Dynamics of nitrogen mineralization and nitrogen cycling functional genes in response to soil pore size distribution

Soil pore distribution influences the permeability of gas, water, and solutes, affecting microbial activities such as nitrogen (N) mineralization. Understanding its impact on N mineralization and the subsequent N transformations is essential for managing compacted paddy soils. This study conducted incubation experiments on two paddy soils from typical Chinese rice regions, Northeastern meadow chernozemic Mollisols, and Southern umbric Ferralsols, under three bulk densities (1.0 g cm −3 , 1.2 g cm −3 , and 1.4 g cm −3 ) to investigate the effects of soil porosity on N mineralization and N cycling functional genes. Although the cumulative mineralized N showed no significant difference, with increased macropores (>100 μm) and mesopores (30–100 μm), Ferralsols exhibited a significantly higher net N mineralization rate from day 0 to day 7, while Mollisols extended the mineralization after day 21. Soil dissolved organic carbon (DOC) had a similar temporal trend to the net N mineralization rate, suggesting DOC was the product of mineralization. Soil microbial biomass carbon (MBC) showed an opposite temporal trend to the net N mineralization rate in Mollisols, suggesting microbial biomass as a key N source for mineralization. Soil pores distribution did not affect nitrification under waterlogged conditions, but it affected nirK , nirS and nosZ genes by altering redox potential and substrates availability in the pore micro-environment. Overall, soil pores over 30 μm were the key pore size ranges affecting the intensity and duration of N mineralization, with different effects on DOC, MBC, and N cycling functional genes in Mollisols and Ferralsols. These findings emphasized the role of pore size in regulating N transformation in waterlogged conditions, contributing to the understanding of the N availability in compacted paddy soils from typical geographic rice-growing regions. • Higher N mineralization rates are associated with macropores (>100 μm) and mesopores (30–100 μm). • Macropores and mesopores increased cumulative N mineralization in Mollisols but only temporarily in Ferralsols. • Microbial biomass serves as a key N source for mineralization in Mollisols, but not in Ferralsols. • Under waterlogged conditions, pore size regulates denitrification in Mollisols, with nosZ gene rising in compacted soils.