¹H-NMR-Based Metabolomic Study of Tomato Cultivars, Heinz and Roma, Grown on Selected Growth Medium and Deep-Water...

Background/Objectives: This study examined the effect of three different cultural media-coconut coir, peat moss, and deep-water culture-on the metabolomic profiles of two tomato cultivars, Heinz and Roma. Tomato fruit quality is influenced by intricate interactions between the genotype and root-zone environment; nevertheless, little is known about how substrate-based systems compare metabolically to deep-water hydroponics. Methods: Fruit samples from both cultivars grown under controlled greenhouse conditions were analyzed using proton nuclear magnetic resonance (¹H-NMR) spectroscopy to identify treatment-dependent biochemical changes. Polar metabolites were extracted using a methanol-water solvent solution and examined using a 600 MHz NMR spectrometer. Spectral datasets were processed and analyzed with multivariate statistical tools such as Principal Component Analysis (PCA), Partial Least Squares Discriminant Analysis (PLS-DA), and Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA). Results: Distinct clustering patterns were observed, indicating both cultivar-specific and cultivation-system-dependent metabolic differentiation. The PCA model displayed excellent explanatory and predictive capacity, while supervised OPLS-DA improved group discrimination, demonstrating that both genotype and growing medium significantly influenced the chemical composition of the fruit. Soluble sugars (glucose, fructose, and sucrose), sugar alcohols, organic acids such as citric and malic acids, and a variety of amino acids involved in nitrogen metabolism and stress reactions were among the key distinguishing factors. Carbohydrate-related spectral areas (3.0-5.5 ppm) were highly associated with treatment separation, indicating that the cultivation system had a significant impact on carbon allocation and energy metabolism. Conclusions: Fruits grown in deep water culture have distinct metabolic fingerprints from those grown on coconut coir and peat moss, implying that root-zone oxygen availability and nutrient dynamics may influence primary and secondary metabolism.