Microbial community dynamics and its correlation with environmental factors in the water of polyculture ponds containing Penaeus japonicus, Portunus trituberculatus and Sinonovacula constricta

Microbes play an important role in circulating material and regulating energy flow and water quality control in aquaculture systems. To reveal the dynamics of microbial community in polyculture pond and the environmental factors affecting this change, one hundred water samples were collected from 4 polyculture ponds containing Penaeus japonicus, Portunus trituberculatus, and different stocking densities of Sinonovacula constricta (SC, 0 kg/ha; SCC1, 37.5 kg/ha; SCC2, 75 kg/ha; and SCC3, 112.5 kg/ha), and the species composition of the microbial community and its association with environmental factors were analyzed. The alpha diversity of the microbial community was significantly different among SC, SCC1, SCC2, and SCC3. The main dominant phyla in polyculture ponds were Cyanobacteria, Proteobacteria, Actinobacteriota, and Bacteroidetes. However, the relative abundances of these dominant phyla in the four ponds varied among months. Additionally, the four ponds had different biomarkers in different months. Bacteroidetes were biomarkers in SC in July and SCC1 in August, and Gemmatimonadetes were biomarkers in SC, SCC1, and SCC3 in November. Cyanobacteria were biomarkers in SC, SCC1, SCC2, and SCC3 in December. Significant differences in the beta diversity of the microbial community were observed among the four ponds (P < 0.05). Based on these results, coculture of S. constricta in shrimp and crab polyculture ponds may alter the species composition of the microbial community, resulting in changes in material cycle. The pH and NH4+ concentration seemed to be the important environmental factors responsible for the differences. The results of this study might be helpful for understanding the microecological environment of polyculture ponds and provide a reference for environmental optimization based on the regulation of the microbial community.