Long-term and large-scale application of mineral fertilizer destroys soil microbial structure and crop quality. To reduce the harm of mineral fertilizer, a 6-year localization experiment was conducted to study the effects of replacing 0 % (CF), 25 % (M25), 50 % (M50), 75 % (M75), and 100 % (M100) of 225 kg ha−1 mineral fertilizer nitrogen with manure nitrogen on soil bacterial community structure and crop quality. The results showed that an increase in soil Longimicrobiaceae elicited a reduction in amylose. The impact of soil bacteria on the soluble sugar showed no significant difference. Compared with CF, substitution treatments significantly reduced Ktedonobacteria and C0119 by 53.42–81.28 %, and significantly decreased cyanobacteria, cellulolysis, aerobic chemoheterotrophy, phototrophy, photoautotrophy and oxygenic photoautotrophy by 3.27–196.58 %, and significantly increased dark sulfur oxidation, dark thiosulfate oxidation, nitrogen fixation and chitinolysis by 15.73–508.50 %. M50, M75, and M100 significantly reduced Holophagae and Subgroup 7 by 24.96–37.91 % relative to CF. M75 significantly increased Chao index, whereas significantly reduced Simpson index compared with M25. The Simpson indices of M75 and M100 were significantly lower than that of CF. Bacillaceae and Env.OPS 17 can be used as the main basis for the classification of soil samples in the equivalent substitution of nitrogen mineral fertilizer with manure.
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