College of Engineering, Peking University, Beijing, 100871, China.
Institute of Ocean Research, Peking University, Beijing, 100871, China.
Environ Microbiol. 2021 Feb;23(2):861-877. doi: 10.1111/1462-2920.15176. Epub 2020 Aug 26.
The bacterial genus Dietzia is widely distributed in various environments. The genomes of 26 diverse strains of Dietzia, including almost all the type strains, were analysed in this study. This analysis revealed a lipid metabolism gene richness, which could explain the ability of Dietzia to live in oil related environments. The pan-genome consists of 83,976 genes assigned into 10,327 gene families, 792 of which are shared by all the genomes of Dietzia. Mathematical extrapolation of the data suggests that the Dietzia pan-genome is open. Both gene duplication and gene loss contributed to the open pan-genome, while horizontal gene transfer was limited. Dietzia strains primarily gained their diverse metabolic capacity through more ancient gene duplications. Phylogenetic analysis of Dietzia isolated from aquatic and terrestrial environments showed two distinct clades from the same ancestor. The genome sizes of Dietzia strains from aquatic environments were significantly larger than those from terrestrial environments, which was mainly due to the occurrence of more gene loss events during the evolutionary progress of the strains from terrestrial environments. The evolutionary history of Dietzia was tightly coupled to environmental conditions, and iron concentrations should be one of the key factors shaping the genomes of the Dietzia lineages.
土壤杆菌属广泛分布于各种环境中。本研究分析了 26 株不同的土壤杆菌属菌株的基因组，包括几乎所有的模式菌株。该分析揭示了土壤杆菌属丰富的脂质代谢基因，这可以解释土壤杆菌属能够在与油相关的环境中生存的能力。泛基因组由 83976 个基因组成，分为 10327 个基因家族，其中 792 个基因家族存在于所有土壤杆菌属的基因组中。数据的数学推断表明，土壤杆菌属的泛基因组是开放的。基因复制和基因缺失都导致了泛基因组的开放性，而水平基因转移是有限的。土壤杆菌属菌株主要通过更古老的基因复制获得了多样化的代谢能力。对来自水生和陆地环境的土壤杆菌属的系统发育分析表明，来自同一祖先的两个不同分支。来自水生环境的土壤杆菌属菌株的基因组大小明显大于来自陆地环境的菌株，这主要是由于陆地环境中菌株的进化过程中发生了更多的基因缺失事件。土壤杆菌属的进化历史与环境条件密切相关，铁浓度应该是塑造土壤杆菌属谱系基因组的关键因素之一。
