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The objective of this research was to evaluate the PGPR effect on nodulation and nitrogen-fixing efficiency of soybean (<i>Glycine</i> max (L.) Merr.) by co-inoculation with <i>Bradyrhizobium</i> <i>diazoefficiens</i> USDA110. Co-inoculation of <i>Bacillus</i> <i>velezensis</i> S141 with USDA110 into soybean resulted in enhanced nodulation and N2-fixing efficiency by producing larger nodules. To understand the role of S141 on soybean and USDA110 symbiosis, putative genes related to IAA biosynthesis were disrupted, suggesting that co-inoculation of USDA110 with S141Δ<i>yhcX</i> reduces the number of large size nodules. It was revealed that <i>yhcX</i> may play a major role in IAA biosynthesis in S141 as well as provide a major impact on soybean growth promotion. The disruption of genes related to cytokinin biosynthesis and co-inoculation of USDA110 with S141Δ<i>IPI</i> reduced the number of very large size nodules, and it appears that IPI might play an important role in nodule size of soybean–<i>Bradyrhizobium</i> symbiosis. However, it was possible that not only IAA and cytokinin but also some other substances secreted from S141 facilitate <i>Bradyrhizobium</i> to trigger bigger nodule formation, resulting in enhanced N2-fixation. Therefore, the ability of S141 with Bradyrhizobium co-inoculation to enhance soybean N2-fixation strategy could be further developed for supreme soybean inoculants.