Greenhouse gas dynamics in Northeast China's black soil paddies: Protozoan regulation of CH₄ and CO₂ emissions under nitrogen input

Paddy fields represent major sources of methane (CH₄) and carbon dioxide (CO₂) emissions, significantly contributing to global climate change. However, the mechanistic role of protozoa—key components of soil microbiota—in mediating greenhouse gas emissions from paddy systems remains poorly understood. This study explored the effects and underlying mechanisms through which protozoa influence CH₄ and CO₂ emissions under nitrogen input conditions. Metagenomics analyses revealed that available phosphorus and nitrate nitrogen are the primary environmental factors shaping the protozoan community structure. Nitrogen fertilization reduces protozoan diversity and enhances CH₄ and CO₂ emissions. During the rice tillering stage, plots without nitrogen fertilization exhibited a 7.41% increase in protozoan diversity, along with 97.45% and 80.75% reductions in CH₄ and CO₂ emissions, respectively. Protozoa were found to regulate the greenhouse gas emission via microbial genes involved in carbon decomposition. Specifically, protozoa dynamically modulated greenhouse gas fluxes via a three-tier metabolic network encompassing carbon fixation, decomposition, and energy conversion. Significant positive correlations were observed between the abundances of Symbiodinium sp. KB8 and key functional genes including amyA, mcrA, and pulA genes. This study offers scientific insights for optimizing nitrogen management in paddy ecosystems, elucidating the ecological roles of protozoan communities as key regulators of soil microecology. Our findings provide guidance for mitigating global warming, protecting food security, and maintaining ecological stability. Manipulating protozoan abundance and diversity may contribute to achieving carbon neutrality in modern agricultural ecosystems. © 2026 Elsevier B.V.