Decadal Resampling Reveals Widespread Increases in Soil Microbial Diversity Associated With Nitrogen Deposition

Simulated manipulation experiments, such as nitrogen addition to mimic atmospheric nitrogen deposition, are widely used in global change research. However, experimental manipulations may differ from real-world environmental change in their intensity, duration, and co-occurrence, leaving long-term changes in soil microbial communities and soil health insufficiently understood. To address this gap, we resampled soils from 38 forest and grassland ecosystems across eastern China in 2009 and 2019 and assessed microbial taxonomic and functional diversity using shotgun metagenomics. Microbial diversity increased by 17% over the decade, accompanied by clear shifts in community composition. Among the environmental variables considered, nitrogen deposition (~19 kg nitrogen ha^-1 year^-1 across ecosystems) was the strongest predictor of changes in seven of 12 microbial community metrics. Larger nitrogen deposition was also associated with increased relative abundances of nitrogen-cycling genes and reduced spatial turnover in microbial community composition. These effects were consistent with a potential alleviation of nitrogen limitation and weakening of deterministic community assembly, although these mechanisms could not be directly established. In addition, increases in genes associated with carbon degradation and phosphorus cycling, together with declines in the relative abundances of pathogens, antibiotic resistance genes, and DNA viruses, coincided with the raise of the composite soil health index. Our findings demonstrate widespread decadal increases in soil microbial diversity and soil health across eastern China, with nitrogen deposition emerging as their strongest environmental factor. These results highlight that microbial responses to long-term ambient environmental change can differ markedly from responses inferred from short-term or high-intensity manipulation experiments.