Microbiome and transcriptome analyses reveal the influence of calcined dolomite application on Eriocheir sinensis in a rice–crab co-culture system

Abstract Co-culture systems of rice and aquatic animals can contribute to the ecological intensification of agriculture by reducing nutrient loss and the need for N fertilizer application and by enhancing nutrient-use efficiency. However, the input of high-protein diets into paddy fields, to facilitate the growth of aquatic animals, has been found to increase N pollution and acidification of the soil. Although soil amendments have been widely used to ameliorate acidic soils, reduce N2O emissions, and improve agronomic production, the relationship between soil amendments and aquatic animal remains unclear. Therefore, this study investigated the effects of calcined dolomite (hereafter referred to as dolomite) as an acidic soil amendment and Ca–Mg supplement in rice–crab co-culture using Eriocheir sinensis crabs (Chinese mitten crabs). High-throughput sequencing was used to examine crab bacterial community composition and crab hepatopancreas biology. Although the water pH was significantly increased in the dolomite group, the number, composition, and diversity of bacteria identified in crab gut microbiome did not vary significantly between the dolomite and control groups. In the dolomite group, the probiotic agents Candidatus Hepatoplasma and Lactobacillus were highly abundant in the crab gut, and immune- and retinol metabolism-related genes were significantly upregulated in the crab hepatopancreas. Overall, dolomite application increased crab health and water pH. Dolomite is a low-cost amendment, with better stability, compared to other soil amendments, thus making it ideal for sustainable and clean rice–aquatic animal co-culture.