Metagenomic insights into kapok-driven nitrogen-cycling hotspots enhancing soil biological resilience in tropical agroforestry systems

Abstract Intensive rice monoculture in tropical regions is increasingly vulnerable to soil degradation, low nitrogen use efficiency (NUE), and amplified nutrient losses under climate change extremes, necessitating sustainable, biologically driven management strategies. This study evaluated the role of traditional kapok–rice agroforestry, integrating the native red silk-cotton tree ( Bombax ceiba ), in regulating soil nutrient dynamics, nitrogen (N) mineralization, microbial biomass, extracellular enzyme activities, and microbial community composition across five rice growth stages (tillering, booting, heading, maturity, and fallow) compared to rice monoculture systems in Changjiang County, Hainan, China. Using a paired-plot design with three independent replicate fields per system, we compared kapok-integrated soils against adjacent rice monoculture controls. Kapok-integrated soils exhibited markedly enhanced fertility relative to monoculture, with soil organic matter increasing by up to 42%, total N by 44–49%, and available N, P, and K by 63%, 133%, and 93%, respectively, at the maturity stage, compared to monoculture controls. Microbial biomass carbon and nitrogen peaked at 397.17 and 362.40 mg kg − 1 , accompanied by significantly higher N-acquiring enzyme activities (N-acetylglucosaminidase and leucine aminopeptidase), indicating intensified microbial functioning. Nitrogen mineralization potential (N o ) and cumulative mineralized N were substantially greater (63.42 and 67.46 mg kg − 1 over 90 days), reflecting improved N retention and cycling capacity under agroforestry management. These enhancements were linked to distinct microbial community shifts dominated by Pseudomonadota, Actinomycetota, Ascomycota, and Bacillariophyta, suggesting increased functional stability and adaptive capacity under climate-sensitive conditions. Overall, kapok–rice agroforestry strengthens soil biological processes, enhances nitrogen cycling, and improves ecosystem resilience, demonstrating its potential as a nature-based, low-input management strategy to mitigate soil degradation and sustain productivity in tropical rice systems under climate change extremes.