Nutrient status of integrated rice-crayfish system impacts the microbial nitrogen-transformation processes in paddy fields and rice yields.

Increasing rice yield is essential for alleviating global food crisis. High soil nutrient level guarantees high rice yields in conventional rice monoculture (RM) systems, but excessive unconsumed nutrients act as pollutants and can even threaten rice growth. The integrated rice-crayfish (IRC) system aims to transfer the excess nutrients from crayfish to paddy fields to improve the comprehensive utilization rate of nutrients and create additional profits, while the responding characteristics of IRC microbial communities in paddy fields and rice yields to the nutrient status remain unclear. Considering the crucial roles of microbiomes in promoting nutrient cycling for crop absorption in rice production progresses, the composition and functional characteristics of soil microbial communities from six IRC farms with variant nutrient statuses in the Yangtze River Delta were surveyed in this study. Compared with RM systems, IRC systems with appropriately improved (p < 0.05) soil quality created favorable nutrient (FN) status accompanied by 15% rice yields increase, while IRC systems with extremely high nutrients (HN) status (p < 0.01) accompanied by 14% rice yields reduction. Soil microbial diversity and network complexity were maintained in FN-IRC systems, but declined in HN-IRC systems, with the Shannon index significantly decreased by 9.2% and network density decreased from 0.135 (in RM) to 0.062. In the FN-IRC systems, the keystone taxa identified by co-occurrence networks displayed inextricably positive correlations with soil nitrification potential (calculated by normalization of amoA gene abundance) and rice yields. While in HN-IRC systems, the large loss of keystone taxa might limit soil nitrogen fixation potential (calculated by normalization of nifH gene abundance), and further rice yields. Our study indicates that soil nutrient management in IRC systems claim attention, and the improvement of nitrogen metabolism is the key to realize agricultural cleaner production.