The application of bio-organic fertilizers can significantly improve soil fertility and crop yield. This study explored how replacing bio-organic fertilizer with equal nitrogen affected potato quality, yield, and soil microbial diversity after a 4-year positioning experiment. The results showed that the application of bio-organic fertilizer instead of 70% chemical fertilizer could significantly increase potato yield by 10.4–155.4% but had no significant effect on quality. Furthermore, replacing chemical fertilizers with bio-organic fertilizers could decrease the number of soil bacterial species, but it did not influence the diversity of soil bacterial and fungal communities. At the phylum level, bio-organic fertilizer application was directly proportional to the abundance of Gemmatimonadota and Ascomycota, but inversely proportional to the abundance of Acidobacteriota and Basidiomycota. At the genus level, Longimicrobiaceae, Lysobacter, and Nocardioides were higher, whereas Vicinamibacteraceae, Gaiella, and Solirubrobacter were lower. Arthrobacter, Parcubacteria, Lautropia, Luteimonas, and Brunneochlamydosporium were the signatures of bio-organic fertilizer treatment and were positively correlated with the potato yield. Thus, in dry climates with little rainfall, partial substitution of chemical fertilizer with higher bioorganic fertilizers can alter the composition of microbial communities in potato rhizosphere soil, thus significantly improving potato yield.
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