Enhanced rice yields are related to pronounced shifts in soil resident bacterial community structures in response to Rhodopseudomonas palustris and Bacillus subtilis inoculation

Microbial inoculation is a promising way to improve soil fertility in an eco-friendly manner. Despite the extensive studies of microbial inoculation used for soil biofertilization, their influences on the soil resident microbial community compositions and functions remain poorly understood. Here, we conducted a 130-day pot experiment to test the effects of single and co-inoculation of Rhodopseudomonas palustris and Bacillus subtilis on soil resident bacterial community through sequencing soil microbial 16S ribosomal RNA gene amplicons, as well as the yield and agronomic traits of the rice plant. Microbial inoculations significantly improved the rice yields by 9.84–17.73% (p < 0.05), and R. palustris and B. subtilis inoculant showed synergistic effects on rice yields. The agronomic traits of the rice plants were rarely influenced by the inoculations. We observed that the Shannon diversity of soil resident bacteria remained; however, the community composition changed profoundly with microbial inoculants. The co-inoculation with R. palustris and B. subtilis led to the shift of the relative abundances of plant growth–promoting bacteria in soils, such as Microbacter. The structural equation modeling suggested that soil bacterial community composition greatly contributed to the yield and agronomic traits of the rice plants (r = −0.36 to −0.88, p < 0.05). The soil bacterial community also indirectly mediated the plant growth by affecting microbial enzymatic activities involved in carbon and phosphorus cycling in soils. In general, microbial inoculants directly and indirectly through mediating the soil resident communities enhanced the rice yields.