Long-Term Effects of Lime and NPK Fertilization on Soil pH, Nitrogen Cycling, and Carbon Depletion: Benefits and Risks

The nutritional use efficiency (NUE) of crops is influenced by changes in soil pH caused by lime fertilizer, which also affects the nitrogen cycle. Lime application shifts soil pH from acidic to neutral, reducing nitrous oxide (N₂O) emissions through the activity of nitrous oxide reductases in microorganisms, while also increasing nitrification rates due to enhanced activity of ammonia-oxidizing archaea (AOA) and bacteria (AOB). Accelerated nitrification leads to higher nitrate (NO₃^-) levels, which, when exceeding crop absorption capacity, pose a significant risk of leaching. This study investigated the effects of long-term NPK and lime fertilizer application on the soil nitrogen cycle using metagenomic analysis. Soil samples from plots treated with NPK alone and NPK with lime for 48 years were analyzed for metagenomic N₂O gas flux, potential nitric oxide rates (PNR), and NUE. Results showed that long-term lime application significantly increased soil pH and reduced N₂O emissions by 27% over 480 hours, with the most notable reduction in the first 24 hours compared to NPK-only treatment. However, NUE did not significantly improve, while PNR increased dramatically, reaching 1442% higher than in NPK-treated soils, indicating a potential risk of nitrate leaching. Metagenomic analysis revealed that nitrogen cycling pathways, including nitrification, were more active in lime-treated soils. Enhanced microbial nitrogen metabolism also increased carbon metabolism associated with degradation, suggesting a risk of soil carbon depletion via the priming effect, as evidenced by reduced total soil carbon and organic matter in lime-treated plots. The findings highlight both the benefits and drawbacks of long-term lime application. While lime improves soil pH and reduces N₂O emissions, it may also increase nitrate leaching and soil carbon depletion. Further research is needed to optimize lime application for sustainable soil management.