Periphyton closes the nitrogen budget gap in rice paddies

Persistent 4%–22% gaps in nitrogen (N) mass balances have hindered sustainable N management in paddy agriculture. Periphyton are known N sinks, yet their role in paddies remains unclear. We used ¹⁵N tracing in 840 paddies across China to quantify periphyton-associated N pools and their fate. Periphyton captured 6%–24% (mean: 12%) of the applied N fertilizer (i.e. ∼0.8 Tg N yr⁻¹ nationwide), effectively accounting for the missing N in previous budgets. Most of the sequestered N was stored as bioavailable ammonium. Partitioning analysis revealed that periphyton-mediated N was subsequently released into residual soil N (512–640 kt), denitrification (56–128 kt) and ammonia volatilization (64–232 kt). Thus, periphyton act as transient N reservoirs, immobilizing N fertilizer early in the growing season and gradually releasing it through biomass decay. This overlooked pathway closes a critical gap in agroecosystem N cycling and supports more precise N management in rice systems.