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Members of the <i>Microvirga</i> genus are metabolically versatile and widely distributed in Nature. However, knowledge of the bacteria that belong to this genus is currently limited to biochemical characteristics. Herein, a novel thermo-tolerant bacterium named <i>Microvirga thermotolerans</i> HR1 was isolated and identified. Based on the 16S rRNA gene sequence analysis, the strain HR1 belonged to the genus <i>Microvirga</i> and was highly similar to <i>Microvirga</i> sp. 17 mud 1-3. The strain could grow at temperatures ranging from 15 to 50 &#176;C with a growth optimum at 40 &#176;C. It exhibited tolerance to pH range of 6.0&#8722;8.0 and salt concentrations up to 0.5% (<i>w/v</i>). It contained ubiquinone 10 as the predominant quinone and added group <b>8</b> as the main fatty acids. Analysis of 11 whole genomes of <i>Microvirga</i> species revealed that <i>Microvirga</i> segregated into two main distinct clades (soil and root nodule) as affected by the isolation source. Members of the soil clade had a high ratio of heat- or radiation-resistant genes, whereas members of the root nodule clade were characterized by a significantly higher abundance of genes involved in symbiotic nitrogen fixation or nodule formation. The taxonomic clustering of <i>Microvirga</i> strains indicated strong functional differentiation and niche-specific adaption.