Machine learning reveals that duration dominates rate in driving soil nitrogen cycling responses to long-term fertilization

Intensive nitrogen fertilization in agricultural ecosystems has profound impacts on soil nitrogen cycling, yet the mechanistic understanding of how long-term nitrogen inputs alter microbial-mediated nitrogen transformations remains limited. While previous research has focused primarily on application rates, the temporal dimension of nitrogen management has been largely overlooked. Here, we present a global meta-analysis of 2,824 observations from 88 field studies specifically examining how nitrogen application duration, rather than just amount, shapes soil nitrogen cycling processes. Machine learning analysis revealed application duration as the dominant driver of nitrogen cycling changes, explaining greater variance than that explained by application rates across all functional genes examined. Long-term nitrogen application (>20 years) dramatically increased ammonia-oxidizing bacteria (AOB) abundance by 904% while modestly affecting ammonia-oxidizing archaea (AOA) by 142%, fundamentally altering the balance of ammonia oxidation processes. In acidic soils with long-term nitrogen application, AOB responses (1,107%) substantially exceeded AOA responses (179%), demonstrating that substrate availability becomes the primary driver of microbial community structure structure under long-term nitrogen enrichment. Our findings demonstrate that nitrogen application duration, more than amount, determines soil nitrogen cycling responses, creating progressive changes with substantial shifts occurring after 20 years of continuous fertilization. These results reveal duration-dependent mechanisms that provide a new framework for nitrogen management, enabling simultaneous maintenance of agricultural productivity and reduction of environmental impacts through duration-optimized application strategies. • The duration of nitrogen application is crucial for predicting N-cycling processes • AOB primarily regulates ammoxidation in soils with long-term nitrogen application • Long-term nitrogen application leading to N enrichment is crucially affecting AOB • Long-term nitrogen application dramatically increased AOB abundance by 903.8%