Methylomonassediminis sp. nov., Methylomonas paludicola sp. nov., and Methylomonas roseola sp. nov.: genomic insights into the evolution of methane oxidation and carotenoid biosynthesis

Abstract

Three reddish-pink, gram-stain-negative, motile, flagellated, short rod-shaped methanotrophs, designated BW4-1T, SPW-1T, and PHL2-19T, were isolated from wetland sediments in South Korea. All three strains possessed intracytoplasmic membranes characteristic of type I methanotrophs and grew with methane or methanol as the sole carbon and energy source. Their major fatty acids were C14:0, C16:0, and summed feature 3 (C16:1ω7c and/or C16:1ω6c). Phylogenetic and phylogenomic analyses placed the strains within the genus Methylomonas, with Methylomonas defluvii OY6T as their closest relative. Despite sharing 99.9–100.0% 16S rRNA gene sequence similarity, the strains were differentiated by genomic and phenotypic characteristics. Pairwise average nucleotide identity and digital DNA–DNA hybridization values among the three strains were 95.0–95.9% and 60.4–66.2%, respectively, supporting their recognition as distinct species. All three strains possessed complete pmoCAB and mmoXYBZDC clusters and pathways linking methane-derived carbon to C30 and C40 carotenoid biosynthesis. PmoA phylogeny supported predominantly vertical inheritance of pmoCAB, whereas the patchy distribution and phylogenetic incongruence of MmoX indicated lineage-specific gain, loss, and possible horizontal transfer of sMMO-associated genes. Ancestral reconstruction further indicated that pMMO-dependent methane oxidation and carotenoid biosynthesis were evolutionarily conserved, whereas the sMMO system was shaped by more dynamic, lineage-specific evolutionary processes. Accordingly, the names Methylomonas sediminis sp. nov. (BW4-1T = KACC 24053T = MCCC 1K10705T), Methylomonas paludicola sp. nov. (SPW-1T = KACC 24052T = MCCC 1K10729T), and Methylomonas roseola sp. nov. (PHL2-19T = KACC 24054T = MCCC 1K10706T) are proposed.