Interaction of Microbiota between Fish and the Environment of an In-Pond Raceway System in a Lake

Due to its ability to collect and remove aquaculture waste, an in-pond raceway system (IPRS) has been used to decrease the uncontrolled waste discharge in the traditional cage aquaculture method in large water bodies. However, when applied to large water bodies, its environmental performance is still lacking. This study focused on analyzing the microbial characteristics and the interaction between largemouth bass (gill and gut) microbiota and the environment (water and sediment) microbiota of an IPRS. Further, it revealed the primary relationship from the perspective of microbiota in the IPRS. The results show that (1) the alpha diversity of microbiota in the water is significantly lower than that of fish and sediment. The relationship between water microbiota and fish microbiota is limited. (2) The water microbiota inside and outside the tank showed high similarity and were not significantly affected by environmental factors. (3) The SourceTrack analysis showed that fish microbiota is one of the primary sources of sediment microbiota, and more than 15% of the sediment microbiota come from fish. Microbes such as Faecalibacterium, Escherichia-Shigella, and Bacteroides can significantly enrich the sediment. Our study revealed the characteristics and preliminary interaction of fish and environmental microbiota in the IPRS. It provided a reference for evaluating microbial health status in the application of IPRS in large water bodies’ aquaculture.