Rice–crayfish farming mode drives distinct soil properties and ecological assembly of soil microbiome

Rice–crayfish farming (RCF) system represents an effective ecological agricultural model characterized by the cyclical spatiotemporal integration of rice farming and crayfish aquaculture. However, the effects of farming mode and stage on soil microbial community structure over time remain insufficiently explored. In this study, we investigated taxonomic and functional changes in soil microbiomes and their associations with soil nutrient fertility in both RCF and rice monoculture (RM) systems. Our findings demonstrated that RCF significantly increased soil pH, total nitrogen (TN), and soil organic carbon (SOC) compared to RM across multiple growth stages ( P < 0.05). Two-way analysis of variance showed that both mode and stage affected the Chao1 index, while the Shannon index was only affected by stage. Microbial community analysis revealed clear structural differences between the two systems ( P < 0.001). Functional prediction indicated lower chemoheterotrophy but higher photoheterotrophy, aromatic degradation, and sulfur cycling in RCF, along with reduced nitrogen cycling function. Co-occurrence network analysis further showed a longer average path length and higher modularity in RCF than in RM. Modules 3 and 6 in RCF were positively correlated with pH, TN, and SOC. Overall, RCF stabilizes the soil environment and selects for specific functionally sensitive taxa, thereby promoting the formation of a highly modular microbial network, which ultimately maintains the synergistic stability of soil nutrients and the microbial community.

IMPORTANCE

The present study comprehensively compared two different farming modes in terms of their soil microbiome structures and the associations between the microbiomes and soil nutrient fertility. Rice–crayfish farming (RCF) model-specific microbial taxa were identified, and their modularity was found in RCF. These findings provide valuable insights into microbial community responses and regulation in ecological agriculture, establishing a robust microbiological foundation for optimizing rice-aquatic animal integrated farming management and advancing sustainable agricultural practices.