By reconstructing a multifunctional intensive microbiome, effective microorganisms (EM) improve the ecological environment of rice–crayfish cocropping

Abstract

Integrated rice and aquaculture farming is a high-intensity agricultural model that efficiently utilizes soil and water resources. However, soil ecological issues caused by overexploitation of this model may jeopardize rice production and food security. Given the requirements of aquatic animal breeding circumstances, the application of biological agents has become the preferred choice for improving the environment in this model. In this study, the rice–crayfish cocropping (RC) model was used as the research object, and the widely used bio-fertilizer Effective Microorganisms (EM) was employed as a biological amendment. This study seeks to clarify the improvement effect of EM on the soil and water environment of the RC model as well as to explore its microbiological mechanism. The findings demonstrated that EM significantly improved the chemical properties of the model, for example, the dissolved oxygen in water increased by about 44%, and the redox potential in soil increased by about 150% over the entire rice growing period. Second, the use of EM reduced the soil microbial diversity while reconstructing a more compact and stable microbial cooccurrence network. The reconstructed community selectively enriched the functions related to photosynthesis and nitrogen transformation to cope with the environmental stresses of low dissolved oxygen or high nitrogen. Subsequently, 30 dominant-ASVs (ASV, Amplicon Sequence Variant) with high abundance, strong functionality, positive correlation with environmental factors, and good representation of the community were identified using correlation analysis, abundance comparison, and model prediction. This study not only verified the application effect of EM in a complex agricultural intensive system but also proved that the community induced by EM has a positive effect on ecosystem multifunctionality and identified the key dominant species. This provides strong evidence for us to understand the microbiological mechanisms of exogenous biological agents in environmental improvement and provides a reference for screening and optimizing functional microbial species in agricultural ecosystems.