Soil bacterial, fungal and ammonia-oxidizing bacterial (AOB) communities in a cultivated black soil (0-20 cm) with different fertilizing treatments [no fertilizer (NoF), chemical fertilizer (CF) and chemical fertilizer plus manure (CFM)] and in a neighboring plot of natural restoration (NR) in Northeast China were investigated using PCR-DGGE and clone method over a period of two years.The cultivated soils were plowed and had a rotation of maize-soybean-wheat.The NR plot was revegetated naturally with grasses since 1985.The PCA and UniFrac analysis showed that the dominant members of the soil bacterial, fungal and AOB communities were primarily regulated by land use and also linked to periods of plant growth and plant residue inputs in the region.There was no distinct difference in dominant members of both bacterial and fungal communities among different fertilizer treatment plots in cultivated black soils.The change of dominant members of fungal communities along with land use and season was more obvious than that of bacterial communities, suggesting greater sensitivity of fungi to vegetation, soil disturbance of tillage and soil physico-chemical properties.Sequence analysis of the DGGE bands revealed that bacteria belonging to Proteobacteria and Actinobacteria, and fungi of the Basidiomycota and Ascomycota inhabit predominantly in the black soil.Phylogenetic analyses of bacterial amoA gene fragments from four treatments showed that AOB in black soilswere distributed in Nitrosospiracluster 1, 2, 3, 4, 7, 9 and 10, while Nitrosospira cluster 3 was dominant in cultivated black soils and Nitrosospira cluster 1 was dominant in NR.We found a new cluster (defined as cluster NR in this study) which was not affiliated with any known AOB cluster.