Enhancing biomass and ecological sustainability in rice–fish cocropping systems through the induction of functional microbiota with compound biogenic bait

Traditional commercial aquatic fish bait (CA) is not conducive to the scientific breeding of rice and fish in cocropping systems, and excessive feeding easily causes environmental pollution in rice fields. In this study, an environment-friendly compound biogenic bait (CB) mixed with plant-derived (PB) and animal-derived (AB) baits was proposed. The rice–crucian carp cocropping system was used as the research object, and the soil microorganisms and fish gut microorganisms were sequenced with high throughput, respectively, to verify the effect of CB application and the microbial mechanism underlying its functional effect. The results showed that the AB and PB components in CB maintain the growth of fish by improving the metabolism-related functions of fish gut microbiome and reducing the abundance of intestinal pathogenic bacteria, including Actinomadura. In particular, the PB components induced soil microbiome, such as Pseudonocardia, that participate in soil nutrient cycling and increase dissolved oxygen in water, which is key for improving rice quality and yield. This is the first study to focus on how different bait components drive key microbial communities to regulate animal–plant–environment relationships in the integrated planting and breeding patterns of paddy fields.