Objective This study aimed to investigate the soil microbial community structure of the rice-fish co-culture system (RF), and compare its microbial functions on carbon and nitrogen cycling to those of rice monoculture system (RM).

Method We sampled soil from paddies during the rice growth season at the site of the Qingtian rice-fish co-culture system, a globally important agricultural cultural heritage. Using high-throughput sequencing technology, we compared the structure and function of soil bacterial and archaeal communities between RF and RM.

Result RF significantly increased the α-diversity of bacterial and archaeal communities, while the dominant phyla or genera remained the same as RM. RF also improved the interactions among soil microbes and the functional diversity of dominant network modules, but its effect on network stability was unclear. Based on FAPROTAX prediction of functions, RF strengthened the positive relationship between methane oxidation and nitrogen fixation compared to RM. However, RF weakened the relationship between nitrification and methane production/denitrification, as well as the relationship between methane oxidation and denitrification. The canonical correlation analysis results demonstrated that, compared to RM, RF reduced the effects of soil organic matter, available N, and available P contents on soil microbial community structure but enhanced the effects of soil total phosphorus content and soil pH.

Conclusion In Qingtian, the traditional rice-fish co-culture system increased the α-diversity of soil microbial communities, global microbial interactions, and the complexity of microbial networks. However, traditional RF simplified the relationships between different microbial functional groups involved in methane and nitrogen cycling. Our findings provide a basis for further research on the microbial ecological processes in rice-aquatic animal co-culture systems.