Effects of Cultivation–Substrate System on Growth, Flowering, Carotenoid Accumulation, and Substrate Microbiology of Three Tagetes patula Cultivars Under Greenhouse and Field Conditions

Tagetes patula is a widely cultivated ornamental plant and a natural source of bioactive compounds. This study evaluated the effects of cultivation–substrate systems on growth, flowering, lutein and zeaxanthin accumulation, substrate microbiological properties, and pest and disease occurrence in three T. patula cultivars (‘Csemő’, ‘Robusta kénsárga’, and ‘Orion’) grown under two greenhouse (peat-based substrate and hydroponics) and three field conditions (peat-based and two peat-free substrates). Greenhouse hydroponics markedly enhanced vegetative growth, resulting in the highest plant height, stem diameter, and shoot biomass, whereas peat-based greenhouse substrates produced the lowest vegetative performance. Flowering responses were more moderate and largely cultivar-dependent: peat-based field conditions supported the highest inflorescence numbers, cv. ‘Orion’ produced the greatest inflorescence biomass, and cv. ‘Robuszta kénsárga’ showed the strongest flowering intensity in peat-based systems. Cultivar ‘Csemő’ consistently accumulated the highest lutein and zeaxanthin concentrations among cultivars. Substrate moisture and microbial activity differed substantially among systems, with peat-free substrates frequently exhibiting elevated enzymatic activity. No fungal diseases were detected; thrips occurred only in greenhouse systems, and spider mites were restricted to cv. ‘Orion’ under hydroponic conditions. Overall, hydroponic and peat-free systems enhanced vegetative growth and microbial activity, whereas flowering and carotenoid accumulation were primarily cultivar-specific, as further supported by correlation analysis and PCA. These findings demonstrate that sustainable peat alternatives and hydroponic systems can effectively support high-quality T. patula production and carotenoid yield.