Rice Rotation System Affects the Spatial Dynamics of the Diazotrophic Community in Paddy Soil of the Yangtze Delta, China

Rice-wheat (RW), rice-fallow (RF), and rice-Chinese milk vetch (RM) are the three major rice rotation systems currently used in the Yangtze Delta of China. However, it remains poorly understood how these systems affect microbial communities in soils. Quantitative polymerase chain reaction (qPCR) and denaturing gradient gel electrophoresis (DGGE) were used to analyze the composition, abundance and diversity of diazotrophic community at different depths in soils under RW, RF and RM treatments. The results showed that rice yields were significantly higher in RM as compared to those in RF and RW in all years from 2011 to 2016. Diazotrophic communities at soil depths of 10–20 cm and 40–80 cm under RM were significantly more diverse than those under the other treatments. Sequences affiliated with Geoalkalibacter spp. showed the greatest abundance under RW at all soil depths, while Desulfovibrio and Pseudacidovorax spp. were both more abundant under RM at the 40–80 cm depth. Redundancy analysis (RDA) identified that the diazotrophic community within the 40–80 cm layer of soil under RM was positively associated with soil macro-aggregates. In conclusion, the RM treatment was characterized by significantly higher diversity of diazotrophic community in subsoil and increased rice yields as compared to the other treatments.