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Application of Zn fertilizer can improve cereal Zn concentration, and affect soil microbial ecology by increasing soil Zn concentration. We investigated the effects of three-year continuous applications of different Zn fertilizers (i.e. , ZnSO 4 and ZnEDTA) on wheat Zn biofortification, soil Zn fractions and bacterial community on a Zn deficient calcareous soil. The results showed that ZnEDTA application induced a higher grain Zn concentration and bioavailability than those in the case of ZnSO 4 application, which met the target of wheat Zn biofortification within three years. Correspondingly, ZnEDTA application resulted in a higher Zn availability in soil than ZnSO 4 application by facilitating Zn transformation into exchangeable and organic matter loosely bound fractions. Bacterial diversity and richness were not affected, but the bacterial community was altered after three years Zn applications. ZnEDTA application significantly decreased the relative abundances of Nocardioides , Arthrobacter , Blastococcus , Gemmatimonas , and Streptomyces as compared with ZnSO 4 application. Meanwhile, ZnEDTA application lowered α-glucosidase, β-glucosidase, and β-xylosidase activities in soil as compared with ZnSO 4 application. These results indicated that ZnEDTA application is an effective practice to achieve wheat Zn biofortification, but attention needs to be paid to the potential environmental risks associated with the decreased activities of microbes and enzymes in soil. • ZnEDTA realized wheat Zn biofortification by higher soil Zn availability than ZnSO4. • ZnEDTA maintained higher soil Zn levels in EX-Zn and LOM-Zn fractions. • Both ZnEDTA and ZnSO4 showed no effects on soil bacterial α-diversity. • ZnEDTA adversely affected soil enzyme activities and bacterial community composition. [ABSTRACT FROM AUTHOR]