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 BW4-1 T , SPW-1 T , and PHL2-19 T , 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 C 14:0 , C 16:0 , and summed feature 3 (C 16:1 ω 7 c and/or C 16:1 ω 6 c ). Phylogenetic and phylogenomic analyses placed the strains within the genus Methylomonas , with Methylomonas defluvii OY6 T 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 C 30 and C 40 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. (BW4-1 T = KACC 24053 T = MCCC 1K10705 T ), Methylomonas paludicola sp. nov. (SPW-1 T = KACC 24052 T = MCCC 1K10729 T ), and Methylomonas roseola sp. nov. (PHL2-19 T = KACC 24054 T = MCCC 1K10706 T ) are proposed.