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Chemical fertilizer application is a common agronomic practice to improve crop productivity and liming is often used to counteract the soil acidification caused by long-term fertilization; however, it is unclear whether liming will counteract the effect of long-term fertilization on soil bacterial community structure and its co-occurrence pattern. Here, we examined the influence of long-term fertilization (NPKS) and liming (L) on soil bacterial community structure and its co-occurrence networks by sequencing 16S rRNA gene amplicons. Our results showed that liming counteracted the influence of long-term fertilization on soil pH, but not on soluble organic carbon (SOC) and electrical conductivity (EC). Long-term fertilization affected the abundance of Acidobacteriia, Deltaproteobacteria and Gammaproteobacteria in the 0–10 cm soil, and that of Deltaproteobacteria, Gammaproteobacteria and Gemmatimonadetes in the 10–20 cm soil; whereas liming affected the abundance of Acidobacteriia, Gammaproteobacteria, and Chloracidobacteria in the 0–10 cm soil and that of Deltaproteobacteria in the 10–20 cm soil. The bacterial community structure in soils with the NPKS-L treatment was different from that with other treatments, and was mainly affected by SOC, EC, and NO 3 − concentration. The link numbers in bacterial co-occurrence networks were decreased by long-term fertilization or liming alone, but were increased by the NPKS-L treatment. Notwithstanding the fact that liming alleviates fertilization-induced soil acidification, this study indicates that liming did not counteract the effect of long-term fertilization on soil bacterial community structure and its co-occurrence pattern, hence cannot recuperate the soil microbial functionality that is changed by long-term fertilization. [ABSTRACT FROM AUTHOR]