Genome Analysis and Biotechnological Potential of Methylomonas sp. 2B, a Novel Carotenoid-Producing Methanotrophic Bacterium

Methanotrophic bacteria have significant potential for various biotechnological applications. Certain biotechnologies, such as single-cell protein production, require fast-growing strains capable of growth on methane or natural gas. This study reports isolation of a novel strain of Methylomonas bacteria, strain 2B, which was obtained from sediments of the mountain River Buu, Krasnodar krai, Russia. Cells were gram-negative, motile, short rods with intracytoplasmic membranes characteristic of type I methanotrophs. Colonies and liquid cultures appeared intense pink. The 16S rRNA gene sequence of strain 2B displayed 96.47–97.91% similarity to those of earlier described Methylomonas species. Complete genome sequence of strain 2B consisted of 5.1 Mb chromosome and 361 kb plasmid. Genome contained three rRNA operons and 4709 protein-coding genes. Gene clusters for both soluble and particulate methane monooxygenases were present. The G+C DNA content was 56.1%. The average nucleotide identity between the genomes of strain 2B and the closest phylogenetic relative M. koyamae Fw12E-YT was 77.6%, indicating that these bacteria represent different species of the genus Methylomonas. The biomass yield of strain 2B during fed-batch and continuous cultivations on natural gas in a bioreactor reached 7.9 ± 0.2 and 5.1 ± 0.3 g cell dry weight L–1, with a protein content of 55 and 65%, respectively. The content of carotenoids during fed-batch cultivation reached 55 μg g–1 biomass. Fast growth along with carotenoid biosynthesis make this bacterium a promising candidate for the production of single-cell protein enriched with carotenoids.