| Abstract: The aquaponics system, as an integrated ecological agriculture model, effectively combines aquaculture and the cultivation of aquatic plants, which not only utilizes the nutrients in the aquaculture water to promote plant growth but also purifies water quality through plant absorption, reducing the discharge of aquaculture waste and providing new ideas for the green transformation of the aquaculture industry. During the operation of the aquaponics system, microorganisms play an important role in elemental cycling, water quality purification, maintaining ecological balance, and regulating the healthy growth of flora and fauna. The co-occurrence of bacteria and microeukaryotic species in aquaculture water is a common ecological phenomenon, yet research on the interactions between bacterial and microeukaryotic communities is still relatively limited. Currently, there is insufficient research on the complexity and structural characteristics of microbial community diversity in aquaculture waters of aquaponics systems, and the interaction relationship between bacteria and microeukaryotic communities remains unclear, which restricts the optimization and regulation of system operation through microbial means. This study constructed an aquaponics system as the experimental group and a recirculating water system as the control group, conducted a 78-day aquaculture experiment, collected water samples from the aquaculture ponds, and employed high-throughput sequencing technology targeting 16S rRNA and 18S rRNA genes to assess the diversity and structural composition of microbial communities in aquaculture waters from different treatment systems. This study revealed the differences in microbial community composition, bacterial networks, microeukaryotic networks, and bacterial-microeukaryotic interaction network structures between different systems, aiming to clarify the differences in bacterial and microeukaryotic community diversity, structure, and composition between the aquaponics system and the recirculating water aquaculture system, and to understand the structural differences in the microbial community co-occurrence networks between systems, providing a theoretical basis for establishing aquaponics systems from a microbial mechanism perspective. The research indicated that the Observed species index, Chao1 index, and Pd_faith index of the bacterial community in the CK group were significantly higher than those in the Aq group (p < 0.05), and there was a significant difference in the structure of the microeukaryotic community (ANOSIM R = 0.082, p = 0.036). There were significant differences in the diversity of bacterial communities and the structure of microeukaryotic communities among different treatment groups. At the phylum level, Bacteroidota and Fusobacteriota exhibited increased relative abundances in the aquaponics group, whereas the relative abundance of Chlorophyta was lower than that in the control group. The relative abundance of Chlorophyta in the aquaponics group continuously decreased over time, while in the recirculating aquaculture group, its relative abundance consistently increased. At the genus level, Flavobacterium, Cetobacterium, and Anurofeca demonstrated higher relative abundances in the aquaponics group than in the control group. There were significant differences in the composition and relative abundance of dominant bacterial and microeukaryotic groups between the Aq and CK groups. Analysis of the microbial community co-occurrence network showed that the bacterial community and microeukaryotic community in the Aq group had more complex interactions and network structures than in the CK group, with more pronounced competition relationships among microbial communities and greater stability. Additionally, the network structure of microeukaryotic communities in both the Aq and CK groups was more complex than that of bacterial communities, with more intense internal competition and greater stability. Bacterial-microeukaryotic interaction network analysis indicated that in the Aq group, Bacteroidota and Chlorophyta were core nodes of the bacterial-microeukaryotic interaction network. In the CK group, Proteobacteria and Fusobacteriota were core nodes of the bacterial-microeukaryotic interaction network. It can be inferred that there are substantial differences in the interaction relationships between bacterial and microeukaryotic communities and the proportion of various groups between the Aq and CK groups, with the interaction relationships between bacterial and microeukaryotic communities in the CK group being more complex and closer than those in the Aq group, which exhibited more antagonistic relationships. This study analyzed the differences in the diversity, composition structure, and co-occurrence networks of bacterial and microeukaryotic communities between the aquaponics and recirculating water aquaculture systems. The growth performance, immunity, and digestive function of fish in the aquaponics system were significantly better than those in the recirculating water aquaculture system, highlighting the advantages of the aquaponics system. This research elucidated the microbial community characteristics of the aquaponics and recirculating water aquaculture systems and revealed the interaction relationships between bacterial and microeukaryotic communities under both aquaculture modes, aiming to provide a microbial theoretical basis for the stable operation of aquaponics systems. |
