Soybean variety influences the advantages of nutrient uptake and yield in soybean/maize intercropping via regulating root–root interaction and rhizobacterial composition

• The effects of soybean varieties BD2 and YC03-3 on plant N and P uptake, growth, yield and the rhizosphere microorganism community were compared in a maize/soybean intercropping system • BD2/maize intercropping enhanced growth and yield more than YC03-3/maize. • BD2/maize intercropping showed alteration in root traits and root–root avoidance, and reduced competition between species unlike in YC03-3/maize intercropping. • BD2/maize intercropping caused more beneficial rhizobacteria recruitment than YC03-3/maize intercropping. Maize/soybean intercropping systems are commonly used in developing countries, but few studies have been performed to elucidate the differences in nutrient efficiency and rhizosphere microbiome, especially when maize is intercropped with different soybean varieties. In this study, field experiments were conducted to compare the growth and yield of two soybean ( Glycine max ) varieties, BD2 and YC03-3, and one maize ( Zea mays ) variety, Huazhen, in mono-cropped and intercropped cultures. The plant biomass and N content of both crops in BD2/maize intercropping were significantly improved compared to their monoculture, but no such effects were observed in the plants of YC03-3/maize intercropping. The yield of BD2 intercropped with maize exhibited a 37.5% increment above that of BD2 in monoculture. Moreover, 19.2–29.1% longer root length of maize and 19.0–39.4% larger root volume of BD2 were observed in BD2/maize intercropping than in monoculture, but no growth advantage was observed in YC03-3/maize intercropping. Maize showed root avoidance when intercropped with BD2, but space competition when intercropped with YC03-3. 16S rRNA amplicon sequencing showed that compared with the monoculture system, rhizobacteria community composition in BD2/maize intercropping changed more significantly than that of the YC03-3/maize intercropping system. In BD2/maize intercropping, most of the rhizobacteria community biomarker bacteria of BD2 were positively correlated with plant biomass, as well as plant P and N content. Maize tended to recruit Rhizobiales and Proteobacteria, which showed positive correlation with plant biomass and N content, respectively, as well as soil available N. In conclusion, soybean varieties determined the advantages of maize/soybean intercropping through root–root interactions and modification of rhizobacteria communities. Our insight emphasizes a linkage between root traits and the rhizobacteria community, which shows the importance of optimizing intercropping systems by selection of appropriate crop varieties.