Genomic and Physiological Properties of a Facultative Methane-Oxidizing Bacterial Strain of Methylocystis sp. from a Wetland

Abstract

Methane-oxidizing bacteria are crucial players in controlling methane emissions. This study aimed to isolate and characterize a novel wetland methanotroph to reveal its role in the wetland environment based on genomic information. Based on phylogenomic analysis, the isolated strain, designated as B8, is a novel species in the genus Methylocystis. Strain B8 grew in a temperature range of 15 °C to 37 °C (optimum 30–35 °C) and a pH range of 6.5 to 10 (optimum 8.5–9). Methane, methanol, and acetate were used as carbon sources. Hydrogen was produced under oxygen-limited conditions. The assembled genome comprised of 3.39 Mbp and 59.9 mol% G + C content. The genome contained two types of particulate methane monooxygenases (pMMO) for low-affinity methane oxidation (pMMO1) and high-affinity methane oxidation (pMMO2). It was revealed that strain B8 might survive atmospheric methane concentration. Furthermore, the genome had various genes for hydrogenase, nitrogen fixation, polyhydroxybutyrate synthesis, and heavy metal resistance. This metabolic versatility of strain B8 might enable its survival in wetland environments.

Phylogeny and Metabolic Potential of the Methanotrophic Lineage MO3 in Beijerinckiaceae from the Paddy Soil through Metagenome-Assembled Genome Reconstruction

“…A novel methanotrophic member of Hyphomicrobiaceae, which contains no known methanotroph yet, is predicted by the presence of MMO-like coding genes in two Hyphomicrobiaceae MAGs recovered from a fen sample [ 14 ]. In addition, MAG analysis can uncover some new features and function details of the well-characterized methanotrophs [ 15 , 16 ]. However, it is important to note that the MAG approach also has some limitations, such as assembly errors and misbinning of fragments from other genomes which may lead to incorrect evolutionary and ecological insights [ 17 , 18 ].…”

Comparative genomic analysis of Methylocystis sp. MJC1 as a platform strain for polyhydroxybutyrate biosynthesis

“…The function of mmoD gene has not been reported yet; however, it has been hypothesized that mmoD might play an important role in binuclear iron cluster assembly [ 48 ]. The presence of sMMO may indicate increased metabolic versatility in comparison to other species that possess only one type of methane monooxygenase because of its ability to utilize methane in the presence or absence of copper in the medium [ 49 ]. Furthermore, sMMO has been shown to have a higher turnover number toward methane than pMMO, suggesting that switching to sMMO expression can lead to a higher growth rate when compared to other Methylocystis strains possessing only pMMO [ 50 ].…”

Microbiome Composition and Dynamics of a Reductive/Oxidative Bioelectrochemical System for Perchloroethylene Removal: Effect of the Feeding Composition

“…The methanotrophic bacterial group of Beijerinckiaceae included the genera Methylocystis , alphaI cluster , and Bosea . Interestingly, the Methylocystis genus comprises aerobic, obligate, and facultative methylotrophic and methanotrophic bacteria capable of utilizing methane and methanol as sole carbon and energy sources ( Jung et al, 2020 ). Members of this genus inhabit different soils, peatlands, and freshwater sediments, and they have been previously shown to be capable of degrading TCE and cis -DCE via aerobic metabolic or co-metabolic pathways ( Uchiyama et al, 1989 ; Nakajima et al, 1992 ; Dolinová et al, 2017 ).…”