FIGURE 8 - available via license: Creative Commons Attribution 4.0 International
Content may be subject to copyright.
| The structure of integrative and conjugative element (ICE) region revealed in the genome of strain KN2 and prophage-associated regions (≥20 Kb) detected in the examined Methylococcus genomes.
Source publication
The bacterial genus Methylococcus, which comprises aerobic thermotolerant methanotrophic cocci, was described half-a-century ago. Over the years, a member of this genus, Methylococcus capsulatus Bath, has become a major model organism to study genomic and metabolic basis of obligate methanotrophy. High biotechnological potential of fast-growing Met...
Context in source publication
Citations
... Previously, it was demonstrated that RubisCO and CO 2 play essential roles in the metabolism of M. capsulatus Bath (Henard et al., 2021). In addition, it was reported that several Methylococcus strains showed a (slight) increase in optical density when hydrogen was added as an additional energy source (Oshkin et al., 2021). Genes encoding the glycolysis and gluconeogenesis pathway, the TCA cycle, and the pentose phosphate pathway were detected (Table S6). ...
Terrestrial geothermal ecosystems are hostile habitats, characterized by large emissions of environmentally relevant gases such as CO 2 , CH 4 , H 2 S and H 2 . These conditions provide a niche for chemolithoautotrophic microorganisms. Methanotrophs of the phylum Verrucomicrobia , which inhabit these ecosystems, can utilize these gases and grow at pH levels below 1 and temperatures up to 65°C. In contrast, methanotrophs of the phylum Proteobacteria are primarily found in various moderate environments. Previously, novel verrucomicrobial methanotrophs were detected and isolated from the geothermal soil of the Favara Grande on the island of Pantelleria, Italy. The detection of pmoA genes, specific for verrucomicrobial and proteobacterial methanotrophs in this environment, and the partially overlapping pH and temperature growth ranges of these isolates suggest that these distinct phylogenetic groups could coexist in the environment. In this report, we present the isolation and characterization of a thermophilic and acid‐tolerant gammaproteobacterial methanotroph (family Methylococcaceae ) from the Favara Grande. This isolate grows at pH values ranging from 3.5 to 7.0 and temperatures from 35°C to 55°C, and diazotrophic growth was demonstrated. Its genome contains genes encoding particulate and soluble methane monooxygenases, XoxF‐ and MxaFI‐type methanol dehydrogenases, and all enzymes of the Calvin cycle. For this novel genus and species, we propose the name ‘ Candidatus Methylocalor cossyra’ CH1.
... Two pmoCAB clusters encoding particulate methane monooxygenase were found in each genome (7), and the Methylococcus capsulatus (Norfolk) genome also possesses a single soluble methane monooxygenase mmoXYBZDCGQSR cluster (8) and a putative copper chaperone (mopE) gene (9). Calcium-dependent (mxaFJGIRSACKLD) and lanthanidedependent (xoxFJ) methanol dehydrogenase gene clusters (10,11) were found in these genomes, with a clade 5 xoxF gene present in each and an additional clade 3 xoxF in Methylocaldum szegediense (Norfolk) (12). Both genomes feature complete gene inventories for tetrahydromethanopterin and tetrahydrofolate-linked formaldehyde oxidation, in addition to formate dehydrogenase genes (13). ...
Here we report the complete genome sequence of two moderately thermophilic methanotrophs isolated from a landfill methane biofilter, Methylococcus capsulatus (Norfolk) and Methylocaldum szegediense (Norfolk).
... Members of the genus Methylococcus are strictly aerobic bacteria that specialize in utilizing methane as the sole electron and carbon source [1]. Methylococcus capsulatus, which includes several described strains (Texas T , Bath, IO1, BH, KN2 and MIR) [2][3][4][5][6], and M. geothermalis IM1 T [7] are the only two species within this genus with validly published names. The recently described isolates Methylococcus sp. ...
... The recently described isolates Methylococcus sp. MC7 [6] and Methylococcus sp. HGS-45 [8] are also potentially novel species within this genus, according to the Genome Taxonomy Database (GDTB) [9,10]. ...
... However, several genera with mesophilic (non-thermophilic/thermotolerant) traits, including Methylogaea, Methyloparacoccus, Methylomagnum, Methyloterricola and 'Methylolobus' [13][14][15][16][17], have been recently added to this list. Physiologically, all characterized Methylococcus strains are moderately thermophilic, growing optimally between 40 and 50 °C [2][3][4][5][6][7][8], and have been isolated from or found in a variety of thermal habitats, including geothermal soils, hot springs, and sugarcane bagasse [4,7,[18][19][20][21]. Members of this genus also inhabit a variety of non-thermal habitats, including freshwater, goldmines, and plant rhizospheres, based on cultivation-independent studies [22][23][24][25]. ...
Strain 16-5 T , a mesophilic methanotroph of the genus Methylococcus , was isolated from rice field soil sampled in Chungcheong Province, Republic of Korea. Strain 16-5 T had both particulate and soluble methane monooxygenases and could only grow on methane and methanol as electron donors. Strain 16-5 T cells are Gram-negative, white to light tan in color, non-motile, non-flagellated, diplococcoid to cocci, and have the typical type I intracytoplasmic membrane system. Strain 16-5 T grew at 18–38 °C (optimum, 27 °C) and at pH 5.0–8.0 (optimum, pH 6.5–7.0). C 16 : 1 ω7 c (38.8%), C 16 : 1 ω 5 c (18.8%), C 16 : 1 ω 6 c (16.8%) and C 16 : 0 (16.9%) were the major fatty acids, and phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unidentified phospholipid were the major polar lipids. The main respiratory quinone was methylene-ubiquinone-8. Strain 16-5 T displayed the highest 16S rRNA gene sequence similarities to other taxonomically recognized members of the genus Methylococcus , i.e. Methylococcus capsulatus Texas T (98.62%) and Methylococcus geothermalis IM1 T (98.49 %), which were its closest relatives. It did, however, differ from all other taxonomically described Methylococcus species due to some phenotypic differences, most notably its inability to grow at temperatures above 38 °C, where other Methylococcus species thrive. Its 4.34 Mbp-sized genome has a DNA G+C content of 62.47 mol%, and multiple genome-based properties such as average nucleotide identity and digital DNA-DNA hybridization value distanced it from its closest relatives. Based on the data presented above, this strain represents the first non-thermotolerant species of the genus Methylococcus . The name Methylococcus mesophilus sp. nov. is proposed, and 16-5 T (=JCM 35359 T =KCTC 82050 T ) is the type strain.
... T he species Methylococcus capsulatus represents aerobic thermotolerant methanotrophic bacteria that are widely distributed in various habitats (1,2) and possess high biotechnological potential. With very few exceptions, characterized strains of this species display only trace growth on methanol (3). Here, we report the complete genome sequence of a new M. capsulatus isolate, strain MIR, which is capable of growth on methanol in the range of concentrations of 0.05 to 3.5% (vol/vol) in a mineral medium (3) during incubation at 42°C (Fig. 1). ...
Methylococcus capsulatus MIR is an aerobic methanotroph that was isolated from an activated sludge sample and is capable of growth on methanol. The finished genome of strain MIR is 3.2 Mb in size. It encodes both MxaFI and XoxF methanol dehydrogenases, as well as three different isozymes of formate dehydrogenase.
... All the aforementioned genes were actively transcribed, based on transcriptomic data. Consequently, participation of Methylococcales in sulfur cycling within these symbiont communities should be considered (61). ...
... The abundant MMO enzymes carried by Methylococcales could be used to transfer ammonia to hydroxylamine via monooxygenation, since the latter is toxic and mutagenic (61,66). Furthermore, hydroxylamine is an intermediate that can be released by aerobic ammonium-oxidizing bacteria and used by other community members (67,68). ...
Remarkably diverse bacteria have been observed as biofilm aggregates on the surface of deep-sea invertebrates that support the growth of hosts through chemosynthetic carbon fixation. Growing evidence also indicates that community-wide interactions, and especially cooperation among symbionts, contribute to overall community productivity. Here, metagenome-guided metatranscriptomic and metabolic analyses were conducted to investigate the taxonomic composition, functions, and potential interactions of symbionts dwelling on the seta of Shinkaia crosnieri lobsters in a methane cold seep. Methylococcales and Thiotrichales dominated the community, followed by the Campylobacteriales, Nitrosococcales, Flavobacteriales, and Chitinophagales Metabolic interactions may be common among the episymbionts since many separate taxon genomes encoded complementary genes within metabolic pathways. Specifically, Thiotrichales could contribute to detoxification of hydroxylamine that is a metabolic by-product of Methylococcales. Further, Nitrosococcales may rely on methanol leaked from Methylococcales cells that efficiently oxidize methane. Elemental sulfur may also serve as a community good that enhances sulfur utilization that benefits the overall community, as evidenced by confocal Raman microscopy. Stable intermediates may connect symbiont metabolic activities in cyclical oxic-hypoxic fluctuating environments, which then enhance overall community functioning. This hypothesis was partially confirmed via in situ experiments. These results highlight the importance of microbe-microbe interactions in symbiosis and deep-sea adaptation. 2022 Xu et al.
Carotenoids are secondary metabolites that exhibit antioxidant properties and are characterized by a striking range of colorations from red to yellow. These natural pigments are synthesized by a wide range of eukaryotic and prokaryotic organisms. Among the latter, carotenoid-producing methanotrophic bacteria, which display fast growth on methane or natural gas, are of particular interest as potential producers of a feed protein enriched with carotenoids. Until recently, Methy-lomonas strain 16a and Methylomonas sp. ZR1 remained the only representatives of the genus for which detailed carotenoid profile was determined. In this study, we analyzed the genome sequences of five strains of Methylomonas species whose pigmentation varied from white and yellow to orange and red, and identified carotenoids produced by these bacteria. Carotenoids synthesized using four pigmented strains included C30 fraction, primarily composed of 4,4'-diaplycopene-4,4'-dioic acid and 4,4'-diaplycopenoic acid, as well as C40 fraction with the major compound represented by 1,1'-dihydroxy-3,4-didehydrolycopene. The genomes of studied Methylomonas strains varied in size between 4.59 and 5.45 Mb and contained 4201-4735 protein-coding genes. These genomes and 35 reference Methylomonas genomes available in the GenBank were examined for the presence of genes encoding carotenoid biosynthesis. Genomes of all pigmented Methylomonas strains harbored genes necessary for the synthesis of 4,4'-diaplycopene-4,4'-dioic acid. Non-pigmented "Methylomonas montana" MW1 T lacked the crtN gene required for carotenoid production. Nearly all strains possessed phytoene desaturases, which explained their ability to naturally synthesize lycopene. Thus, members of the genus Methylomonas can potentially be considered as producers of C30 and C40 carotenoids from methane.
