Genomic Studies on the Thermotolerant Methanotroph Methylococcus sp. COMITA G2

Abstract In silico analysis of the complete genome sequence of potential single-cell protein (SCP) producer, the thermotolerant methanotroph Methylococcus strain COMITA G2, was performed to clarify its taxonomic position and metabolic features. Based on phylogenetic analysis of 16S rRNA gene sequences, the closest taxonomically described phylogenetic relatives of strain COMITA G2 were Methylococcus capsulatus TexasT (98.72% similarity) and Methylococcus capsulatus Bath (98.8%). Other closely related validated species were Methylococcus mesophilus 16-5T and Methylococcus geothermalis IM1T (97.86 and 97.73%, respectively). The strain COMITA G2 shared average nucleotide identity (ANI) values of 89.29% with M. capsulatus TexasT and 85.86% with M. geothermalis IM1T. On the basis of genetic and phylogenetic data, strain COMITA G2 may represent a novel species of the genus Methylococcus. Phylogenomic analysis has shown that COMITA G2 forms a well-supported clade with partially described cultured strains Methylococcus sp. GBS-15 and Methylococcus sp. BF19-07 demonstrating 100% identity of the 16S rRNA gene sequence and ANI of 99.99 and 99.45%, respectively. Comparative analysis of the COMITA G2 genomic inventory confirmed the high conservation of methane oxidation and assimilation pathways in representatives of the genus Methylococcus and revealed several distinctive features in the central metabolic pathways. Unique metabolic features have been identified, including the phosphoacetyltransferase (PTA) and pyruvate carboxylase genes, which are absent in Methylococcus capsulatus representatives, and duplication of glucose-6-phosphate dehydrogenase/6-phosphogluconate dehydrogenase genes. We have also identified clusters of exopolysaccharide biosynthesis genes and two regions of intact prophages. The conducted genomic analysis establishes the taxonomic novelty of COMITA G2 strain and facilitates the identification of genetic targets for its modification in order to improve biotechnological potential.