Sustainable Soil Management: The Dynamic Impact of Combined Use of Crop Rotation and Fertilizers from Agri-Food and Sulfur Hydrocarbon Refining Processes Wastes

Sustainable agriculture increasingly relies on strategies that improve soil fertility while reducing the environmental footprint of chemical inputs. The primary objective of this research was to disentangle the individual and combined effects of crop rotation and fertilization on soil quality. This study aimed to determine whether the effectiveness of fertilization was modified by rotational practices—exploring whether these interactions were additive, antagonistic, or synergistic. This study assessed the impact of two-year open-field crop rotations—broccoli–tomato and broccoli–pepper—combined with organic and mineral fertilization on soil chemical and biological properties. Treatments included sulfur bentonite enriched with orange waste (SBO), horse manure (HM), mineral fertilizer (NPK), and an unfertilized control (CTR). Soil samples were collected after each crop cycle and analyzed for enzymatic activities (fluorescein diacetate hydrolase, dehydrogenase, catalase), microbial biomass carbon (MBC), organic matter, total nitrogen, and macro- and micronutrient content. The results showed that organic amendments, particularly SBO and HM, significantly increased microbial activity, MBC, and nutrient availability compared to NPK and CTR. Organic treatments also led to a reduction in soil pH (−12%) and a more balanced ionic profile, enhancing soil biological fertility across both rotations. By contrast, the NPK treatments favored higher nitrate and chloride concentrations (3.5 and 4.6 mg * g −1 dw, respectively) but did not improve biological indicators. Improvements were more pronounced in the second crop cycle, suggesting the cumulative benefits of organic amendments over time. These findings highlight the potential of combining organic fertilization with crop rotation to enhance soil health and support long-term sustainability in horticultural systems.