Objectives Microbial fertilizer is effective to improve soil fertility and promote crop growth. We studied the effects of single- and co-inoculation of two microbial fertilizers on rice rhizosphere and rhizoplane bacterial diversity and function.

Methods A rice pot experiment was conducted, and four treatments were set up, i.e. clean water as control, single inoculation of Rhodopseudomonas palustris (R. palustris), single inoculation of Bacillus subtilis (B. subtilis), and co-inoculation of both (Mix). At harvest of rice, soil samples were collected around rice plant of 10 cm × 10 cm× 10 cm, and rhizoplane and rhizosphere samples were separated from the soil samples, to determine bacterial diversity and function by 16S rDNA high-throughput sequencing and functional prediction.

Results All the three biofertilizer treatments increased rice yield and the setting rate, of which Mix treatment increased the most by 13.7% and 17.2%, respectively. All the three biofertilizer treatments did not change soil physicochemical properties significantly at harvest stage of rice. Compared with control, the application of the two functional bacteria did not significantly affect the diversity and function of rhizosphere bacterial community, but single-inoculation of B. subtilis and co-inoculation reduced Chao1 richness and Shannon-Wiener index of rhizoplane bacterial community. An increase in the relative abundance of rhizoplane dominant phylum Proteobacteria (average increase of 3%, 10% and 13% by single-inoculation of R. palustris, single-inoculation of B. subtilis and co-inoculation of both, respectively) was found. Microbial fertilizer treatments caused variations in the dominant genera, such as increasing the relative abundances of Novosphingobium, Flavobacterium and Rhizobium and reducing those of Anaeromyxobacter, Bradyrhizobium, Pleomorphomonas, Nocardioides, Propionicimonas and Methanobacterium, changed rhizoplane bacterial community structure, and increased their functional gene abundance. The abundance of both rhizosphere and rhizoplane bacterial genes involved in metabolism, genetic information processing, environmental information processing, and cellular processes were positively correlated with panicle seed setting rate (r = 0.60–0.68, P< 0.05). The increase of functional gene abundance was related to the change of dominant genera, and such change in rhizoplane bacterial community had a greater impact on the bacterial functional gene abundance.

Conclusion Application of R. palustris improved rice yields significantly, and its co-inoculation with B. subtilis was more effective than single-inoculation. Compared with control, both co-inoculation and single-inoculation changed the rhizoplane bacterial diversity and increased the abundance of dominant bacteria and functional genes. The effect of co-inoculation on bacterial community was similar to single-inoculation of B. subtilis, but different with that of single-inoculation of R. palustris. Microbial fertilizer can indirectly promote crop growth by affecting the diversity of root zone bacterial communities.