Metagenomic Insight into the Impact of Soil Nutrients and Microbial Community Structure on Greenhouse Gas Emissions: A Case Study in Giant Rice–Fish Co-Cultured Mode

This study investigates the impact of environmental changes induced by systematic manipulation of flooding depth and breeding density on greenhouse gas emissions in the field-based giant rice–fish hybrid farming model. Compared with traditional agricultural practices, increasing cultured density in giant rice–fish co-cultivation significantly alleviated the adverse consequences of flooding on soil nutrient dynamics, microbial activity community structure, and greenhouse gas emissions. Relative to the traditional alternating wet and dry irrigation, the soil concentrations of ammonium, total nitrogen, and phosphate significantly increased. Cultured fish had significantly increased soil microbial biomass carbon, nitrogen, and phosphorus contents and improved soil β-glucosidase and aryl-sulfatase activates relative to flooding alone. Cultured fish increased the relative abundances of Actinobacteria, Nitrospirae, Planctomycetes, Verrucomicrobia, and Aminicenantes. An increasing cultured fish density reduced cumulative methane and nitrous oxide emissions and GWP (global warming potential). Relative to the continuous flooding throughout the growing period, cumulative methane emissions and GWP in the flooding with high-density cultured fish were reduced by 5.32% and 1.48%, respectively. Notably, this co-cultivation strategy has the potential to transform traditional practices for sustainable agriculture. Nevertheless, it is imperative to remain vigilant about the potential consequences of greenhouse gas emissions associated with these innovative practices. Continuous monitoring and refinement are essential to ensure the long-term sustainability and viability of this agricultural approach.