The relatively new research discipline of Eco-Metabolomics is the application of metabolomics techniques to ecology with the aim to characterise biochemical interactions of organisms across different spatial and temporal scales. Metabolomics is an untargeted biochemical approach to measure many thousands of metabolites in different species, including plants and animals. Changes in metabolite concentrations can provide mechanistic evidence for biochemical processes that are relevant at ecological scales. These include physiological, phenotypic and morphological responses of plants and communities to environmental changes and also interactions with other organisms. Traditionally, research in biochemistry and ecology comes from two different directions and is performed at distinct spatiotemporal scales. Biochemical studies most often focus on intrinsic processes in individuals at physiological and cellular scales. Generally, they take a bottom-up approach scaling up cellular processes from spatiotemporally fine to coarser scales. Ecological studies usually focus on extrinsic processes acting upon organisms at population and community scales and typically study top-down and bottom-up processes in combination. Eco-Metabolomics is a transdisciplinary research discipline that links biochemistry and ecology and connects the distinct spatiotemporal scales. In this review, we focus on approaches to study chemical and biochemical interactions of plants at various ecological levels, mainly plant–organismal interactions, and discuss related examples from other domains. We present recent developments and highlight advancements in Eco-Metabolomics over the last decade from various angles. We further address the five key challenges: (1) complex experimental designs and large variation of metabolite profiles; (2) feature extraction; (3) metabolite identification; (4) statistical analyses; and (5) bioinformatics software tools and workflows. The presented solutions to these challenges will advance connecting the distinct spatiotemporal scales and bridging biochemistry and ecology.

Arthropod herbivores cause substantial economic costs that drive an increasing need to develop environmentally sustainable approaches to herbivore control. Increasing plant diversity is expected to limit herbivory by altering plant-herbivore and predator-herbivore interactions, but the simultaneous influence of these interactions on herbivore impacts remains unexplored. We compiled 487 arthropod food webs in two long-running grassland biodiversity experiments in Europe and North America to investigate whether and how increasing plant diversity can reduce the impacts of herbivores on plants. We show that plants lose just under half as much energy to arthropod herbivores when in high-diversity mixtures versus monocultures and reveal that plant diversity decreases effects of herbivores on plants by simultaneously benefiting predators and reducing average herbivore food quality. These findings demonstrate that conserving plant diversity is crucial for maintaining interactions in food webs that provide natural control of herbivore pests.

Species‐rich plant communities can induce unique soil biotic legacy effects through changing the abundance and composition of soil biota. These soil legacy effects can cause feedbacks to influence plant performance. In addition, soil biota can induce (defensive) secondary metabolites in shoots and roots and thus affect plant–herbivore interactions. We hypothesize that plant diversity‐driven soil biotic legacy effects elicit changes in the shoot and root metabolome. We tested this hypothesis by establishing an experiment with four plant species. We grew plants in a sterile substrate inoculated with soil conditioned by different plant species communities: (a) monocultures of either of the four species, (b) the four species in a mixture, (c) an eight species mixture including all four species or (d) a sterile inoculum. After at least 8 weeks in the field, we estimated shoot herbivory. At the same time, we took root and shoot samples for metabolomics analyses by liquid chromatography quadrupole time‐of‐flight mass spectrometry. We found that shoot and root metabolomes of all plants grown in sterile soil differed significantly from those grown in living soil. The plant metabolomes in living soils differed by species and tissue. Across all species, shoots displayed a greater richness of secondary metabolites than roots. The richness of secondary metabolites differed by species and among living soils. The conditioning species richness significantly affected the Shannon diversity of secondary metabolites in Centaurea jacea. Shoot herbivory positively correlated with the richness and Shannon diversity of secondary metabolites in Leucanthemum vulgare. We detected multiple metabolites that together explained up to 88% of the variation in herbivory in the shoots of C. jacea and Plantago lanceolata. Synthesis. Our findings suggest that plant diversity‐driven shifts in soil biota elicit changes in the composition and diversity of shoot and root secondary metabolites. However, these plant responses and their effect on shoot herbivores are species‐specific. Tracking changes in plant secondary chemistry in response to soil biotic legacy effects will help to understand the mechanisms that govern species‐specific plant–plant and plant–herbivore interactions.