Metagenomic insights into carbon and nitrogen cycling functions in an integrated rice-crayfish farming system with straw return

Straw return is an important strategy for agricultural residue utilization, and functional microbial communities are known to play a pivotal role in straw decomposition and nutrient cycling. Nevertheless, the decomposition dynamics and associated microbial functional outcomes in rice-aquaculture systems remain poorly documented. This study established a rice-crayfish integrated system with straw return and assessed the mechanisms of straw decomposition and the resulting improvement on soil fertility through soil physicochemical characterization, enzyme activity assays, and metagenomic sequencing. Soil samples were obtained in July (PF7, the rice transplanting stage following the crayfish farming period) and November (PF11, the post-harvest field drying period), with surrounding ditches as controls (CK7 and CK11). The results showed that straw was effectively decomposed, releasing potassium and nitrogen nutrients, while urease and cellulase activities were markedly increased in the paddy field. Metagenomic analysis revealed that Pseudomonadota was the dominant phylum, whereas Euryarchaeota and Nitrososphaerota exhibited the most pronounced changes, with their abundances in PF11 being 0.23-fold and 10.57-fold of those in CK11, respectively. In the C cycle, C degradation was the most abundant pathway, in which amino acid degradation (primarily derived from crayfish farming) dominated, followed by aromatic compound degradation (associated with straw decomposition). For the methane metabolic pathway, the greenhouse gas emission potential was reduced, as evidenced by lower mcrA abundances in PF than in CK. N cycling was primarily mediated through organic N metabolism (81.63–84.14%), with the remaining fraction dominated by nitrification and denitrification. Furthermore, the relevant analysis consistently indicated that C cycling genes occupy more central positions and TN showed a negative effect on these genes. Collectively, this integrated system was associated with straw decomposition, facilitated terminal organic C and N mineralization, while greenhouse gas-related functional potentials were reduced, supporting sustainable straw utilization in rice-crayfish agroecosystems.