Soil pH modulates microbial nitrogen allocation in soil via compositional and metabolic shifts across forests in Japan

Abstract Ammonium release (ammonification) and uptake (immobilization) by soil microbial communities are fundamental processes of forest nitrogen (N) cycling, representing major N fluxes that influence plant productivity and ecosystem N retention. However, because these processes involve diverse metabolic pathways distributed across many taxa, they are difficult to evaluate using gene‐ or taxon‐specific approaches, and it remains unclear how microbial community structure governs the patterns of these processes. In this study, we examined how the abundance, taxonomic composition, richness, and metabolic capabilities of microbial communities regulate ammonium‐related N cycling processes across a wide range of forests in Japan, using rRNA gene sequencing and quantification, shotgun metagenomics, and ¹⁵ N tracer assays. Across the full gradients of soil pH and N content, microbial abundance was primarily correlated with the absolute rates of N cycling processes, while taxonomic composition and richness were more strongly correlated with N allocation—that is, the balance among ammonium release, ammonium uptake, and subsequent nitrification. Soils with higher pH supported taxonomic compositions linked to enhanced ammonium release and nitrification, whereas lower‐pH soils hosted compositions associated with greater ammonium uptake and retention. Notably, the regulatory influence of taxonomic composition on N allocation was pronounced within the higher‐pH range but diminished within the lower‐pH range. Despite this environmental dependency, N allocation by soil microbial communities was ultimately constrained by their overall metabolic capabilities. In higher‐pH soils, microbial communities were enriched in metabolic functions related to nutrient acquisition and respiratory N transformations, supporting increased ammonium release and N mobility. By contrast, microbial communities in lower‐pH soils were enriched in stress‐adaptive functions, which promoted ammonium retention and limited N transformations—thereby diminishing the regulatory influence in N cycling. Together, our findings provide a mechanistic understanding of how microbial community structure and metabolic capabilities regulate ammonium‐related N cycling processes across forests under varying environmental conditions.