Peer-Reviewed Publication – Science China Press

Rice paddies are among the world’s most important agroecosystems, feeding more than half of the global population. Nitrogen (N) fertilizer is essential for high yields, yet low N-use efficiency leads to substantial environmental costs, including ammonia volatilization, greenhouse-gas emissions, and downstream eutrophication. A major obstacle to improving N management is that many paddy-field N budgets do not fully close: despite careful accounting of crop uptake, soil retention, and gaseous and hydrological losses, the fate of about 4–22% of applied fertilizer N remains uncounted for.

In the paper newly published in National Science Review, a team led by Dr. Yonghong Wu at the Institute of Soil Science, Chinese Academy of Sciences, identifies a previously overlooked microbial N sink that can account for this missing fraction. periphyton, a thin microbial community that develops at the soil–water interface in flooded paddies. Periphyton is composed of algae, bacteria, and extracellular polymeric substances, forming a dense microhabitat with strong capacities for nutrient uptake, transformation, and temporary storage.

To quantify the fraction of fertilizer N intercepted by periphyton and to resolve its subsequent fate, we combined a nationwide field survey with ¹⁵N isotope tracer experiments. From 2016 to 2019, periphyton was sampled from 840 rice fields spanning more than 93% of China’s rice-growing area. Periphyton biomass and nitrogen content were measured and subsequently upscaled to provincial and national levels. In parallel, in situ ¹⁵N-labeled urea experiments were conducted across three representative climatic zones—temperate, subtropical, and tropical—to track the incorporation of fertilizer-derived N into periphyton throughout the rice-growing season.

The results demonstrate that periphyton consistently captures a substantial fraction of applied fertilizer N. Across provinces, periphyton accounted for 6–24% of fertilizer inputs, with a national average of approximately 12%. When scaled up, periphyton was estimated to store about 0.8 teragrams of N annually in China’s paddy fields—closely matching the magnitude of the long-standing “unaccounted” N fraction reported in previous budget analyses.

The ¹⁵N tracer experiments provided direct, mechanistic support for this inference. Periphyton recovered 9.3 ± 1.6% of fertilizer N at the tropical site, 11.4 ± 1.6% at the subtropical site, and 21.3 ± 3.8% at the temperate site, yielding a cross-site mean of approximately 14%. The close agreement between national-scale upscaling and independent isotope tracing reinforces the conclusion that periphyton represents a widespread and quantifiable component of paddy-field N cycling.

Beyond the quantity captured, the chemical form of stored N indicates that periphyton functions as a transient and potentially recyclable N pool. Across all sites, ammonium (NH₄⁺) dominated inorganic N within periphyton and exceeded nitrate (NO₃⁻) by at least one order of magnitude. Moreover, NH₄⁺ accumulation exhibited a clear climatic gradient (temperate > subtropical > tropical), suggesting that temperature-sensitive microbial processes regulate periphyton N dynamics.

Using ¹⁵N-based partitioning, we further estimated that periphyton-associated N is subsequently redistributed along multiple pathways. Approximately 19–24% returns to the soil residual N pool, 8–29% is lost via ammonia volatilization, and 7–16% is associated with denitrification-related gaseous losses. The remaining fraction persists temporarily within periphyton biomass and can later re-enter the paddy system through periphyton decomposition.

By explicitly incorporating periphyton as a short-term N reservoir and redistribution hub, this study closes the paddy-field N budget gap and refines both the conceptual and quantitative frameworks used to evaluate fertilizer fate. These findings further suggest that synchronizing periphyton N release with crop demand,through targeted water management or optimized fertilization timing, could enhance internal N recycling, reduce unnecessary fertilizer inputs, and minimize trade-offs associated with gaseous N losses.

Published Date: March 3, 2026