Reconstruction of soil microbiome and elemental cycling by a synthetic microbial community: A sustainable strategy for improving paddy soil fertility and rice production under agrochemical reduction

Abstract

Intensive rice cultivation often relies on substantial agrochemical inputs to maintain soil fertility and crop productivity, creating challenges for sustainable paddy management. In the present study, a field trial combined with metagenomic sequencing was performed to uncover the responses of rice, paddy soil, and the soil microbiome to a synthetic microbial community (SynCom) containing some photosynthetic bacteria and Bacillus species under a 50% reduction in agrochemical inputs. Agronomic detection showed SynCom increased rice yield by 3.4%, elevated polished rice rate and grain protein, and drastically reduced the yellow rice and lodging rate. Continuous soil monitoring demonstrated obvious increases in soil organic matter, available nitrogen, and total phosphorus across the whole growing period. Metagenomic analyses further illustrated that SynCom restructured soil microbiota, enriched nutrient-metabolizing taxa including Nitrospirota, Chloroflexota, and Anaeromyxobacter, and might have strengthened positive interspecific cooperation of microbes. Additionally, the increased abundance of some functional pathways associated with C/N/S/P mineralization potentially promoted soil nutrient activation. This study reveals the multi-level regulatory pathway of SynCom and supplies theoretical support for green, chemical-saving sustainable rice production.