Lineage-specific evolution of , a close relative of , during habitat adaptation.

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.