Effects of farming mode on sediment–water microbial communities and functional potential in rice field eel (Monopterus albus) culture systems

Aquaculture-related environmental problems have attracted increasing attention, particularly in intensive rice field eel ( Monopterus albus ) farming, where high feeding inputs and waste accumulation may accelerate water eutrophication and sediment deterioration. Although microbial responses to cage culture and rice-based integrated farming have been reported, systematic metagenomic comparisons between these two farming modes across both water and sediment remain limited. In this study, shotgun metagenomic sequencing was used to compare microbial community composition and functional potential in water and sediment from rice–eel rotation and cage-culture systems at the stocking and harvest stages. The results revealed clear differences between the two farming modes, especially in sediment. The rice–eel rotation system was enriched in soil- and nutrient-cycling-associated taxa, including Nitrospira , and showed broader metabolic potential related to xenobiotic biodegradation and nutrient transformation. In contrast, the cage-culture system displayed stronger enrichment of taxa associated with reductive metabolism and methanogenesis, particularly at the later culture stage, together with greater representation of functions related to genetic information processing and energy metabolism. Functional annotation further suggested tighter coupling of carbon, nitrogen, and sulfur cycling pathways in the rice–eel rotation system in autumn, whereas the cage-culture system showed stronger signatures associated with reductive sediment processes and potential water-column ecological risk. Overall, these results indicate that farming mode strongly influences the sediment–water microbiome of M. albus culture systems, and suggest that rice–eel rotation may support a more functionally balanced microbial environment for sustainable aquaculture management.