The alphaproteobacterial genus Bradyrhizobium has been best known as N₂-fixing members that nodulate legumes, supported by the nif and nod gene clusters. Recent environmental surveys show that Bradyrhizobium represents one of the most abundant free-living bacterial lineages in the world’s soils. However, our understanding of Bradyrhizobium comes largely from symbiotic members, biasing the current knowledge of their ecology and evolution. Here, we report the genomes of 88 Bradyrhizobium strains derived from diverse soil samples, including both nif-carrying and non-nif-carrying free-living (nod free) members. Phylogenomic analyses of these and 252 publicly available Bradyrhizobium genomes indicate that nif-carrying free-living members independently evolved from symbiotic ancestors (carrying both nif and nod) multiple times. Intriguingly, the nif phylogeny shows that the vast majority of nif-carrying free-living members comprise an independent cluster, indicating that horizontal gene transfer promotes nif expansion among the free-living Bradyrhizobium. Comparative genomics analysis identifies that the nif genes found in free-living Bradyrhizobium are located on a unique genomic island of ~50 kb equipped with genes potentially involved in coping with oxygen tension. We further analyze amplicon sequencing data to show that Bradyrhizobium members presumably carrying this nif island are widespread in a variety of environments. Given the dominance of Bradyrhizobium in world’s soils, our findings have implications for global nitrogen cycles and agricultural research.

阿尔法变形菌属慢生根瘤菌最出名的是在nif和nod基因簇的支持下使豆科植物结瘤的 N _{2固定成员。}最近的环境调查表明，慢生根瘤菌是世界土壤中最丰富的自由生活细菌谱系之一。然而，我们对慢生根瘤菌的理解主要来自共生成员，偏向于目前对其生态和进化的认识。在这里，我们报告了来自不同土壤样品的 88种慢生根瘤菌菌株的基因组，包括携带nif和非携带nif的自由生活（点头免费）会员。对这些和 252 个可公开获得的慢生根瘤菌基因组的系统基因组分析表明，携带nif的自由生活成员多次独立地从共生祖先（携带nif和nod）进化而来。有趣的是，nif系统发育表明绝大多数携带nif的自由生活成员组成一个独立的簇，这表明水平基因转移促进了自由生活的慢生根瘤菌中的nif扩增。比较基因组学分析确定了在自由生活的慢生根瘤菌中发现的nif基因位于一个独特的约 50 kb 的基因组岛上，配备有可能参与应对氧张力的基因。我们进一步分析扩增子测序数据以表明可能携带该nif岛的慢生根瘤菌成员广泛存在于各种环境中。鉴于慢生根瘤菌在世界土壤中的主导地位，我们的研究结果对全球氮循环和农业研究具有重要意义。