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Microbiome Diversity and Dynamics in Lotus–Fish Co-Culture Versus Intensive Pond Systems: Implications for Sustainable Aquaculture
by
Qianqian Zeng
1,†, 
Ziyi Wang
1,†,
Zhongyuan Shen
1,
Wuhui Li
1,2,
Kaikun Luo
1,
Qinbo Qin
1,2,
Shengnan Li
1,* and
Qianhong Gu
1,* 1
Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha 410081, China
2
Hunan Yuelu Mountain Science and Technology Co. Ltd. Amid at Aquatic Breeding, Changsha 410081, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Biology 2025, 14(8), 1092; https://doi.org/10.3390/biology14081092
Submission received: 18 July 2025
/
Revised: 13 August 2025
/
Accepted: 14 August 2025
/
Published: 20 August 2025
(This article belongs to the Collection Feature Papers in Microbial Biology)
Simple Summary
This study employed integrated metagenomic and environmental analyses to elucidate the ecological roles of microbial communities (viruses, archaea, fungi) in lotus–fish co-culture (LFC) systems versus intensive pond culture (IPC), focusing on their impacts on water quality, sediment health, fish gut immunity, and ecosystem sustainability. The LFC system efficiently decreased the concentration of total nitrogen, total phosphorus, chemical oxygen demand in water, and organic matter in sediment via plant–microbe symbiosis. Simultaneously, LFC mediated the structure of microbial communities: archaea enhanced ammonia oxidation and organic matter degradation, which helped counterbalance methanogenesis, whereas the richness of fungi in sediment and fish gut promoted ecological self-purification. The suppression of viral diversity in water helped to reduce pathogen risks. LFC advances sustainable aquaculture by strengthening ecological resilience and health in large-scale operations, achieving dual goals of high productivity and environmental stewardship via closed-loop resource cycling.
Abstract
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, showing higher ecological self-purification ability and sustainability potential in LFC. Collectively, LFC's optimized archaeal–fungal networks strengthened host immunity and environmental resilience, while viral community suppression reduced pathogen risks. These findings elucidate microbiome-driven mechanisms underlying LFC’s ecological advantages, providing a framework for designing sustainable aquaculture systems through microbial community modulation.
