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.

We would like to thank the German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, funded by DFG grant FZT-118, for supporting the workshop that allowed 32 researchers to come together and discuss current challenges in Eco-Metabolomics, as well as the iDiv publication fund for covering open access costs. Kristian Peters acknowledges funding from the European Commission PhenoMeNal Grant EC654241 and by the Leibniz Association. Christian Ristok acknowledges funding by the German Federal Environmental Foundation (DBU). Oliver Alka, Steffen Neumann, and Christoph Ruttkies acknowledge BMBF funding (grants 031A535A and 031L0107) as part of the German Network of Bioinformatics Infrastructures (de.NBI). Onno Calf is supported by grant number 823.01.007 of the open programme of the Netherlands Organisations for Scientific Research (NWO-ALW). Mirka Macel is supported by a grant of the Green defense Against Pest (GAP) program, project 13552, Stichting voor de Technische Wetenschappen (STW), The Netherlands.