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Evolutionary origin and ecological implication of a unique nif island in free-living Bradyrhizobium lineages

Abstract

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.

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Fig. 1: The maximum-likelihood phylogenomic tree of Bradyrhizobium and inferred lifestyle evolutionary history.
Fig. 2: Nif gene phylogeny of Bradyrhizobium.
Fig. 3: The comparison of the gene arrangement of the nif gene cluster located in the nif island and in the symbiosis island.
Fig. 4: Normalized abundance of free-living and symbiotic nifH of Bradyrhizobium in amplicon sequencing samples collected from different types of environments.

Data availability

The genomic sequences and raw reads of the 88 sequenced Bradyrhizobium and five Afipia strains are available at NCBI BioProject (accession: PRJNA698083).

Code availability

The Python [72] and Ruby [73] codes used for phylogenomic and comparative genomics analyses are deposited in the online repository https://github.com/luolab-cuhk/Bradyrhizobium-Nif-HGT.

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Acknowledgements

We thank Xiaoyuan Feng for help with genome assembly. We appreciate Shuang Wang and Jie Liu for providing soil samples and Jianjun Xu for assisting in sample collection. We are grateful to Xingqin Lin for her helpful suggestions in medium design. We also thank Qin Li, Yan Li, Xiaojun Wang, Xiao Chu, Hao Zhang, Danli Luo and Mei Xie for their helpful discussion. This work was supported by the National Natural Science Foundation of China (92051113), the Hong Kong Research Grants Council Area of Excellence Scheme (AoE/M-403/16), the Direct Grant of CUHK (4053495), and The CUHK Impact Postdoctoral Fellowship Scheme to SW.

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Tao, J., Wang, S., Liao, T. et al. Evolutionary origin and ecological implication of a unique nif island in free-living Bradyrhizobium lineages. ISME J (2021). https://doi.org/10.1038/s41396-021-01002-z

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