Climate change and an increasing population, present a massive global challenge with respect to environmentally sustainable nutritious food production. Crop yield enhancements, through breeding, are decreasing, whilst agricultural intensification is constrained by emerging, re-emerging, and endemic pests and pathogens, accounting for ~30% of global crop losses, as well as mounting abiotic stress pressures, due to climate change. Metabolomics approaches have previously contributed to our knowledge within the fields of molecular plant pathology and plant–insect interactions. However, these remain incredibly challenging targets, due to the vast diversity in metabolite volatility and polarity, heterogeneous mixtures of pathogen and plant cells, as well as rapid rates of metabolite turn-over. Unravelling the systematic biochemical responses of plants to various individual and combined stresses, involves monitoring signaling compounds, secondary messengers, phytohormones, and defensive and protective chemicals. This demands both targeted and untargeted metabolomics approaches, as well as a range of enzymatic assays, protein assays, and proteomic and transcriptomic technologies. In this review, we focus upon the technical and biological challenges of measuring the metabolome associated with plant stress. We illustrate the challenges, with relevant examples from bacterial and fungal molecular pathologies, plant–insect interactions, and abiotic and combined stress in the environment. We also discuss future prospects from both the perspective of key innovative metabolomic technologies and their deployment in breeding for stress resistance.

Auxins are commonly used for commercial propagation of chrysanthemums by stem cuttings. Recent studies imply that these root-promoting hormones also affect plant defense responses. The underlying motive of this study stems from the serendipitous observation that water dipping of auxin-coated cuttings beneficially affected thrips herbivory. Therefore, the primary objective of this investigation was to explore the role of indole-3-butyric acid (IBA) in relation to herbivore susceptibility in chrysanthemum. We observed contrasting findings concerning the physical presence of IBA and it’s role in promoting susceptibility of cuttings to thrips, which may in part be explained by the phenotypical variations of cuttings generated from mother plants. Nonetheless, we repeatedly demonstrated considerable protection, in some experiments up to 37%, against thrips and leaf miner upon water dipping of IBA-coated cuttings. Assessment of polyphenol oxidase activity (PPO), 14 days after dipping treatment, suggests that neither direct induction nor priming of plant defenses are involved. Future experiments aimed at understanding the early signaling events may help to explain the underlying mechanisms involved in conferring herbivore protection. We propose a dual role for auxins in early integrated pest management strategies to maximize plant development and minimize herbivory through feasible, cost-effective water dipping treatments.