Archaea are the predominant and responsive ammonia oxidizing prokaryotes in a red paddy soil receiving green manures

Application of green manures is an effective approach to optimizing N management in paddy soils. Nitrification is a key process in the N cycle and ammonia oxidization is the first and typically limiting step in nitrification. In this study, we investigated the changes of ammonium oxidizing prokaryotes after the application of green manure in a red paddy soil using pot experiments. The experiment included four treatments; milk vetch-rice, radish-rice, ryegrass-rice and winter fallow-rice. The nitrification potential was measured, and the abundance and community of amoA genes from ammonia-oxidizing archaea (AOA) and bacteria (AOB) were quantified. The results showed that the AOA to AOB ratios ranged from 7 to 80, and that the milk vetch treatment increased the abundances of AOA and AOB. The abundance of AOA showed negative correlations with nitrification potential and NH4+-N, and positive correlation with soil pH in the acidic red paddy soil. DNA sequence analyses revealed that the Nitrososphaera and Nitrosospira were the dominant clusters of AOA and AOB, respectively. The dominant clusters of AOA were significantly changed by utilization of green manures, especially radish. Partial least squares path modeling analysis showed that green manures exerted larger effects on the abundances of AOA than on AOB, and the community structure of AOA had the strongest effect on nitrification potential. The high abundance of AOA found in this study and their responsiveness to green manuring suggests that AOA are critically important for soil ammonia oxidation in these soils and more sensitive to green manuring than AOB.