Interactive Effect of Soil Properties and Microbial Functional Genes on Methane and Nitrous Oxide Emissions in Rice Paddies: A Global Meta-Analysis

Rice paddies are a major anthropogenic source of methane (CH₄) and nitrous oxide (N₂O), yet the interactive roles of soil properties and microbial functional groups in regulating both gases remain poorly quantified. While individual studies have examined CH₄ and N₂O separately, an integrated assessment of their shared drivers across diverse field conditions is lacking. Here, we synthesized 74 paired observations to evaluate how soil properties and microbial gene abundance jointly influence CH₄ and N₂O emissions in rice paddies and to assess mitigation patterns associated with common management practices. Neutral soil pH (6.5–7.5) and strongly reduced conditions (Eh  –90 mV) increased CH₄ emissions by up to 800%, higher than non-reduced conditions (Eh > 0 mV), whereas rising nitrate (NO₃⁻) availability suppressed CH₄ emissions by 58%. Moderate mcrA increased CH₄ by 54%, and high nosZ increased emissions by 103%, while elevated pmoA and ammonia-oxidizing bacteria (AOB) suppressed CH₄. In contrast, N₂O emissions increased with higher pmoA abundance (+70%) but declined under elevated NH₄+. Random forest identified AOB and NO₃⁻ as the strongest predictors of CH₄, while AOB and NH₄⁺ governed N₂O. Organic amendments increased emissions by up to 62.1%, whereas biochar consistently reduced both gases. The most consistent mitigation pattern was biochar with 120–180 kg N ha⁻¹, which suppressed carbon cycling, nitrification, and denitrification genes (path coefficients ranged from –0.28 to –0.49). These findings suggest soil-microbe interaction underpins CH₄ and N₂O emissions in rice paddies and highlight biochar-based nutrient management as a promising mitigation strategy.