Microbial synergistic interactions shape the heavy metal speciation preferences between paddy and upland soils

Heavy metal contamination in agricultural soils poses escalating ecological risks, necessitating urgent remediation strategies. Through integrated approaches including soil sample collection, ecological network analysis, functional bacterial strain isolation, and validation via soil simulation experiments, this study systematically investigated the bacterial regulation of metal speciation in contrasting paddy and upland ecosystems within the middle Yangtze River Basin. Findings revealed that upland microbial communities functioned to reduce heavy metal mobility compared with paddy systems. Sphingomonas-dominated microbial alliances drove heavy metal speciation into residual fraction through synergistic interactions. Dual culture experiments demonstrated that microbial synergistic interactions enhanced Cd adsorption capacity in 67.71 % of combinations, while soil incubation experiments confirmed that Sphingomonas significantly enhanced the complexity of co-occurrence networks and reduced Risk Assessment Code (RAC) values for As, Cd, and Zn by 7.74 %, 8.13 %, and 7.02 %, respectively. Mechanistically, genomic analyses identified metal-responsive two-component systems enabling stress adaptation and detoxification. Furthermore, the microbial-physicochemical coupling between Sphingomonas and soil organic matter (SOM) indirectly reduced SOM-mediated ecological risks. The global distribution of Sphingomonas underscores its widespread role in regulating ecological risks. These findings transcend traditional single-strain bioremediation paradigms, establishing synergistic interactions as critical determinants in metal speciation control. The study provides a theoretical foundation for cross-ecosystem remediation technologies.