Fertilization decreases compositional variation of paddy bacterial community across geographical gradient

•Spatial variation of paddy bacterial community is mainly shaped by geographic factor.•The distance decay relationship rate is flattened by NPK and OM fertilizations.•Fertilizations decrease sensitivity of paddy bacterial community to changes.•Community homogeneity profits agroecosystem stability and yield sustainability.

Fertilization is one of the most common agricultural practices to meet an increasing global demand for food products. Few investigations have been reported on spatial variation of microbial community composition in response to fertilizations in agroecosystems at a large scale. To improve the related understandings, we have evaluated the taxonomic and phylogenetic diversities of bacterial taxa in response to three fertilization strategies in six paddy experiment sites spanning across subtropical China. We found the large-scale compositional variation of paddy bacterial community is shaped by both geographic location and environmental selection, and the former is the dominant factor. The slopes of distance-decay relationships (DDR) are flattened by fertilizations, NPK (mineral NPK fertilizers) and OM (mineral NPK fertilizers plus organic amendments) when compared to Control. A flattened DDR implies that bacterial community composition is greatly homogenized by fertilizations in paddies. It is also inferred that fertilization decreases sensitivity of bacterial community to geographic and environmental factors, which is speculated to be beneficial for agroecosystem stability and yield sustainability. Results from this investigation correlate microscopic agroecosystem with macroscopic agricultural practices.