Input of plant material may strongly change decomposition rates of soil organic matter (SOM), i.e. causing priming effect (PE), but the underlying mechanisms are largely unknown. We found that rice straw addition in anoxic Fuyang (F) rice field soil stimulated CH4 production from SOM at the expense of CO2, whereas in Uruguay (U) soil it suppressed SOM degradation to CO2 plus CH4 (negative PE). Reciprocal inoculation experiments with non-sterile and sterile soils showed that the soils always displayed the effect of rice straw characteristic for the live microbial community rather than for the soil physicochemical properties. Pyrosequencing of 16S rRNA genes showed that bacterial communities in these soil samples were separated into two clusters (F and U). Symbiobacterium was abundant or dominant in microbiota from U soil, but negligible in those from F soil. Network analysis indicated that the bacterial populations involved in SOM decomposition were different between soils of F and U clusters; moreover, they were more tightly connected to methanogens in U than in F clusters. Ultimately, our results suggested that the PE of rice straw is mediated by the composition and activity of soil microbial community.