Frog Density and Growth Stage of Rice Impact Paddy Field and Gut Microbial Communities in Rice–Frog Co-Cropping Models

The black-spotted frog (<i>Pelophylax nigromaculatus</i>) is a common economic species in the rice-frog ecological cropping mode. The present study investigated microbial community structures in paddy water and black-spotted frog's guts across rice monoculture and low-/high-density rice-frog co-cropping systems at four rice growth stages. Proteobacteria dominate in paddy water, while frog guts are enriched in Firmicutes and Actinobacteriota. The frog density shows no impact on the α-diversity, but rice growth stages significantly alter the Shannon, Simpson, and Pielou_e indices (<i>p</i> < 0.01). Co-cropping may promote amino acid synthesis, elemental cycling, and stress tolerance in paddy water microbiota, which are more diverse than gut microbiota. Strong correlations exist between paddy water and gut microbiotas, with <i>Limnohabitans</i> being linked to gut diversity (<i>p</i> < 0.05). Low-density co-cropping enhances <i>Xenorhabdus</i>, which is beneficial for pest control and stabilizes gut microbiota. The results of this study offer insights for managing rice-frog systems based on rice growth stages.