| Summary: | Fertilization is one of the most common agricultural practices to achieve high yield. Although microbes play a critical role in nutrient cycling and organic matter decomposition, knowledge of the long-term responses of the soil bacterial community to organic and inorganic fertilizers is still limited. This study was conducted to evaluate the effects of century-long organic (manure), inorganic (NPK), and no fertilization (control) treatments on soil bacterial community structure under continuous winter wheat (<i>Triticum aestivum</i> L.) cultivation. Fertilization treatments altered the richness, diversity and composition of the soil bacterial community. Compared with the control, manure significantly increased the operational taxonomic units (OTUs), Chao 1 and Shannon indices, and taxonomic groups, while NPK significantly decreased these parameters. Fertilization treatments did not alter the types of dominant phyla but did significantly affect their relative abundances. <i>Acidobacteria</i> and <i>Proteobacteria</i> were the most dominant phyla in all treatments. Manure led to enrichment of most phyla, with a diazotrophic group, <i>Cyanobacteria</i>, being an exception; NPK reduced most phyla, but enriched <i>Chloroflexi</i>; control led to promotion of <i>Cyanobacteria</i>. Soil pH and NO<sub>3</sub><sup>−</sup> were two dominant parameters influencing the bacterial community structure. Soil pH positively correlated with the relative abundances of <i>Proteobacteria</i> and <i>Gemmatimonadetes</i> but negatively correlated with those of <i>Acidobacteria</i> and <i>Chloroflexi</i>; NO<sub>3</sub><sup>−</sup> negatively correlated with the relative abundance of <i>Cyanobacteria</i>, which was 14–52 times higher in control than the fertilized soils. <i>Cyanobacteria</i>, especially <i>M. paludosus</i> and <i>L. appalachiana</i>, could be the key players in maintaining wheat productivity in the century-long unfertilized control.
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