Long-term warming and elevated CO₂ increase ammonia-oxidizing microbial communities and accelerate nitrification in paddy soil

Soil nitrification is a crucial process that increases nitrogen (N) availability for plants and drives nitrous oxide (N₂O) emissions and nitrate (NO₃⁻) leaching. Ongoing climate warming and elevated CO₂ in the atmosphere may affect nitrification in opposite directions. However, their interactions are not known, especially in the long-term and in flooded conditions common in paddy soils. We conducted a long-term (9 years) field experiment with simultaneous manipulation of temperature (+2 °C above ambient) and CO₂ (+60–100 ppm above ambient) to evaluate the impacts of warming and CO₂ enrichment on the community structure, diversity, and population size of ammonia-oxidizing archaea (AOA) and bacteria (AOB), soil nitrification and physico-chemical characteristics. Elevated CO₂ increased soil organic carbon (SOC) content (18%), microbial biomass N (65%), and carbon (27%). These changes accompanied an increment in AOB functional-gene abundance (181%) and soil nitrification rate (96%). Elevated temperature also increased (58%) soil nitrification rate. The combination of warming and CO₂ enrichment enhanced AOB gene abundance (232%) and nitrification rate (133%). Impacts of these climate change factors on nitrification strongly depended on AOB gene abundance and microbial biomass, but not on AOA abundance. Higher root C inputs by rhizodeposition and pH under these climate change factors explained the substantial increases in AOB gene abundance, as nutrient-rich and alkaline soils favor AOB growth. By contrast, the AOA community was less sensitive to these climate change factors. Community composition, diversity, and richness of nitrifiers were remarkably resilient in response to individual and interactive impacts of warming and elevated CO₂. Consequently, climate change will increase AOB population size but without community restructuring and will increase nitrification in paddy soils, which enhances N availability with consequences for crop productivity, N₂O emissions, and NO₃⁻ leaching.