Shifts of bacterial community structure and function in long-term soybean monoculture

Crop monoculture affects soil microbial community structure and diversity, but it is unclear which differences occur in microbial functions after the alteration of the bacterial community during crop monoculture. We investigated the diversity, functional groups and metabolic functions of bacteria under soybean rotation (RS), 2-year (SS) and 27-year (CS) soybean monoculture systems using high-throughput sequencing and functional prediction based on FAPROTAX and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Original soil sample (OS) was taken as a reference point. Our results showed that CS had a lower abundance of the bacterial amoA gene than either RS or SS. Bacterial community differed more in OS than that in RS, SS and CS, and SS and CS had similar bacterial community and that they differed from RS. CS showed a lower relative abundance of predicted functional groups in terms of aerobic chemoheterotrophy, nitrate reduction and photoheterotrophy. KEGG annotation showed greater negative effects on the bacterial functional metabolism than positive effects in CS compared to RS. Redundancy analysis indicated that the predicted functional groups might be related to organic carbon and total nitrogen concentration, and that KEGG pathways were mainly affected by soil pH and available nitrogen.Abbreviations RS: soybean rotation; SS: two-year soybean monoculture; CS: long-term soybean monoculture; AOB: ammonia-oxidizing bacteria; qPCR: quantitative real-time PCR; OTUs: operational taxonomic units; SOC: soil organic carbon; TN: total nitrogen; AN: available nitrogen; TP: total phosphorus; AP: available phosphorus; AK: available potassium; PCoA: Principal coordinate analysis; KEGG: the Kyoto Encyclopedia of Genes and Genomes; RDA: redundancy analysis.