Nowadays farmers are interested in moving to organic cultivation. The purpose of this experiment was to compare two organic, with or without effective microorganisms (EM), and one conventional greenhouse pepper cropping systems. We focused on the study of the macronutrients nitrogen, phosphorus, and potassium (N, P, K) concentrations in leaves plants, soil, and soil solution during the full production cycle to detect any plant nutrient deficiencies and differences in crop yield for the three different treatments. Foliar analyses showed good concentrations of nutrients with conventional treatment, but P was low with organic ones. However, P content in soil was high, because this element is easily precipitated in carbonated soil. Pepper yield was higher in conventional treatment and no differences in productivity were found between the two organic treatments. The role of EM was not clear on the development of plants and fruits; however it seems to influence the N mineralization in organic treatments.
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