Vermicompost-Based Substrates and a PGPR Consortium Improve the Nutraceutical Quality of Greenhouse Tomato (Solanum lycopersicum L.) in a Semi-Hydroponic System

Tomato (Solanum lycopersicum L.) is a globally important vegetable, prized for its nutritional value and antioxidant content. Given the increasing demand for foods with health-promoting properties and the need for sustainable production practices, this study evaluated the impact of different growth substrates combined with plant growth-promoting rhizobacteria (PGPR) inoculation on the yield and nutraceutical quality of greenhouse tomatoes grown in a semi-hydroponic system. ‘Nereida’ variety saladette tomato plants were either inoculated with a single PGPR consortium (1 × 108 CFU mL−1) or uninoculated. Three substrates were used: a chemical fertilization control and a sand-vermicompost mixture with two inherent levels of phosphorus (253 and 442 ppm). The chemically fertilized substrate without inoculation served as the control treatment. The results indicated that the chemically fertilized substrate presented a significantly higher yield per square meter (p < 0.05), reaching values of 5.20 ± 0.70 kg m−2 and 4.83 ± 0.35 kg m−2 in the control treatment. However, fruits grown in the vermicompost-based substrate with higher phosphorus content (442 ppm) and PGPR inoculation exhibited significantly greater antioxidant capacity (54.16 µmol TE g−1 FW) and higher concentrations of vitamin C (14.03 mg·100 g−1 FW), lycopene (47.68 mg·100 g−1 FW), flavonoids, carotenoids, and glutathione. This represented an increase of 28–45% in bioactive compounds including lycopene, vitamin C, flavonoids, carotenoids, and glutathione compared to the chemical control. While the interaction between substrate and inoculation was significant only for soluble solids, both factors independently and additively contributed to the enhancement of nutraceutical parameters. These findings suggest that the use of vermicompost-based substrates, particularly those with higher phosphorus content, in combination with PGPR inoculation, is a promising strategy to enhance the accumulation of health-promoting bioactive compounds in tomato fruits, despite a trade-off in total yield.