Metabolomics and Metabolic Profiling: Investigation of Dynamic Plant-Environment Interactions at the Functional Level

  • Dominik Skoneczny
  • Paul A. Weston
  • Leslie A. WestonEmail author


Sessile plants routinely face challenges associated with environmental extremes or neighbouring competitors, and have therefore developed mechanisms that allow them to withstand constant exposure to these diverse abiotic and biotic stressors. In some cases, the response to plant stress can be manifested on demand by the plant (so-called inducible responses), while other responses are expressed constitutively and are available at all times to counter the stressor. Thus, it can be said that environment shapes a plant’s physiology and, in turn, also impacts the functioning of ecosystems. Interactions between plants, their competitors, and the environment are always dynamic and as a result often difficult to characterize. It is therefore not surprising that recent studies of such complex interactions have utilised a multitude of advanced techniques for experimentation, and have eventually led to an enhanced understanding of the physiological basis for these interactions. This chapter explores the most common applications of metabolomics in plant ecophysiology research by providing an overview of typical instrumentation and workflows used by plant scientists along with a discussion of the experimental outcomes of such studies.


  1. Akula R, Ravishankar GA (2011) Influence of abiotic stress signals on secondary metabolites in plants. Plant Signal Behav 6:1720–1731CrossRefGoogle Scholar
  2. Arbona V, Manzi M, Ollas C, Gómez-Cadenas A (2013) Metabolomics as a tool to investigate abiotic stress tolerance in plants. Int J Mol Sci 14:4885CrossRefPubMedPubMedCentralGoogle Scholar
  3. Bino RJ, Hall RD, Fiehn O, Kopka J, Saito K, Draper J, Nikolau BJ, Mendes P, Roessner-Tunali U, Beale MH, Trethewey RN, Lange BM, Wurtele ES, Sumner LW (2004) Potential of metabolomics as a functional genomics tool. Trends Plant Sci 9:418–425CrossRefPubMedGoogle Scholar
  4. Bunnik EM, Le Roch KG (2013) An introduction to functional genomics and systems biology. Adv Wound Care 2:490–498CrossRefGoogle Scholar
  5. Claude E, Jones EA, Pringle SD (2017) DESI Mass Spectrometry Imaging (MSI). In: Cole LM (ed) Imaging mass spectrometry: methods and protocols. Springer New York, New York, pp 65–75CrossRefGoogle Scholar
  6. van Dam NM, Bouwmeester HJ (2016) Metabolomics in the rhizosphere: tapping into belowground chemical communication. Trends Plant Sci 21:256–265CrossRefPubMedGoogle Scholar
  7. Dunn WB, Ellis DI (2005) Metabolomics: current analytical platforms and methodologies. Trends Anal Chem 24:285–294CrossRefGoogle Scholar
  8. El-Aneed A, Cohen A, Banoub J (2009) Mass spectrometry. Review of the basics: electrospray, MALDI, and commonly used mass analyzers. Appl Spectrosc Rev 44:210–230CrossRefGoogle Scholar
  9. Franceschi VR, Krokene P, Christiansen E, Krekling T (2005) Anatomical and chemical defenses of conifer bark against bark beetles and other pests. New Phytol 167:353–376CrossRefPubMedGoogle Scholar
  10. Fuchs B, Süß R, Schiller J (2010) An update of MALDI-TOF mass spectrometry in lipid research. Prog Lipid Res 49:450–475CrossRefPubMedGoogle Scholar
  11. García A, Godzien J, López-Gonzálvez A, Barbas C (2017) Capillary electrophoresis mass spectrometry as a tool for untargeted metabolomics. Bioanalysis 9:99–130CrossRefPubMedGoogle Scholar
  12. Gargallo-Garriga A, Sardans J, Pérez-Trujillo M, Oravec M, Urban O, Jentsch A, Kreyling J, Beierkuhnlein C, Parella T, Peñuelas J (2015) Warming differentially influences the effects of drought on stoichiometry and metabolomics in shoots and roots. New Phytol 207:591–603CrossRefPubMedGoogle Scholar
  13. Hagel J, Facchini P (2008) Plant metabolomics: analytical platforms and integration with functional genomics. Phytochem Rev 7:479–497CrossRefGoogle Scholar
  14. Heyman HM, Dubery IA (2016) The potential of mass spectrometry imaging in plant metabolomics: a review. Phytochem Rev 15:297–316CrossRefGoogle Scholar
  15. Hill CB, Roessner U (2014) Advances in high-throughput untargeted LC-MS analysis for plant metabolomics. Future Science eBook Series “Advanced LC-MS applicafions for metabolomics”. Future Science Group, LondonGoogle Scholar
  16. Jänkänpää HJ, Mishra Y, Schröder WP, Jansson S (2012) Metabolic profiling reveals metabolic shifts in Arabidopsis plants grown under different light conditions. Plant Cell Environ 35:1824–1836CrossRefPubMedGoogle Scholar
  17. Kim HK, Verpoorte R (2010) Sample preparation for plant metabolomics. Phytochem Anal 21:4–13CrossRefPubMedGoogle Scholar
  18. Lee CE (2002) Evolutionary genetics of invasive species. Trends Ecol Evol 17:386–391CrossRefGoogle Scholar
  19. Leiss K, Choi Y, Abdel-Farid I, Verpoorte R, Klinkhamer PL (2009) NMR metabolomics of thrips (Frankliniella occidentalis) resistance in Senecio hybrids. J Chem Ecol 35:219–229CrossRefPubMedGoogle Scholar
  20. Maldini M, Natella F, Baima S, Morelli G, Scaccini C, Langridge J, Astarita G (2015) Untargeted metabolomics reveals predominant alterations in lipid metabolism following light exposure in broccoli sprouts. Int J Mol Sci 16:13678–13691CrossRefPubMedPubMedCentralGoogle Scholar
  21. Martínez-Arranz I, Mayo R, Pérez-Cormenzana M, Mincholé I, Salazar L, Alonso C, Mato JM (2015) Data in support of enhancing metabolomics research through data mining. Data Brief 3:155–164CrossRefPubMedPubMedCentralGoogle Scholar
  22. Metlen KL, Aschehoug ET, Callaway RM (2009) Plant behavioural ecology: dynamic plasticity in secondary metabolites. Plant Cell Environ 32:641–653CrossRefPubMedGoogle Scholar
  23. Mwendwa JM, Weston PA, Fomsgaard I, Laursen BB, Brown WB, Wu H, Rebetzke G, Quinn JC, Weston LA (2016) Metabolic profiling for benzoxazinoids in weed-suppressive and early vigour wheat genotypes. In: Conference proceedings of the 20th Australasian weeds conference, pp. 353–357. Weeds Society of Western AustraliaGoogle Scholar
  24. Pan Z, Raftery D (2007) Comparing and combining NMR spectroscopy and mass spectrometry in metabolomics. Anal Bioanal Chem 387:525–527CrossRefPubMedGoogle Scholar
  25. Ramautar R, de Jong GJ (2014) Recent developments in liquid-phase separation techniques for metabolomics. Bioanalysis 6:1011–1026CrossRefPubMedGoogle Scholar
  26. Rochfort S (2005) Metabolomics reviewed: a new “omics” platform technology for systems biology and implications for natural products research. J Nat Prod 68:1813–1820CrossRefPubMedGoogle Scholar
  27. Roessner U, Bacic A (2009) Metabolomics in plant research. Aust Biochem 40:9–11Google Scholar
  28. Roessner U, Luedemann A, Brust D, Fiehn O, Linke T, Willmitzer L, Fernie AR (2001) Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems. Plant Cell Online 13:11–29CrossRefGoogle Scholar
  29. Ryalls JMW, Moore BD, Riegler M, Johnson SN (2016) Above–belowground herbivore interactions in mixed plant communities are influenced by altered precipitation patterns. Front Plant Sci 7:345CrossRefPubMedPubMedCentralGoogle Scholar
  30. Saito K, Matsuda F (2010) Metabolomics for functional genomics, systems biology, and biotechnology. Annu Rev Plant Biol 61:463–489CrossRefPubMedGoogle Scholar
  31. Schauer N, Fernie AR (2006) Plant metabolomics: towards biological function and mechanism. Trends Plant Sci 11:508–516CrossRefPubMedGoogle Scholar
  32. Schuman MC, Baldwin IT (2016) The layers of plant responses to insect herbivores. Annu Rev Entomol 61:373–394CrossRefPubMedGoogle Scholar
  33. Skoneczny D, Weston PA, Zhu X, Gurr GM, Callaway RM, Weston LA (2015) Metabolic profiling of pyrrolizidine alkaloids in foliage of two Echium spp. invaders in Australia—a case of novel weapons? Int J Mol Sci 16:26721–26737CrossRefPubMedPubMedCentralGoogle Scholar
  34. Skoneczny D, Weston PA, Zhu X, Gurr GM, Callaway RM, Barrow RA, Weston LA (2017) Metabolic profiling and identification of shikonins in root periderm of two invasive Echium spp. Weeds in Australia Molecules 22:330Google Scholar
  35. Smolinska A, Blanchet L, Buydens LMC, Wijmenga SS (2012) NMR and pattern recognition methods in metabolomics: from data acquisition to biomarker discovery: a review. Anal Chim Acta 750:82–97CrossRefGoogle Scholar
  36. Sumner LW, Amberg A, Barrett D, Beale MH, Beger R, Daykin CA, Fan TW-M, Fiehn O, Goodacre R, Griffin JL (2007) Proposed minimum reporting standards for chemical analysis. Metabolomics 3:211–221CrossRefPubMedPubMedCentralGoogle Scholar
  37. Swenson TL, Jenkins S, Bowen BP, Northen TR (2015) Untargeted soil metabolomics methods for analysis of extractable organic matter. Soil Biol Biochem 80:189–198CrossRefGoogle Scholar
  38. Viant MR, Sommer U (2013) Mass spectrometry based environmental metabolomics: a primer and review. Metabolomics 9:144–158CrossRefGoogle Scholar
  39. Vidkjær NH, Wollenweber B, Gislum R, Jensen K-MV, Fomsgaard IS (2015) Are ant feces nutrients for plants? A metabolomics approach to elucidate the nutritional effects on plants hosting weaver ants. Metabolomics 11:1013–1028CrossRefGoogle Scholar
  40. Watson JT, Sparkman OD (2007) Introduction to mass spectrometry: instrumentation, applications, and strategies for data interpretation. Wiley, Chichester, p 862CrossRefGoogle Scholar
  41. Weston P, Weston L, Hildebrand S (2013) Metabolic profiling in Echium plantagineum: Presence of bioactive pyrrolizidine alkaloids and napthoquinones from accessions across southeastern Australia. Phytochem Rev 12(1–7):831e837Google Scholar
  42. Weston LA, Skoneczny D, Weston PA, Weidenhamer JD (2015) Metabolic profiling: an overview – new approaches for the detection and functional anlysis of biologically active secondary plant products. J Allelochem Interact 2:15–27Google Scholar
  43. Wittstock U, Gershenzon J (2002) Constitutive plant toxins and their role in defense against herbivores and pathogens. Curr Opin Plant Biol 5:300–307CrossRefPubMedGoogle Scholar
  44. Yan D, Afifi L, Jeon C, Trivedi M, Chang HW, Lee K, Liao W (2017) The metabolomics of psoriatic disease. Psoriasis 7:1–15CrossRefPubMedGoogle Scholar
  45. Ye M, Song Y, Long J, Wang R, Baerson SR, Pan Z, Zhu-Salzman K, Xie J, Cai K, Luo S (2013) Priming of jasmonate-mediated antiherbivore defense responses in rice by silicon. PNAS 110:3631–3639CrossRefGoogle Scholar
  46. Zhang A, Sun H, Wang P, Han Y, Wang X (2012) Modern analytical techniques in metabolomics analysis. Analyst 137:293–300CrossRefPubMedGoogle Scholar
  47. Zhu X, Skoneczny D, Weidenhamer JD, Mwendwa JM, Weston PA, Gurr GM, Callaway RM, Weston LA (2016) Identification and localization of bioactive naphthoquinones in the roots and rhizosphere of Paterson’s curse (Echium plantagineum), a noxious invader. J Exp Bot 67:3777–3788CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Dominik Skoneczny
    • 1
    • 2
  • Paul A. Weston
    • 1
    • 2
  • Leslie A. Weston
    • 1
    • 2
    Email author
  1. 1.Graham Centre for Agricultural InnovationCharles Sturt UniversityWagga WaggaAustralia
  2. 2.School of Agricultural and Wine SciencesCharles Sturt UniversityWagga WaggaAustralia

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