Abstract
Individual applications of biochar (B) or organic manure (M) have been reported to improve soil fertility and plant performance. Their synergistic effects on paddy soil physicochemical properties, microbial communities, and rice productivity remain under explored. This study investigated the effects of B (20 t ha(− 1)), M (15 t ha(− 1)), and their combined application (BM, 10 + 7.5 t ha(− 1)) on soil physicochemical properties, microbial communities, rice plant growth and yield. Our findings revealed that B, M, and BM significantly improved soil physicochemical properties compared to control (CK). BM enhanced total nitrogen and available phosphorus by 34% and 26%, respectively, compared to CK. Soil pH, soil organic carbon, available nitrogen, and available potassium showed higher values in all treatments compared to the CK, with no significant differences among B, M, or their combined applications. Chlorophyll a, b, plant growth, dry matter and yield attributes showed the trend of BM > M > B > CK. These changes were attributed to the enhancement of beneficial soil bacteria, including Proteobacteria, Firmicutes, Actinobacteria and Bacteroidota in the BM treatment. Individual biochar treatment reduced Chloroflexi and Firmicutes but increased Proteobacteria and Actinobacteria. In contrast, individual manure application enhanced Firmicutes and Nitrospirota. Among fungal communities, Chaetomium and Pinnularia showed higher relative abundances in the combined treatment, playing roles in organic matter decomposition and plant growth, respectively. We conclude that the integrated use of biochar and manure enhances rice performance primarily by fostering a soil microbiome conducive to nutrient cycling and plant growth. Combined B + M application is therefore recommended as a sustainable strategy for improving paddy soil quality and crop yield. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-025-06834-x.