Long-Term Field Fertilization Significantly Alters Community Structure of Ammonia-Oxidizing Bacteria rather than Archaea in a Paddy Soil

Long-term field fertilization experiments may provide useful insight into the relative contributions of NH3-oxidizing bacteria (AOB) and NH3-oxidizing archaea (AOA) to soil nitrification. In this study, the abundance and composition of AOB and AOA were investigated in bulk soil from paddy field plots (4 by 5 m) that received no fertilization (CK), 180 kg urea N ha(-1) yr(-1) (NPK), or 180 kg urea N plus 4500 kg rice (Oryza sativa L.) straw ha(-1) yr(-1) (NPK./OM) since 1988 (each with three replicated plots). Our results clearly indicate that long-term fertilization (22 yr) significantly altered the community structure of AOB rather than AOA in the soil within fertilized plots compared with the CK plot. Quantitative polymerase chain reaction analysis of the amoA genes that encode the ammonia monooxygenase subunit A revealed that the AOB in the fertilized plots were 50 times more abundant than in the CK plot. Denaturing gradient gel electrophoresis fingerprinting of the amoA genes demonstrated a drastic shift in the AOB community structure, resulting in highly enriched AOB similar to Nitrosospira cluster 3 in the fertilized plots. In contrast, the population size and composition of the AOA community remained largely unchanged in all plots. Furthermore, a positive correlation was observed between the bacterial rather than archaeal amoA gene copy numbers and potential nitrification activity among the soils. The distinct responses of AOA and AOB to long-term field fertilization were probably related to the availability of NH3. Our results suggest that AOB might play major roles in the NH3 oxidation that occurs in bulk soil under the in situ fertilized paddy field conditions tested in this study.