Effects of an Organic Medium-Enclosed Trough System on Growth, Yield, Nutritional Composition, and UHPLC-QTOF-MS Metabolites of Chilli Pepper (Capsicum annuum L.)

Climate change and water scarcity pose threats to smallholder chilli pepper (Capsicum annuum L.) production, necessitating affordable and resource-efficient cultivation systems. This study assessed the effects of an Organic Medium-Enclosed Trough (OMET) system on the growth, yield, irrigation demand, nutritional, and UHPLC-QTOF-MS metabolite composition of chilli pepper under a randomised complete block design (n = 36) in a greenhouse. OMET significantly (p ≤ 0.05) increased plant height by 224%, stem diameter by approximately 43.7%, root length (57%), branch number (120%), fruit number per plant (133%), fruit length (70%), fruit width (48%), and fruit weight (204%). Cumulative irrigation water use was 44% lower under OMET (2400 mL) than under non-OMET (5350 mL). OMET increased protein (to 33.8% in leaves) and carbohydrate (to 45.4% in pods). OMET enhanced macronutrients Ca, K, and S and several micronutrients in leaves and pods. Sixteen amino acids were quantified, most of which were upregulated under OMET, with aspartic acid (Asp) being the most abundant. UHPLC-QTOF-MS untargeted metabolomics detected 38 metabolites, predominantly flavonoids and diterpenoid glycosides. Collectively, OMET improved chilli pepper growth, yield, nutrient density, and water-use efficiency without additional chemical fertiliser application, while nutrient cycling was achieved through the return of plant residues, offering smallholder farmers a practical, climate-resilient production option.