Distinct responses of ammonia-oxidizing bacteria and archaea to green manure combined with reduced chemical fertilizer in a paddy soil

Purpose: Ammonia oxidation is the rate-limiting step in nitrification. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are the key drivers of the nitrogen cycle. Chinese milk vetch (MV) has the potential to substitute for part of chemical fertilizer, but it remains unclear how MV is able to replace N fertilizer. The purpose of this study was to investigate the rice yield, soil properties, potential nitrification activity (PNA), abundances, and community structures of ammonia oxidizers in a paddy soil under MV combinations of different rates of chemical fertilizer. Materials and methods: This study was conducted at a long-term Experimental Station of the Fujian Academy of Agricultural Sciences, Fuzhou, China. The treatments included a control (without fertilization), NPK (chemical fertilizer), MF80 (MV plus 80% NPK), MF60 (MV plus 60% NPK), and MF40 (MV plus 40% NPK). Soil samples were collected after the rice harvest. We determined the soil physico-chemical properties and PNA. The abundances and community structures of AOB and AOA were assessed using their ammonia monooxygenase (amoA) genes. Quantitative PCR was used to determine the gene abundance, and Illumina Miseq sequencing was used to explore the diversity of AOB and AOA. Results and discussion: MV significantly increased the soil organic matter and PNA in comparison to the NPK. The available nitrogen content was higher in the MV treatments than in the control and NPK. Compared to the NPK, the application of MV increased the AOB abundance but decreased that of AOA. The abundance of AOA was higher in the control and NPK, but lower in the MV treatments than that of AOB. PNA was significantly positively correlated with the AOB abundance. The primary dominant OTU of the AOB group was Nitrosospira. MV significantly affected the AOB community, while no impact on the AOA community was observed. Principal coordinate analysis showed that the MV treatments were significantly distinct from those of the control and NPK. Redundancy analysis indicated that the soil OM, TN, AN, pH, and PNA were significantly correlated to the AOB community structure. Conclusions: This study demonstrated that MV combined with reduced chemical fertilizer would contribute to the improvement of soil fertility and PNA, resulting in rice yield comparable to that of the NPK. MV had a stronger effect on the AOB community than did chemical fertilizer. AOB played a more important role than AOA in the ammonia oxidation in this soil.