Integrated Rice-Snail-Crayfish Farming System Shapes Soil Microbial Community by Enhancing pH and Microbial Biomass in South Subtropical China

Within the framework of sustainable agriculture, the integrated rice-snail-crayfish farming system has been recognized as a highly efficient agroecological approach that enhances crop production while minimizing the application of chemical fertilizers and pesticides. Nonetheless, the mechanisms by which this system influences soil microbial community composition to achieve these benefits remain unknown. In this study, we focused on traditional rice farming (TR), the integrated rice-snail-crayfish (R-S-C) farming system, and mono-rice farming (CK), and systematically examined the impacts of these farming systems on soil chemical properties, microbial biomass, enzyme activity, and microbial community composition. Our results showed that the R-S-C significantly increased soil pH, microbial biomass carbon (MBC), and the MBC/microbial biomass phosphorus (MBP) ratio compared to TR, as well as the peroxidase activity. Moreover, the R-S-C significantly increased soil total phospholipid fatty acid (PLFA), bacterial PLFAs, Gram-negative bacterial (GN) PLFAs, anaerobic bacteria PLFAs, arbuscular mycorrhizal fungi (AMF) abundances, and the bacteria/fungi ratio compared to the other two systems. However, the soil microbial α-diversity indices, including Shannon–Wiener index (H), Simpson index (D), and Pielou evenness index (J), were significantly lower in the R-S-C system than in the other two systems. Further exploration suggested that soil pH, microbial biomass nitrogen (MBN), the MBN/total nitrogen (TN) ratio, and the MBC/MBP ratio were critical factors governing microbial community composition under the three farming practices. Notably, soil pH alone accounted for 64.5% of the observed variation in microbial community composition. Path analysis using partial least squares structural equation modeling further revealed the pathways by which the R-S-C system enhanced total PLFAs, AMF, and gram-positive bacteria by regulating the soil pH and MBN/TN ratio. This study provides insights into the regulatory mechanisms driving soil microbial communities in the R-S-C system and offers a theoretical foundation for developing sustainable agricultural management practices.