Sample Preparation for Forest Tree Metabolomics

Abstract

Plant growth, development, and survival results from the adjustment of various metabolic processes in response to internal and external factors. Because metabolites are spatiotemporal and environment dependent, the use of metabolomics to elucidate how and to what extent plant metabolism adjusts in response to environmental alterations has increased in the last decades, including studies focused on forest trees. However, trees are known to be complex biological matrices to work with. Despite the great advances in analytical technologies to separate and detect metabolites and in the use of sophisticated tools, such as machine learning for data analysis and interpretation, these approaches cannot compensate for inappropriate sample preparation. Thus, to ensure a high-quality metabolomics analysis, special attention should be given to the initial steps of the sample preparation workflow, which include experimental design, sampling, quenching, and metabolite extraction. In this chapter, we present an overview of the key points to be considered in forest tree metabolomics experiments. We first summarize the critical steps in setting up the experimental design, followed by the methods used for sampling different tree tissues and fluids (e.g. leaves, wood, phloem sap, xylem sap, and root), including analysis at single-cell resolution and without cell or tissue separation. Stable isotope labeling strategies as well as issues related to metabolite extraction (e.g. solvent polarity) are also discussed.