Green manuring inhibits nitrification in a typical paddy soil by changing the contributions of ammonia-oxidizing archaea and bacteria

Rice–rice–green manure rotations in south China are characterized by high efficiency and good environmental performance, and the application of green manure plays an important role in N management. Nitrification is a key process in N cycling and is highly correlated with the N utilization of crops and with leaching losses. As a potential N loss pathway, the nitrification process and nitrifiers as affected by green manuring are of critical importance. A pot experiment covering green manure-double rice rotation was conducted to evaluate the effects of green manure and N fertilizer on soil nitrification and to achieve a mechanistic understanding of underlying processes in an alkaline paddy soil. Soil nitrification potential (NP) and the recovered nitrification potential (RNP) were measured. Relative contributions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in soil nitrification were studied using specific bacterial inhibitors. In the alkaline paddy soil, soil NP and nitrate concentrations were significantly decreased by green manuring but increased with increasing N fertilization. Soil nitrification was dominated by AOB and that the relative contributions of AOB to RNP ranged from 65% to 79% at different sampling stages despite the larger abundance of AOA amoA gene numbers. RNP and the contribution of AOB to RNP were significantly increased by N fertilizer, whereas the contribution of AOA was decreased by green manuring. We concluded that the application of inorganic N enhanced NP while green manures reduced it, which is consistent with the variation of observed soil nitrate concentrations. These results indicate that the utilization of winter green manure is an effective practice to improve N management in paddy rice.