Skip to main content

Computational Metabolomics to Elucidate Molecular Signaling and Regulatory Mechanisms Associated with Biostimulant-Mediated Growth Promotion and Abiotic Stress Tolerance in Crop Plants

  • Protocol
  • First Online:
Plant Abiotic Stress Signaling

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2642))

Abstract

Biostimulants show potentials as sustainable strategies for improved crop development and stress resilience. However, the cellular and molecular mechanisms, in particular the signaling and regulatory events, governing the agronomically observed positive effects of biostimulants on plants remain enigmatic, thus hampering novel formulation and exploration of biostimulants. Metabolomics offers opportunities to elucidate metabolic and regulatory processes that define biostimulant-induced changes in the plant’s biochemistry and physiology, thus contributing to decode the modes of action of biostimulants. Here, we describe an application of metabolomics to elucidate biostimulant effects on crop plants. Using the case study of a humic substance (HS)-based biostimulant applied on maize plants, under normal and nutrient-starved stress conditions, this chapter proposes key methodological guidance and considerations of computational metabolomics approach to investigate metabolic and regulatory reconfiguration and networks underlying biostimulant-induced physiological changes in plants. Computational metabolome mining tools, in the Global Natural Products Social Molecular Networking (GNPS) ecosystem, are highlighted as well as metabolic pathway and network analysis for biological interpretation of the data.

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

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 189.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. du Jardin P (2015) Plant biostimulants: definition, concept, main categories and regulation. Sci Hortic (Amsterdam) 196:3–14. https://doi.org/10.1016/j.scienta.2015.09.021

    Article  CAS  Google Scholar 

  2. Yakhin OI, Lubyanov AA, Yakhin IA et al (2017) Biostimulants in plant science: a global perspective. Front Plant Sci 7:1–32. https://doi.org/10.3389/fpls.2016.02049

    Article  Google Scholar 

  3. Ricci M, Tilbury L, Daridon B et al (2019) General principles to justify plant biostimulant claims. Front Plant Sci 10:1–8. https://doi.org/10.3389/fpls.2019.00494

    Article  Google Scholar 

  4. Francesca S, Arena C, Hay Mele B et al (2020) The use of a plant-based biostimulant improves plant performances and fruit quality in tomato plants grown at elevated temperatures. Agronomy 10:363. https://doi.org/10.3390/agronomy10030363

    Article  CAS  Google Scholar 

  5. Paul K, Sorrentino M, Lucini L et al (2019) Understanding the biostimulant action of vegetal-derived protein hydrolysates by high-throughput plant phenotyping and metabolomics: a case study on tomato. Front Plant Sci 10:1–17. https://doi.org/10.3389/fpls.2019.00047

    Article  Google Scholar 

  6. Chele KH, Steenkamp P, Piater LA et al (2021) A global metabolic map defines the effects of a Si-based biostimulant on tomato plants under normal and saline conditions. Metabolites 11:820. https://doi.org/10.3390/metabo11120820

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Othibeng K, Nephali L, Ramabulana AT et al (2021) A metabolic choreography of maize plants treated with a humic substance-based biostimulant under normal and starved conditions. Metabolites 11:403. https://doi.org/10.3390/metabo11060403

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Rouphael Y, Lucini L, Miras-Moreno B et al (2020) Metabolomic responses of maize shoots and roots elicited by combinatorial seed treatments with microbial and non-microbial biostimulants. Front Microbiol 11:1–13. https://doi.org/10.3389/fmicb.2020.00664

    Article  Google Scholar 

  9. Nephali L, Moodley V, Piater L et al (2021) A metabolomic landscape of maize plants treated with a microbial biostimulant under well-watered and drought conditions. Front Plant Sci 12:1–15. https://doi.org/10.3389/fpls.2021.676632

    Article  Google Scholar 

  10. Lephatsi M, Nephali L, Meyer V et al (2022) Molecular mechanisms associated with microbial biostimulant-mediated growth enhancement, priming and drought stress tolerance in maize plants. Sci Rep 12:1–18. https://doi.org/10.1038/s41598-022-14570-7

    Article  CAS  Google Scholar 

  11. Likić VA, McConville MJ, Lithgow T et al (2010) Systems biology: the next frontier for bioinformatics. Adv Bioinforma 2010:268925. https://doi.org/10.1155/2010/268925

    Article  Google Scholar 

  12. Tugizimana F, Engel J, Salek R et al (2020) The disruptive 4IR in the life sciences: metabolomics. In: Doorsamy W, Paul BS, Marwala T (eds) The disruptive fourth industrial revolution: technology, society and beyond. Springer Nature, Cham

    Google Scholar 

  13. Aron AT, Gentry EC, McPhail KL et al (2020) Reproducible molecular networking of untargeted mass spectrometry data using GNPS. Nat Protoc 15:1954–1991. https://doi.org/10.1038/s41596-020-0317-5

    Article  CAS  PubMed  Google Scholar 

  14. van der Hooft JJJ, Wandy J, Barrett MP et al (2016) Topic modeling for untargeted substructure exploration in metabolomics. Proc Natl Acad Sci U S A 113:13738–13743. https://doi.org/10.1073/pnas.1608041113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. da Silva RR, Wang M, Nothias LF et al (2018) Propagating annotations of molecular networks using in silico fragmentation. PLoS Comput Biol 14:1–26. https://doi.org/10.1371/journal.pcbi.1006089

    Article  CAS  Google Scholar 

  16. Rogers S, Ong CW, Wandy J et al (2019) Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra. Faraday Discuss 218:284–302. https://doi.org/10.1039/c8fd00235e

    Article  CAS  PubMed  Google Scholar 

  17. Quinn RA, Nothias LF, Vining O et al (2017) Molecular networking as a drug discovery, drug metabolism, and precision medicine strategy. Trends Pharmacol Sci 38:143–154. https://doi.org/10.1016/j.tips.2016.10.011

    Article  CAS  PubMed  Google Scholar 

  18. Nothias LF, Petras D, Schmid R et al (2020) Feature-based molecular networking in the GNPS analysis environment. Nat Methods 17:905–908. https://doi.org/10.1038/s41592-020-0933-6

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Beniddir MA, Kang KB, Genta-Jouve G et al (2021) Advances in decomposing complex metabolite mixtures using substructure- and network-based computational metabolomics approaches. Nat Prod Rep 38:1967–1993. https://doi.org/10.1039/d1np00023c

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Djoumbou Feunang Y, Eisner R, Knox C et al (2016) ClassyFire: automated chemical classification with a comprehensive, computable taxonomy. J Cheminform 8:1–20. https://doi.org/10.1186/s13321-016-0174-y

    Article  Google Scholar 

  21. Ernst M, Kang KB, Caraballo-Rodríguez AM et al (2019) MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools. Metabolites 16:144. https://doi.org/10.3390/metabo9070144

    Article  CAS  Google Scholar 

  22. Chong J, Soufan O, Li C et al (2018) MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis. Nucleic Acids Res 46:W486–W494. https://doi.org/10.1093/nar/gky310

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Liang X, Zhang L, Natarajan SK et al (2013) Proline mechanisms of stress survival. Antioxid Redox Signal 19:998–1011. https://doi.org/10.1089/ars.2012.5074

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

Shimadzu South Africa Ltd. are gratefully thanked for the support with access to the LCMS-8050 system. Omnia Group Ltd., the South African Cultivar and Technology Agency (SACTA), and the South Africa National Research Foundation (NRF) are duly acknowledged for scholarships to Lerato Nephali and Kgalaletso Othibeng.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Fidele Tugizimana .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Othibeng, K., Nephali, L., Tugizimana, F. (2023). Computational Metabolomics to Elucidate Molecular Signaling and Regulatory Mechanisms Associated with Biostimulant-Mediated Growth Promotion and Abiotic Stress Tolerance in Crop Plants. In: Couée, I. (eds) Plant Abiotic Stress Signaling. Methods in Molecular Biology, vol 2642. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3044-0_9

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-3044-0_9

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3043-3

  • Online ISBN: 978-1-0716-3044-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics