Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR.
Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.
ISME J. 2021 Nov;15(11):3195-3206. doi: 10.1038/s41396-021-01002-z. Epub 2021 May 14.
The alphaproteobacterial genus Bradyrhizobium has been best known as N-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.
α变形菌属中的慢生根瘤菌一直以来以能够与豆科植物共生固氮而闻名，这一特性主要由 nif 和 nod 基因簇来支持。最近的环境调查显示，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了解主要来自共生成员，这使得我们对其生态学和进化的现有知识产生了偏差。在这里，我们报告了 88 株源自不同土壤样本的慢生根瘤菌菌株的基因组，其中包括携带 nif 的共生成员和不携带 nif 的自由生活（无 nod）成员。对这些菌株和 252 株公开可得的慢生根瘤菌基因组的系统发育基因组分析表明，携带 nif 的自由生活成员多次独立于共生祖先（同时携带 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 的自由生活成员构成一个独立的集群，这表明水平基因转移促进了自由生活慢生根瘤菌中 nif 的扩张。比较基因组学分析确定，在自由生活慢生根瘤菌中发现的 nif 基因位于一个约 50kb 的独特基因组岛上，该岛配备了可能有助于应对氧张力的基因。我们进一步分析了扩增子测序数据，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。
