Integrated rice–crayfish farming system is a highly efficient artificial ecosystem in which the rice (Oryza sativa) variety ‘Jianzhen 2′ is cultivated in waterlogged paddy fields along with crayfish (Procambarus clarkii). We investigated soil carbon fractions and microbial community structure by phospholipid fatty acids (PLFA) analysis in a 10-year field experiment using an integrated rice–crayfish (CR) model and a rice monoculture (MR) model at soil depths of 0–10 cm, 10–20 cm, 20–30 cm, and 30–40 cm. Compared with the MR model, the CR model had significantly more total organic carbon, particulate organic carbon, and dissolved organic carbon contents in all of the layers examined and microbial biomass carbon content in the 20–40 cm layer. Principal components analysis revealed that microbial community composition in the CR model differed from that in the MR model in the 20–30 cm layer. Higher proportions of gram–negative bacteria, aerobic bacteria and fungi in the 20–30 cm soil layer were observed for the CR model than the MR model. These results indicate that the CR model increases soil carbon levels, and strongly affects microbial community composition and structure in the deeper layers of soil, thereby accelerating subsurface soil nutrient cycling.

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This study presents an investigation of soil chemical properties and microbial community diversity by Biolog ECO analysis in a seven-year field experiment using winter flooded fallow + no straw returning (W), winter flooded fallow + straw returning (WS), and winter flooded fallow + straw returning + crayfish farming (WSC) at soil depths of 0–10 cm and 10–20 cm. Compared with the WS treatment, the WSC treatment had significantly higher total organic carbon (TOC) content in the 0–10 cm layer as well as greater available nitrogen (AN) and total nitrogen (TN) contents and acid phosphatase and sucrase activities in the 10–20 cm layer, while the pH value, total reducing substances, and Fe2+ content in the 0–20 cm layer were considerably lower. The WSC treatment improved the microbial species abundance in the 10–20 cm layer and the utilization rate of carbon sources in the 0–20 cm layer compared with the WS treatment. The soil microbial species abundance, microbial community diversity, and utilization rate of carbon sources in all of the layers examined were significantly higher in the WSC treatment than in the W treatment. The results indicate that straw returning under the rice-crayfish integrated system improves the contents of TOC, TN, and AN, decreases reducing substances properties, increases acid phosphatase and sucrase activities, and improves microbial community functional diversity, thereby contributing to the improvement of soil quality and the long-term sustainable development of the rice-crayfish integrated system.