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Summary Receiving nodulation and nitrogen fixation genes does not guarantee rhizobia an effective symbiosis with legumes. Here, variations in gene content were determined for three Sinorhizobium species showing contrasting symbiotic efficiency on soybeans. A nitrate‐reduction gene cluster absent in S. sojae was found to be essential for symbiotic adaptations of S. fredii and S . sp. III. In S. fredii , the deletion mutation of...