Microbiome Diversity and Dynamics in Lotus–Fish Co-Culture Versus Intensive Pond Systems: Implications for Sustainable Aquaculture

作者：Qianqian Zeng, Ziyi Wang, Zhongyuan Shen, Wuhui Li, Kaikun Luo, Qinbo Qin, Shengnan Li, Qianhong Gu · 发表于：Biology · 年份：2025 · DOI：10.3390/biology14081092 · 被引用次数：2 · 研究领域：Aquaculture disease management and microbiota、Microbial Community Ecology and Physiology、Gut microbiota and health

The lotus–fish co-culture (LFC) system leverages plant–fish symbiosis to optimize aqua-culture environments, enhancing both economic and ecological yields. However, the eco-logical mechanisms of microbial communities in LFC systems remain poorly understood, particularly regarding the functional roles of fungi, archaea, and viruses. This study compared microbiota (viruses, archaea, fungi) in water, sediment, and fish (crucian carp) gut of LFC and intensive pond culture (IPC) systems using integrated metagenomic and environmental analyses. Results demonstrated that LFC significantly reduced concentrations of total nitrogen, total phosphorus, and nitrite nitrogen and chemical oxygen demand in water, and organic matter and total nitrogen in sediment compared to IPC. Community diversity analysis, LefSe, and KEGG annotation revealed suppressed viral diversity in LFC, yet increased complexity and stability of intestinal virus communities compared to IPC. Archaeal and functional analyses revealed significantly enhanced ammonia oxidation and OM decomposition in LFC versus IPC, promoting methane metabolism equilibrium and sediment organic matter decomposition. Moreover, crucian carp intestines in LFC harbored abundant Methanobacteria, which contributed to maintaining a low hydrogen partial pressure, suppressing facultative anaerobes and reducing intestinal infection risk. The abundance of fungi in sediment and crucian carp intestine in LFC was significantly higher than that in IPC, sho...