Comparative Genomic Analysis Reveals the Metabolism and Evolution of the Thermophilic Archaeal GenusMetallosphaera

Members of the genusMetallosphaeraare widely found in sulfur-rich and metal-laden environments, but their physiological and ecological roles remain poorly understood. Here, we sequencedMetallosphaera tengchongensisRic-A, a strain isolated from the Tengchong hot spring in Yunnan Province, China, and performed a comparative genome analysis with otherMetallosphaeragenomes. The genome ofM. tengchongensishad an average nucleotide identity (ANI) of approximately 70% to that ofMetallosphaera cuprina. Genessqr,tth,sir,tqo,hdr,tst,soe, andsdoassociated with sulfur oxidation, and gene clustersfoxandcbsinvolved in iron oxidation existed in allMetallosphaeragenomes. However, the adenosine-5 '-phosphosulfate (APS) pathway was only detected inMetallosphaera sedulaandMetallosphaera yellowstonensis, and several subunits offoxcluster were lost inM. cuprina. The complete 3-hydroxypropionate/4-hydroxybutyrate cycle and dicarboxylate/4-hydroxybutyrate cycle involved in carbon fixation were found in allMetallosphaeragenomes. A large number of gene family gain events occurred inM. yellowstonensisandM. sedula, whereas gene family loss events occurred frequently inM. cuprina.Pervasive strong purifying selection was found acting on the gene families ofMetallosphaera, of which transcription-related genes underwent the strongest purifying selection. In contrast, genes related to prophages, transposons, and defense mechanisms were under weaker purifying pressure. Taken together, this study expands knowledge of the genomic traits ofMetallosphaeraspecies and sheds light on their evolution.