Microorganisms, including bacteria, fungi, and protists, are key drivers in aquatic ecosystems, maintaining ecological balance and normal material circulation, playing vital roles in ecosystem functions and biogeochemical processes. To evaluate the environmental impact of different river crab polyculture practices, we set up two different river crab (Eriocheir sinensis) polyculture practices: one where river crabs were cultured with mandarin fish (Siniperca chuatsi), silver carp (Hypophthalmichthys molitrix), and freshwater fish stone moroko (Pseudorasbora parva), and another where river crabs were cultured just with mandarin fish and silver carp. These two polyculture practices were referred to as PC and MC, respectively. We analyzed the water bacterial, fungal, and protist communities in the PC and MC groups using 16S, ITS, and 18S ribosomal RNA high-throughput sequencing. We found that the PC group obviously increased the diversity of microbial communities and altered their composition. The bacterial community held the narrowest habitat niche and exhibited the weakest environmental adaption compared to fungal and protist communities. The PC group altered the co-occurrence networks of bacteria, fungi, and protist, leading to more complex and stable communities of fungi and protist. Furthermore, the PC group shifted the assembly mechanism of the bacterial community from being predominantly deterministic to predominantly stochastic processes, with relatively minor impacts on the fungal and protist communities. Environmental factors, especially dissolved oxygen (DO), were significantly associated with the communities of bacteria, fungi, and protists, with DO being the major contributor to changes in the microbial communities. Our results suggest that the polyculture of river crab with mandarin fish, silver carp, and stone moroko was an effective and viable attempt, and it was superior in terms of microbial community diversity and stability.

Integrated aquaculture, centered around polyculture involving multiple species, is a typical practice for the sustainable development of the aquaculture industry, capable of enhancing resource utilization efficiency, environmental stability, and overall productivity through establishing symbiotic interactions among species. This study employed multi-amplicon high-throughput sequencing to assess the ecological impacts of two polyculture methods involving river crabs on sediment bacteria, fungi, and protists. One method involved polyculturing river crabs with mandarin fish, silver carp, and the stone moroko (SPC), and the other involved polyculturing river crabs with only mandarin fish and silver carp (SMC). The results showed that, compared to the SMC group, the SPC group remarkably increased the Chao1 index of bacterial communities in pond sediment and decreased the Pielou_J index of protists. The relative abundances of all fungal phyla and most dominant bacterial and protistan phyla (top 10 in relative abundance) in the SPC group were considerably different from those in the SMC group. In the co-occurrence networks of bacterial, fungal, and protistan communities, the numbers of edges and nodes were higher in the SPC group than in the SMC group, and the habitat niche breadth of bacterial community was also notably increased in the SPC group. The levels of total carbon (TC), total nitrogen (TN), and phosphates within pond sediment in the SPC group were obviously lower than those in the SMC group, and were significantly correlated with the microbial communities, with TC being identified as the primary contributor driving changes in the microbial communities. All the findings collectively demonstrate that the polyculture of river crabs with mandarin fish, silver carp, and the stone moroko enhances the stability of bacterial, fungal, and protistan communities in sediment and enhances resource utilization efficiency in aquaculture, thereby preventing the environmental risks associated with excessive nutrient accumulation in sediment. Polyculture systems integrating river crabs with mandarin fish, silver carp, and the stone moroko represent a sustainable aquaculture model with significant ecological benefits.