Metabolomic insights into volatile and non-volatile compounds in organic tomato fruits: a pathway-based approach

Organic food is in rising demand, yet the chemical diversity and metabolic mechanisms in organic crops remain underexplored. This study aims to apply pathway-based metabolomics to elucidate the metabolic networks differentially regulated in organic crops, using tomato fruits as a case study. Two tomato cultivars, ‘Estiva’ and ‘Tomimaru Muchoo,’ were collected from three farming systems: organic field, organic high-tunnel, and conventional field. Based on a literature search and pathway enrichment analysis, 17 potential metabolic pathways were identified. A total of 91 metabolites, comprising 67 non-volatile and 24 volatile compounds, within these pathways were targeted and analyzed using metabolomics. Metabolites were mapped and discussed based on the pathway networks, and 27 statistically differential markers (p-value < 0.05, fold-change > 1.3, and VIP score > 0.7) were identified as potential biomarkers. This pathway-based metabolomics approach effectively highlights the metabolic differences between groups (e.g., organic field vs. conventional field) and the associated mechanisms. The knowledge obtained from this study will serve as preliminary data for applications in food and agricultural fields, ranging from crop quality control to the optimization of cultivation practices.