Effects of the Rice–Red Claw Crayfish (Cherax quadricarinatus) Co-Culture System on the Soil Quality in Paddy Fields

Soil degradation is closely related to the core issue of food security, making the assessment and monitoring of paddy soil quality particularly important. To clarify the impact of a rice–red claw crayfish co-culture on paddy soil quality, this research established two experimental groups: a rice monoculture and a rice–red claw crayfish co-culture. Using 16S rRNA and 18S rRNA sequencing technologies, we systematically compared soil characteristics, microbial diversity, and community composition under the two modes. Principal component analysis based on a minimum data set was employed to integrate soil property parameters with bacterial and eukaryotic microbial community indicators for a comprehensive assessment of the paddy soil quality index. The results showed that the rice–red claw crayfish co-culture substantially increased soil total nitrogen, available nitrogen, total phosphorus, available potassium, and cation exchange capacity. Simultaneously, the rice–red claw crayfish co-culture significantly influenced the beta diversity and composition of bacterial and eukaryotic microbial communities, significantly increasing the relative abundances of Bacteroidota, Cyanobacteria, Verrucomicrobiota, Arthropoda, Cryptomycota, and Nematoda. The soil quality index under the rice–red claw crayfish co-culture was markedly higher than that under the rice monoculture. In summary, a rice–red claw crayfish co-culture can enhance soil fertility and improve overall soil quality. By incorporating microbial community parameters into the evaluation index system, this study confirms that the rice–red claw crayfish co-culture system is indeed a sustainable agricultural practice, providing a theoretical basis for refining the soil quality assessment framework for rice–aquatic animal-integrated farming systems.