Long-term continuous cropping of soybean is comparable to crop rotation in mediating microbial abundance, diversity and community composition

•CC13 and CR5 significantly increased soil pH, and available nutrients in contrast to CC3 and CC5.•soil pH and C/N was primary factors regulating the shifts of bacterial and fungal community structures.•CC13 and CR5 increased beneficial microbial populations, while decreased the relative abundance of pathogenic fungi.•CC13 and CR5 harbor more complex co-occurrence network than CC3 and CC5.