A practical guide to implementing metabolomics in plant ecology and biodiversity research

Abstract Ecologists study the interactions between plants and their changing biotic and abiotic environments. These interactions are directly mediated by the chemical phenotypes of the plants i.e. their metabolomes. In consequence, the study of these metabolomes (a branch of analytical chemistry called metabolomics) is a powerful tool for describing the chemical aspects of plant ecology. The application of metabolomics to ecology is growing because of current technical developments in high throughput and high-resolution mass spectrometry. Advanced metabolomics allows the combination of traditional plant phenotypic traits (biomass, flowering probability) with plant chemical phenotypes. The combination of ecology and the analytical chemistry of advanced metabolomics has given rise to a new discipline, that of “ecometabolomics.” However, realizing the true potential of ecometabolomics is hindered because its constituent disciplines differ greatly in their experimental approaches, workflows and norms. These differences present challenges that must be overcome if the two constituent disciplines are to be successfully integrated and the potential of ecometabolomics successfully realized. In our EcoMetabolomics facility at the German Centre for integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, we have, since 2016, built up expertise on bringing metabolomics into ecology research. Our experience tells us that the main challenges of combining the two disciplines pertain to technical and experimental issues or are related to differences in scientific background knowledge between metabolomicists and ecologists. Technical and experimental challenges in ecometabolomics occur mainly when experimental conditions are such that it is hard to take samples of good quality for metabolomic analysis. Moreover, ecologists taking metabolomic samples in the field often face challenges in obtaining enough replicates, providing proper storage conditions and meeting export regulations (Nagoya protocols, phytosanitary regulations). We have also noticed that ecologists lack knowledge of the dynamics of plant metabolomes, e.g. how they change over the day. And that ecologists often have unrealistic expectations about how fast the data can be processed and how many unknown compounds of interest it is possible to identify in non-model species. This lack of knowledge may cause unproductive collaborations between ecologists and metabolomicists. In this chapter, we share our experience in ecometabolomics projects by describing the main challenges in combining different areas of expertise. We aim to provide strategies and practical solutions, particularly for project management, training, advising on experimental workflows before sampling and communicating realistic outcomes of the metabolomic analysis. We believe these strategies will help ecologists and metabolomics experts collaborate more effectively and fruitfully.