Watermelon-Sesbania rotation enhance soil quality in greenhouses systems by driving soil properties and functional microorganisms

Continuous monoculture of watermelon in greenhouses often leads to soil degradation by disrupting microbial communities and nutrient cycling, yet effective mitigation strategies remain unclear. In this study, we conducted a three-year experiment to investigate the effects of watermelon-Sesbania rotation on soil chemical properties, microbial diversity (bacterial, fungal, archaeal, and viral), community composition, and functional gene profiles related to carbon, nitrogen, phosphorus, and sulfur cycling. We show that a three-year Sesbania rotation significantly improves soil properties compared to continuous watermelon monoculture, increasing soil organic matter by 103%, total nitrogen by 53%, available nitrogen by 48%, and available phosphorus by 98%. Extended rotations particularly enhanced beneficial microorganisms, including bacteria (e.g., Chloracidobacterium, Rubrivivax, Pyrinomonas) and archaea (Methanohalophilus), which promote carbon fixation and nitrogen cycling while suppressing monoculture-associated pathogens. Both bacterial and fungal community structures (beta diversity) changed significantly under rotation treatments. Additionally, functional genes related to carbon, nitrogen, and phosphorus metabolism (e.g., rbcS, nasB, gntK) were significantly enriched in rotated soils, driven primarily by improved nutrient availability and pH. The soil quality index increased by 92.5% in the three-year rotation, with total nitrogen and organic matter identified as the main drivers. Our findings, for the first time, demonstrate that watermelon-Sesbania rotation can improve soil quality in greenhouse systems by driving soil properties and functional microorganisms, and that these effects are enhanced over time with increasing rotation duration, overcoming common barriers associated with continuous cropping in greenhouse production systems. We recommend a minimum rotation period of three years to achieve substantial improvements in soil health and sustainability.