Metagenomics-Based Analysis of Microbial Community Structure and Function Composition in Aquaculture Pond for Chinese Mitten Crab (Eriocheir sinensis)

The structure and function of microbial communities in aquaculture water bodies are important in the aquaculture ecosystem. To comprehensively and systematically evaluate the structure and functional composition of the microbial community in the water during Chinese mitten crab (Eriocheir sinensis) cultivation, the water quality indicators in the crab pond in Chongming District, Shanghai were monitored monthly from June to October 2022. The microbial species and functional structural characteristics in the water environment during the breeding period were analyzed based on metagenomics technology, and their relationships with environmental factors were discussed. The results showed that the major water quality indicators that exceeded the standard in the breeding pond were pH, permanganate index, total phosphorus, and total nitrogen. During the breeding period, the diversity of the microbial community in the water body from June to August and the richness of the microbial community from July to August were high, and the dominant microbial phyla in the water body were mainly Proteobacteria, Bacteroidetes, Actinobacteria, Verrucomicrobia, Cyanobacteria, and Uroviricota. At the genus level, the top 10 dominant genera regarding abundance were significantly different among multiple groups. For example, the abundances of Microcystis bacteria in July and unclassified_o_Caudovirales viruses in August–October were significantly higher than those in other months. The primary function of microorganisms is metabolism, including energy metabolism, global and overview maps, and amino acid metabolism. Notable differences are present in the functional composition of different months; particularly, the abundance of metabolic pathways in June–July was significantly higher than that in August–October, and the dominant bacteria (Proteobacteria, Actinobacteria, and Bacteroidetes) were major contributors to the aforementioned functions. The influence trends of environmental factors on the structure and functional composition of microbial communities were consistent. Chlorophyll a and pH had the most significant impact on the structure and functional composition of microbial communities, whereas dissolved oxygen and total phosphorus had a slightly weaker impact. The pathogenic bacteria with a relatively large abundance in aquaculture water bodies are Salmonella enterica, Edwardsiella ictaluri, and Staphylococcus aureus. The research results provide basic data for the study of microbial community structure and functional composition in water bodies of Chinese mitten crab breeding ponds and can provide a theoretical basis for aquaculture water quality control and ecosystem construction.