Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea.
Department of Life Science, Chung-Ang University, Seoul, South Korea.
Appl Environ Microbiol. 2024 Mar 20;90(3):e0209123. doi: 10.1128/aem.02091-23. Epub 2024 Feb 27.
The novel genus that lacks nitrogenase was recently reclassified from the genus. The genomes of species isolated from water were smaller and had higher GC contents than those of species. Six species lacking nitrogenase were found to exhibit low similarity in the average nucleotide identity values to the other 24 species. Therefore, they were classified as the non-N-fixing lineage (N-ML), an evolutionary intermediate species. The results of our phylogenomic analyses and the loss of Rhizobiales-specific indicated that species may have evolved from species through an ecological transition. Halotolerant and alkali-resistant and belonging to N-ML possessed many tripartite ATP-independent periplasmic transporter and sodium/proton antiporter subunits composed of seven genes (). These genes were not present in the N-fixing lineage (ML), suggesting that genes acquired for adaptation to highly saline and alkaline environments were lost during the evolution of ML as the habitat changed to soil. Land-to-water habitat changes in species, close relatives of species, could have influenced their genomic evolution by the gain and loss of genes. Our study indicated that lineage-specific evolution could have played a significant role in shaping their genome architecture and conferring their ability to thrive in different habitats.IMPORTANCEPhylogenetic analyses revealed that the lineage (AL) and non-N-fixing lineage (N-ML) were monophyletically grouped into distinct clusters separate from the N-fixing lineage (ML). The N-ML, an evolutionary intermediate species having characteristics of both ancestral and descendant species, could provide a genomic snapshot of the genetic changes that occur during adaptation. Genomic analyses of AL, N-ML, and ML revealed that changes in the levels of genes related to transporters, chemotaxis, and nitrogen fixation likely reflect adaptations to different environmental conditions. Our study sheds light on the complex and dynamic nature of the evolution of rhizobia in response to changes in their environment and highlights the crucial role of genomic analysis in understanding these processes.
最近，一个缺乏固氮酶的新属从 属中重新分类。从水中分离出的 种的基因组较小，GC 含量较高，而 种的基因组较大。发现六个缺乏固氮酶的 种与其他 24 个 种的平均核苷酸同一性值相似度较低。因此，它们被归类为非固氮系（N-ML），这是一种进化中间种。我们的系统基因组分析结果和 Rhizobiales 特异性基因的丢失表明， 种可能通过生态过渡从 种进化而来。耐盐和耐碱的 N-ML 中的 和 具有许多由七个基因组成的三部分 ATP 独立周质转运蛋白和钠/质子反向转运蛋白亚基（）。这些基因不存在于固氮系（ML）中，这表明在 ML 进化过程中，由于栖息地变为土壤，适应高盐和碱性环境的基因被丢失。 种是 种的近亲，其从陆地到水的栖息地变化可能通过基因的获得和丢失影响其基因组进化。我们的研究表明，谱系特异性进化可能在塑造它们的基因组结构和赋予它们在不同栖息地中茁壮成长的能力方面发挥了重要作用。
重要的是，系统发育分析表明，AL 系（AL）和非固氮系（N-ML）是单系分组的，与固氮系（ML）分开。N-ML 是一种进化中间种，具有祖先和后代种的特征，它可以提供适应过程中发生的遗传变化的基因组快照。对 AL、N-ML 和 ML 的基因组分析表明，与转运蛋白、趋化性和固氮相关的基因水平的变化可能反映了对不同环境条件的适应。我们的研究揭示了根瘤菌在应对环境变化时进化的复杂和动态性质，并强调了基因组分析在理解这些过程中的关键作用。
