Effect of beneficial microbes applications on nutritional profiles of organic tomatoes revealed by LC‐MS‐qTOF metabolomics

Background: The use of microorganisms and biostimulants is increasingly supported in agriculture because of their advantageous impact on plant disease management, growth enhancement and the synthesis of beneficial bioactive secondary metabolites (SMs). Tomato (Solanum lycopersicum) is an important crop and is consumed worldwide because it is an excellent source of natural compounds (i.e. beta-carotene and flavonoids) and minerals useful for human health. Although the positive effects of individual microbial applications are well-documented, the impact of microbial consortia is underexplored. Results: In this study, the improvement of nutritional value of tomato (S. lycopersicum var. Heinz), by use of beneficial microorganisms, including selected strains of Streptomyces microflavus (S), Trichoderma harzianum (M10) and Trichoderma afroharzianum (T22), has been investigated. These microbes were applied on tomato plants, either as single inoculants or as microbial consortia. The effects were evaluated through statistical analysis of biological parameters. T22 treatments exhibited a significant increase in plant height (107.30 cm) compared to both control and M10-based treatments (104.30 and 102.80 cm, respectively). The similarities observed in plant height between S-treated plants (105.70 cm) and those treated with the combination of S and T22 (106.60 cm) highlight the potential beneficial effects of microbial consortia. Moreover, the berries were subjected to an untargeted metabolomic analysis by liquid chromatography-mass spectrometry-quadrupole-time of flight that led to the identification of eighteen metabolites, including tomatine and its derivatives solafloridine. Multivariate analysis demonstrated differences in berries metabolic profiles, depending on the treatment applied. Specifically, T22-based treatment increased the accumulation of most of the identified metabolites compared to untreated plants, whereas combined treatment S + T22 induced a major accumulation of solafloridine. Conclusion: Field microbial applications significantly induced the metabolic profile change of tomato and the accumulation of metabolites with nutraceutical value. © 2025 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.