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A total of 155 nodule isolates that originated from seven sites in Northwest China were characterized by PCR-RFLP of the 16S rRNA gene and sequence analysis of multiple core genes (16S rRNA, recA , atpD , and glnII ) in order to investigate the diversity and biogeography of Glycine soja -nodulating rhizobia. Among the isolates, 80 were Ensifer fredii , 19 were Ensifer morelense , 49 were Rhizobium radiobacter , and 7 were putative novel Rhizobium species. The phylogenies of E. fredii and E. morelense isolates in a concatenate tree (assembly of all housekeeping genes) were generally consistent with those in individual gene trees. However, incongruence was found in the phylogenies of the different genes of Rhizobium isolates, indicating that lateral transfer or recombination possibly occurred in these gene loci. Despite their species identity, all the isolates in this study formed a single lineage related to E. fredii in nodA and nifH gene phylogenies, which also indicated that the symbiotic genes were laterally transferred between different species. Biogeographic patterns were found at the species and strain genomic type levels, as revealed by BOXA1R fingerprinting, demonstrating that the evolution of rhizobial populations in different geographic locations was related to soil types, altitude and spatial effects. This study is the first to report that E. morelense , R. radiobacter , and Rhizobium sp. are microsymbionts of G. soja , as well as showing that the diversity of G. soja rhizobia is enhanced and new rhizobia have evolved in Northwest China. [ABSTRACT FROM AUTHOR]