Fig. 1

The workflow for systematically assessing the sustainability of the RCFP and other aquaculture models from the perspective of aquaculture model-specific microbial community patterns, multi-kingdom interactions, horizontal gene transfer (HGT) events, and environmental factors driving microbial community divergence. A Water, sediment, crayfish gut, and crab gut samples were collected from four representative aquaculture models: crab-crayfish culture model (CCFP), crab culture model (CP), crayfish culture model (CFP), and rice- crayfish co-culture model (RCFP). B The inhabiting habitats for the microbial community. C The aquaculture model-specific microbial community patterns of water, sediment, crayfish gut, and crab gut habitats. D Comparison of multi-kingdom interactions (bacteria, archaea, viruses, and eukaryotes) between RCFP and other aquaculture models in water, sediment, and crayfish gut habitats, respectively. E HGT events detecting across kingdoms between RCFP and other aquaculture models in water, sediment, and crayfish gut habitats, respectively. F The response of the multi-kingdom microbial community to environmental factors