Abstract:Application of green manure is an effective measure to improve soil fertility and crop yield, which is very important to the structure and diversity of soil microbial community. [Objective] To study the effect of green fertilizer combined with nitrogen fertilizer on microbial community structure in karst paddy soil, clarify the interaction among microorganisms, soil environmental factors, and crop yield, and thereby provide theoretical basis and evidence for the replacement of nitrogen fertilizer with green manure in karst area. [Methods] A three-year experiment was carried out on the typical karst paddy soil with the following four treatments: winter fallow + no nitrogen fertilizer (CK), winter fallow + nitrogen fertilizer (N), green manure + no nitrogen fertilizer (M), and green fertilizer + nitrogen fertilizer (MN). Soil microorganisms were sequenced with high throughput sequencing technology to analyze the effect of different fertilization treatments on bacterial and fungal communities. [Results] Compared with CK, MN significantly increased the early rice yield, and the content of soil organic matter (SOM), total nitrogen (TN), available nitrogen (AN), and available potassium (AK), and decreased the content of available phosphorus (AP). Compared with other treatments, MN significantly raised soil bacterial richness and diversity, while the richness and diversity of fungal community decreased in MN. Chloroflexi, Proteobacteria, and Acidobacteria dominated the bacteria, and Ascomycota, Basidiomycota, and Zygomycota were dominant fungal taxa in the karst paddy soil. Redundancy analysis (RDA) revealed that soil AK was the key factor affecting the composition of soil bacterial community. Co-occurrence network analysis indicated that there were mostly synergistic and reciprocal relationships among microorganisms. The main bacterial groups were from Chloroflexi and Proteobacteria, and the main fungal groups were Ascomycota and Basidiomycota. [Conclusion] The combined use of green manure and nitrogen fertilizer can help increase soil nutrient content, and the effect is better than that of the application of chemical green alone or nitrogen fertilizer alone. Moreover, the combination can improve soil microbiological properties. This study provides evidence for the substitution of green fertilizer for nitrogen fertilizer in karst area.