Straw Incorporation Promotes CO2 Emission from Urea Under Controlled Irrigation While Facilitating Its Microbial Assimilation Under Flooded Conditions

The fate of urea-derived carbon (urea-C) in paddy soils is poorly understood. Although urea-C is generally considered to be rapidly mineralized and released as CO2, a fraction may be retained in soil through physicochemical and microbial processes. Here, we used 13C-labeled urea combined with 13C-phospholipid fatty acid stable isotope probing (13C-PLFA-SIP) to determine the fate of urea-C under contrasting long-term irrigation and straw management practices and to identify the microbial groups involved in its assimilation. Soil CO2 efflux peaked on day 5, whereas the proportion of urea-derived CO2 in total soil CO2 efflux generally peaked on day 3. Both subsequently declined during the observation period. Cumulative urea-C loss as CO2 accounted for 36–60% of the applied C, with straw return stimulating early CO2 release and the greatest loss occurring under controlled irrigation combined with straw return. Nevertheless, a measurable fraction of urea-C remained in the soil, declining to approximately 10% of the applied C by day 21, with greater retention under flooded irrigation. Controlled irrigation combined with straw return increased microbial biomass and the fungal-to-bacterial (F/B) and Gram-positive-to-Gram-negative (GP/GN) ratios. 13C-PLFA-SIP further revealed distinct microbial partitioning of urea-C: flooded irrigation promoted incorporation into general and Gram-positive bacteria, whereas controlled irrigation favored Actinomycetes and fungi. Straw return increased urea-C incorporation into Actinomycetes and decreased its incorporation into Gram-positive bacteria under both irrigation regimes, while enhancing incorporation into Gram-negative bacteria only under controlled irrigation.