Objectives Taking the typical cold waterlogged paddy fields in the South China as a research object, the effects of chemical fertilizers combined with different manures on the grain yield of paddy rice and the abundance of soil nitrogen-cycling microbes were compared. The study could provide scientific basis for the theory and practice of nitrogen mobilization, nitrogen redirection control and use efficiency, and fertilizer application scheme for high yield in cold waterlogged fields.

Methods A three year-study was conducted to analyze the influences of the fertilizers combined with different organic manures on nutrient mobilization, rice yield and the abundance of nitrogen-cycling bacteria in cold waterlogged soils on the basis of soil properties, enzymatic characteristics and real-time quantification PCR. The field experiment included four treatments: chemical fertilizers (CK), chemical fertilizers combined with pig manure (PIM), chemical fertilizers combined with cattle manure (CAM) or chemical fertilizers combined with chicken manure (CHM).

Results The grain yields responded positively to both CHM and CAM application, and were increased by 10.2% and 7.6% over the yield of CK, respectively. The soil pH, organic carbon, total nitrogen content and ammonium nitrogen content were all increased after continuous application of CHM or CAM. The abundance of microbial genes related to soil nitrogen-cycling was significantly enhanced by the additions of the three fertilizer formulations. Furthermore, the 16s rDNA abundance of bacteria and archae bacteria, and amoA (ammonia monooxygenase) abundance of ammonia-oxidizing archaea (AOA) and anaerobic oxidizing bacteria (AOB) presented consistent increasing patterns, and the highest abundances were exhibited in the CHM-treated soil and the increase rate of bacteria 16s rDNA was smaller than others. However, the gene abundances of nitrite reducate ( nirK, nirS) and nitrous oxide reducate ( nosZ) responded differently to the fertilizer formulations. Correlation analysis showed that the contents of soil organic carbon and total nitrogen appeared to be the key factors influencing the abundance and diversity of AOA-, AOB-, nirK-and nirS-type denitrifying bacteria.

Conclusion The application of the fertilizers combined with chicken manure could significantly increase the contents of soil ammonium nitrogen and available phosphate, improve the gene abundances of bacteria, archaebacteria, AOA and AOB-type amoA and enhance the activities of soil urease, protease and phosphatase, thereby improving the productivity of cold waterlogged soils.