Effects of Stocking Densities on Mud Crab Production and Microbial Community Dynamics in the Integrated Saline Tolerant Rice–Mud Crab (Scylla paramamosain) System

Coastal saline-alkali areas represent huge under-exploited land and water resources. Due to the high salinity, there exists a great discrepancy between the benefits derived from the cultivation of agricultural crops and the cost in terms of manpower and material resources. The mud crab Scylla paramamosain can survive across a wide range of salinity, making it an excellent aquaculture species in crop–fish co-cropping in coastal saline-alkali areas. However, detailed research concerning economic and ecological efficiency remains unclear. This study investigated the effect of stocking density of S. paramamosain co-cropping with salt-tolerant rice on the economic benefits, physiochemical parameters, and the microecological changes. By elaborate management of aquaculture and rice cropping, together with the comprehensive investigation of physiochemical influence on paddy water and soil, microbial community alteration, and functional gene dynamics, we found that an appropriate density of 6000 ind/ha generated the highest net profit, which is more than 9-fold higher than the rice monoculture. In addition, nutrient inflow increased the environmental burden of higher stocking densities. Microbial community composition and structure were altered, as shown by the 16S amplicon sequencing of water and soil samples. Functional gene chips confirmed that the carbon, nitrogen, sulfur, and phosphorus cycle genes in the microbial community contributed to the microecological function. This study proposes a new salt-tolerant rice–mud crab integrated culture mode, which is customized for the underdeveloped saline-alkali areas, and will be helpful in promoting aquaculture as well as sustainable development.