Nitrogen Leaching and Diversity of Ammonia-Oxidizing Archaea and Bacteria in Rice–Frog Co-Cultivation

Rice–frog co-culture is an organic farming practice known to effectively reduce nitrogen (N) loss from paddy fields. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) mediate the rate-limiting step of nitrification; however, their relative contributions to this process remain unclear in certain soil types. This study aimed to evaluate the effects of rice–frog co-culture on N leaching and the associated AOA and AOB communities. A two-year field experiment was conducted in Shanghai, comparing three cultivation patterns: conventional rice (CR), green rice–frog (GR) co-cultivation, and organic rice–frog co-cultivation (OR). Nitrogen leaching was monitored, soil properties were analyzed, and the abundance and community composition of AOA and AOB were assessed. Nitrogen leaching losses were significantly lower in GR and OR than in CR, by 14.82% and 28.45%, respectively. Ammonium (NH4+) was the predominant form of leached N, accounting for 58.10%, 56.20%, and 49.02% of the total N in CR, GR, and OR, respectively. Rice–frog co-culture significantly increased amoA gene copy numbers of AOA but suppressed those of AOB. The community structures of both AOA and AOB were strongly influenced by soil properties, including NH4+, soil organic carbon (SOC), total nitrogen (TN), and pH. Specifically, the AOA community was primarily shaped by NH4+ and SOC, whereas the AOB community was mainly driven by SOC content. These findings indicate that integrated rice–frog co-cultivation systems mitigate nitrogen leaching losses, modify soil physicochemical properties, and shift the abundance and community composition of ammonia-oxidizing archaea and bacteria.