Long-term integrated rice-crayfish culture disrupts the microbial communities in paddy soil

The integrated rice-crayfish culture (IRCC) mode has been developed for more than twenty years in China, but little information could be obtained on the microbial communities in paddy soil under this mode. This study used 16SrRNA and ITS Illumina high-throughput sequencing to investigate microbial communities, diversity, and function in paddy soil under different IRCC times (0, 2, 4, 6, and 10 years). With increasing culture time, IRCC mode altered the relative abundance of dominant taxa, showing a significant decrease in the relative abundance of Actinobacteria and Chytridiomycota, with an increase in Proteobacteria and Firmicutes. The species richness and diversity of bacteria/fungi in 10-year IRCC paddy soil were significantly lower than in other groups (P < 0.05). Bacterial functional potential prediction by PICRUSt2 and phenotype prediction by BugBase showed that long-term IRCC significantly reduced the relative abundance of carbohydrate metabolism and increased the relative abundance of pathogenic potential and anaerobic phenotype (P < 0.05). Saprotrophs and pathotrophs dominated the fungal communities, and higher relative abundances of the plant pathogens, fungal parasites and lichen pathogens were found in IRCC soil (2- and 4-year) (P < 0.05). Microbial communities were mainly influenced by ammonium nitrogen, nitrate nitrogen, soil moisture content, and total carbon. Long-term IRCC could significantly change microbial communities and functions, while reducing microbial diversity in paddy soil. A "resting period" is recommended to ensure the sustainable development of ecological agriculture in paddy fields.