics, 2021, vol. 48, no. 9, pp. 863–866. https://doi.org/10.1016/j.jgg.2021.07.007

    Article  PubMed  Google Scholar 

  9. Kato, K., Kuroki, K., and Shimizu, Y., Cancer Res., 2020, vol. 80, no. 16. https://doi.org/10.1158/1538-7445.Am2020-1020

  10. Genghof, D.S., J. Bacteriol., 1970, vol. 103, no. 2, pp. 475–478. https://doi.org/10.1128/jb.103.2.475-478.1970

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Liu, S.H., Li, J., Huang, J.A., Liu, Z.H., and **ong, L.G., Trends Food Sci. Tech., 2021, vol. 114, pp. 540–551. https://doi.org/10.1016/j.tifs.2021.06.006

    Article  CAS  Google Scholar 

  12. Tarkowski, L.P., Signorelli, S., and Hofte, M., Plant Cell Environ., 2020, vol. 43, no. 5, pp. 1103–1116. https://doi.org/10.1111/pce.13734

    Article  CAS  PubMed  Google Scholar 

  13. Lin, X.L., Li, K., Yang, Z., Chen, B.G., and Zhang, T., Phytomedicine, 2020, vol. 66. https://doi.org/10.1016/j.phymed.2019.153112

  14. Ni, D.W., Xu, W., Zhu, Y.Y., Pang, X.Y., Lv, J.P., and Mu, W.M., Crit. Rev. Biotechnol., 2021, vol. 41, no. 1, pp. 34–46. https://doi.org/10.1080/07388551.2020.1844622

    Article  CAS  PubMed  Google Scholar 

  15. Yadav, U.P., Ivakov, A., Feil, R., Duan, G.Y., Walther, D., Giavalisco, P., et al., J. Exp. Bot., 2014, vol. 65, no. 4, pp. 1051–1068. https://doi.org/10.1093/jxb/ert457

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Kehrer, D.F., Soepenberg, O., Loos, W.J., Verweij, J., and Sparreboom, A., Anticancer Drugs, 2001, vol. 12, no. 2, pp. 89–105. https://doi.org/10.1097/00001813-200102000-00002

    Article  CAS  PubMed  Google Scholar 

  17. Ruan, Q.Y., Patel, G., Wang, J.Y., Luo, E.H., Zhou, W., Sieniawska, E., et al., Food Chem. Toxicol., 2021, vol. 151, p. 112113. https://doi.org/10.1016/j.fct.2021.112113

    Article  CAS  PubMed  Google Scholar 

  18. Han, X., Bao, X.F., Wang, C.X., **e, J., Song, X.J., Dai, P., et al., Nat. Prod. Res., 2021, vol. 35, no. 7, pp. 1115–1121. https://doi.org/10.1080/14786419.2019.1641807

    Article  CAS  PubMed  Google Scholar 

  19. Kang, H., Jang, S.W., Pak, J.H., and Shim, S., Mol. Cell Biochem., 2015, vol. 403, nos. 1–2, pp. 85–94. https://doi.org/10.1007/s11010-015-2339-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Palem, P.P.C., Kuriakose, G.C., and Jayabaskaran, C., PLoS One, 2016, vol. 11, no. 4, p. e0153111. https://doi.org/10.1371/journal.pone.0144476

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Liu, D.S., Huang, Y.L., Li, C.M., Ma, L.Y., Pan, X.H., Ferreira, D., et al., Rec. Nat. Prod., 2016, vol. 10, no. 6, pp. 708–713.

    CAS  Google Scholar 

  22. Jung, J.H., Kwon, T.R., Jeong, S.J., Kim, E.O., Sohn, E.J., Yun, M., et al., J. Evidence-Based Complementary Altern. Med., 2013, vol. 2013, p. 805639. https://doi.org/10.1155/2013/805639

    Article  Google Scholar 

  23. Ding, H., Wang, J.P., Deng, S.P., Gan, J.L., Li, B.X., Yao, L.L., et al., Nat. Prod. Res., 2022, pp. 1–9. https://doi.org/10.1080/14786419.2022.2080207

  24. Yan, C., Liu, W.Y., Li, J., Deng, Y.L., Chen, S.H., and Liu, H.J., Rsc. Adv., 2018, vol. 8, no. 27, pp. 14823–14828. https://doi.org/10.1039/c8ra02430h

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Song, Y.P., Fang, S.T., Miao, F.P., Yin, X.L., and Ji, N.Y., J. Nat. Prod., 2018, vol. 81, no. 11, pp. 2553–2559. https://doi.org/10.1021/acs.jnatprod.8b00714

    Article  CAS  PubMed  Google Scholar 

  26. Parvandi, M., Rezadoost, H., and Farzaneh, M., Lett. Appl. Microbiol., 2021, vol. 73, no. 5, pp. 569–578. https://doi.org/10.1111/lam.13542

    Article  CAS  PubMed  Google Scholar 

  27. Jurkiewicz, A., Lesniewska, E., Ciesla, M., Gorjao, N., Kantidakis, T., White, R.J., et al., Mol. Cell. Biol., 2019, vol. 40, no. 1. https://doi.org/10.1128/MCB.00294-19

  28. Seguin, V., Gente, S., Heutte, N., Verite, P., Kientz-Bouchart, V., Sage, L., et al., World Mycotoxin J., 2014, vol. 7, no. 3, pp. 321–328. https://doi.org/10.3920/Wmj2013.1619

    Article  CAS  Google Scholar 

  29. **, Z., Yan, W., **, H., Ge, C., and Xu, Y., Oncol. Lett., 2016, vol. 12, no. 2, pp. 971–976. https://doi.org/10.3892/ol.2016.4716

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Zhang, H., Jiang, H., Zhang, H., Liu, J., Hu, X., and Chen, L., Eur. J. Pharmacol., 2019, vol. 858, p. 172477. https://doi.org/10.1016/j.ejphar.2019.172477

    Article  CAS  PubMed  Google Scholar 

  31. Dwibedi, V. and Saxena, S., Appl. Biochem. Biotechnol., 2018, vol. 186, no. 2, pp. 476–495. https://doi.org/10.1007/s12010-018-2755-x

    Article  CAS  PubMed  Google Scholar 

  32. Tabata, N., Tomoda, H., Masuma, R., Iwai, Y., and Omura, S., J. Antibiot. (Tokyo), 1995, vol. 48, no. 1, pp. 53–58. https://doi.org/10.7164/antibiotics.48.53

    Article  CAS  Google Scholar 

  33. Gilbert, M.K., Mack, B.M., Wei, Q., Bland, J.M., Bhatnagar, D., and Cary, J.W., Microbiol. Res., 2016, vol. 182, pp. 150–161. https://doi.org/10.1016/j.micres.2015.08.007

    Article  CAS  PubMed  Google Scholar 

  34. Chaudhary, A.K., Dhakal, D., and Sohng, J.K., Biomed. Res. Int., 2013, vol. 2013, pp. 968518. https://doi.org/10.1155/2013/968518

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Liu, R., Bao, Z.X., Zhao, P.J., and Li, G.H., Molecules, 2021, vol. 26, no. 11, pp. 3311. https://doi.org/10.3390/molecules26113311

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Funding

This study was supported by grant from the National Science Foundation of China (81973416).

Author information

Authors and Affiliations

  1. School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Key Laboratory of Characteristic Chinese Medicinal Resources in Southwest China, Chengdu, China

    L. Li, C.-B. Li, Y.-H. Wu, B. Li, Y.-R. Wu & Z.-Y. Yan

Authors
  1. L. Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. C.-B. Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Y.-H. Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. B. Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Y.-R. Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Z.-Y. Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Z.-Y. Yan.

Ethics declarations

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

Supplementary Information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Li, L., Li, CB., Wu, YH. et al. Combining Metabolomics and Metagenomics to Analyze the Biosynthetic Potential of Culturable Endophytic Fungi Isolated from Salvia miltiorrhiza. Appl Biochem Microbiol 59, 659–672 (2023). https://doi.org/10.1134/S0003683823050095

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S0003683823050095

Keywords:

Search

Navigation