Background and aims While intensive fertilization has wide-ranging impact on microbial communities, its effects on microbial recolonization of soil niches and associated enzyme activities as well as hotspots distribution remain underexplored. Methods Using soil zymography and high-throughput sequencing, we investigated the hotspots and activities of C-, N- and P-acquiring hydrolases, as well as bacterial community dynamics across hotspots, coldspots, and root endosphere within rice rhizosphere in sterilized and non-sterilized soils following NPK fertilization. Results Bacterial community reassembly after sterilization was primarily governed by compartment niches rather than by fertilization, although fertilization accelerated bacterial recovery by increasing diversity and network complexity. Specifically, the dominant taxa and major contributor of genes encoding hydrolases in the rhizosphere of non-sterilized soil shifted from Actinomycetota (K-strategists) to Pseudomonadota and Bacillota (r-strategists). In contrast, root endosphere communities had greater resilience during recolonization and likely supported rice growth by expanding enzyme hotspots area. Higher enzyme activities in hotspots, compared to coldspots, correlated strongly with increased bacterial network complexity, and less with differences in diversity and overall community composition. Fertilization triggered a trade-off between enzyme activities and hotspots area, with increased activities for β-glucosidase and leucine aminopeptidase but reduced hotspots area, whereas acid phosphatase had the opposite trend. Conclusion The trade-offs between enzyme activities and hotspots area highlight the micro-scale spatial heterogeneity in nutrient mobilization in paddy soils, suggesting adaptive strategies that plants and microorganisms use to regulate nutrient investment. These findings provide valuable insights for optimizing fertilization management to accelerate microbial processes and enzyme-mediated nutrient cycling. Graphical Abstract

Rice is one of the world’s most important staple crops and a major source of agricultural methane emissions. Breeding strategies such as photosynthate allocation modification and biomass enhancement ...