Alterations in Soil Bacterial Community and Its Assembly Process within Paddy Field Induced by Integrated Rice–Giant River Prawn (Macrobrachium rosenbergii) Farming

Abstract

Integrated rice–aquatic animal farming has become a vital strategy for enhancing food security. To assess the effects of integrated rice–giant river prawn (Macrobrachium rosenbergii) farming (IRPF) on agricultural ecosystems, we used 16S rRNA gene sequencing to analyze soil bacterial communities in comparison with traditional rice monoculture (RM). Our study revealed that the IRPF did not significantly affect the diversity of the soil bacterial community. However, during the initial culture stage, IRPF markedly increased the relative abundance of the phylum candidate division NC10 and the genus Candidatus Methylomirabilis, enhancing nitrogen-cycling-related functions within the bacterial community. Additionally, IRPF reduced the complexity and stability of these communities in the early to middle culture stages. While stochastic processes usually dominate the assembly of these communities, IRPF restricted bacterial migration and reduced the influence of these stochastic processes. Furthermore, IRPF had a significant impact on environmental factors within paddy soils, strongly correlating with shifts in bacterial communities, particularly through variations in soil nitrite concentration. In conclusion, the influence of IRPF on the bacterial community in paddy soils was primarily observed during the early and middle culture stages, and the impacts of IRPF on the soil bacterial community were primarily driven by environmental changes, especially soil nitrite concentration. These findings provide theoretical insights and a reference for understanding the microbiological impacts of different integrated rice–fish farming systems on agricultural ecosystems.