Microbial mechanisms mediate divergent ecosystem responses to nitrogen and phosphorus enrichment

Anthropogenic nitrogen (N) and phosphorus (P) deposition are intensifying nutrient imbalances in ecosystems. However, the microbial mechanisms governing ecosystem responses to chronic N–P enrichment remain poorly resolved and are inadequately represented in ecosystem models. Here, we integrated multi-source and multi-scale observations, from functional genes and enzymes to ecosystem fluxes, into a newly developed microbial-enzyme-mediated Carbon–Nitrogen–Phosphorus model (MEND-CNP). This model-microbiome fusion enables multi-year continuous simulations of nutrient enrichment in a subtropical forest, offering mechanistic insights beyond the reach of experiments alone. Our results refined and extended the Nitrogen Saturation Hypotheses (NSH) by resolving microbial pathways previously unaccounted for in model frameworks. Specifically, after N saturation, N addition enhanced denitrification, suppressed biological N fixation, and reduced soil C:N ratios. We further demonstrated that excess N-induced acidification constrained nitrifying microorganisms and their associated enzymes, thereby mechanistically explaining the observed declines in nitrification in subtropical forests, in contrast to NSH paradigms derived from temperate ecosystems. We also identified process-level controls of increased N₂O emissions, including accelerated NO₃⁻ to N₂O conversion and suppressed N₂O to N₂ reduction. Furthermore, P addition stimulated microbial biomass and elevated microbial N demand, reversing N cycling trajectories induced by N enrichment. This divergent effect was further influenced by N availability, revealing a spectrum of single- and multi-element limitations. By embedding gene-informed microbial physiology into a process-based CNP framework, our study established a mechanistic bridge between microbiome dynamics and ecosystem-scale nutrient cycling, advancing predictive understanding of biogeochemical feedbacks under accelerating global change.