A research team led by Prof. YAN Xiaoyuan from the Institute of Soil Science, Chinese Academy of Sciences, has revealed that nitrogen gas (N2) emissions from rice paddies mainly originate from soil organic nitrogen rather than fertilizer. The study, published in PNAS, also introduces a new mechanism termed the “microbial nitrogen pump,” reshaping the understanding of nitrogen cycling in agricultural systems.
Rice feeds more than half of the global population, yet its production relies heavily on nitrogen fertilizers. In China, nitrogen application rates in rice fields typically reach 200–300 kg per hectare—two to three times higher than in many other regions of the world, while nitrogen use efficiency remains below 40%.
A substantial fraction of applied nitrogen is lost to the environment, with N2 representing the largest but least understood pathway. Because N2 accounts for about 78% of air, distinguishing soil-emitted N2 from background levels has long posed a major technical challenge. As a result, it has been widely assumed that N2 emissions primarily originate from fertilizer nitrogen, despite of limited direct evidence.
To address this long-standing question, the research team combined 15N isotope tracing with membrane inlet mass spectrometry (MIMS) to establish an in-situ observation methodology. This approach enabled simultaneous measurement of N2, ammonia (NH3), and nitrous oxide (N2O) emissions throughout the entire rice growing season, while partitioning their sources.
The results showed that 72%–75% of N2 emissions came from soil organic nitrogen, not fertilizer nitrogen. This finding was independently confirmed in a 14-year long-term fertilization experiment.
In contrast, NH3 emissions were mainly derived from applied fertilizer, while N2O emissions originated from both soil and fertilizer sources. The study also identified a seasonal “trade-off” pattern: NH3 volatilization dominated nitrogen losses in early growth stages, whereas N2 emissions became dominant later in the season.
Based on these observations, the researchers proposed the “microbial nitrogen pump” mechanism.
Following fertilizer application, urea-derived ammonium (NH4+) is rapidly assimilated by soil microbes to support growth, creating a carbon:nitrogen stoichiometric imbalance. To restore this balance, microbial activities accelerate the decomposition of native soil organic matter, mobilizing soil organic nitrogen (SON) and releasing large amounts of soil-derived NH4+. This “old nitrogen” is subsequently converted into N2 through nitrification and denitrification processes and released into the atmosphere. The mineralized SON is only partially replenished through microbial N turnover.
“In other words, fertilizer does not directly turn into nitrogen gas. Instead, it activates soil nitrogen pools, indirectly driving larger nitrogen losses,” said Prof. XIA Longlong, a professor from the research team.
This mechanism provides the first systematic explanation linking fertilization, microbial processes, soil organic nitrogen mineralization, and gaseous nitrogen loss.
Beyond fundamental insights, the research highlights practical implications for reducing nitrogen loss. The team found that hybrid rice varieties improve nitrogen uptake efficiency and microbial nitrogen utilization, reducing yield-scaled gaseous nitrogen losses by approximately 43% while maintaining high productivity.
This suggests that integrating crop breeding with soil–microbe regulation could help achieve both high yields and lower environmental impacts.
By identifying soil organic nitrogen as the dominant source of N2 emissions, this study fundamentally revises the understanding of nitrogen cycling in rice ecosystems. It provides a new theoretical framework for improving nitrogen use efficiency, refining global nitrogen budgets, and developing sustainable agricultural practices.
Notably, the study was featured as a cover article in PNAS, representing one of the very few cover papers on soil nutrient cycling in the past two decades, and highlighting its broad international significance.
Fig. A microbial nitrogen pump driving distinct sources of soil gaseous nitrogen losses from flooded rice systems. (Image by YAN Xiaoyuan’s team)
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