A gradual shift in the evaluation of crop quality has taken place, led by analytical scientists with the advancement of instrumentation and system-based technology (system biology). Metabolomics, one of the emerging omics techniques, provides a complete and unbiased chemical analysis within an organism. Information obtained through metabolomic analysis may range from identifying beneficial compounds for human health to toxicants, can help solve challenges faced by the agricultural industry. Current phytochemical studies focusing on organically-grown crops have typically focused on individual compounds or classes of compounds that may be affected by production practices. This study compared metabolomic profiles between organic and conventionally-grown tomato (Solanum lycopersicon) fruit to systemically access the quality and nutritional value of tomatoes under different growing conditions. Two tomato cultivars (‘Estiva’ and ‘Tomimaru Muchoo’) were grown with three different treatments (organic field, organic high-tunnel, and conventional field) and were assessed for metabolomic analysis using gas chromatography‒mass spectrometry (GC‒MS) and liquid chromatography‒mass spectrometry (LC‒MS). Target metabolites included various primary and secondary metabolites covering a wide range of metabolic pathways, involving citrate cycle, pyruvate metabolism, amino acid biosynthesis, alkaloids biosynthesis, shikimate pathway, salicylic acid pathway, plant hormone biosynthesis, phenylpropanoid biosynthesis, flavone, flavonol, and flavonoid biosynthesis, anthocyanin biosynthesis, and so on. Differentially expressed metabolites (potential biomarkers) between organic and conventional tomatoes were selected, and a core metabolic network was identified by pathway enrichment analysis. Major variations between groups were observed in the network related to plant secondary metabolisms (e.g., plant defense signaling). This is likely due to varying amounts of external stresses between organic and conventional tomatoes by the difference in pesticide input. The organic high-tunnel group also showed some distinct metabolic responses within the secondary metabolisms, probably because of its unique growing conditions. The selected biomarkers and identified metabolic network provided insights into biochemical processes influenced by different cultivation methods. This work will contribute to the evaluation of organic farming practices in the US.
