Methane oxidation in stream sediments
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PROVIDER: PRJEB23592 | ENA |
REPOSITORIES: ENA
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Project description:Methanotrophs, which help regulate atmospheric levels of methane, are active in diverse natural and man-made environments. This range of habitats and the feast-famine cycles seen by many environmental methanotrophs suggest that methanotrophs dynamically mediate rates of methane oxidation. Global methane budgets require ways to account for this variability in time and space. Functional gene biomarker transcripts are increasingly being studied to inform the dynamics of diverse biogeochemical cycles. Previously, per-cell transcript levels of the methane oxidation biomarker, pmoA, were found to vary quantitatively with respect to methane oxidation rates in model aerobic methanotroph, Methylosinus trichosporium OB3b. In the present study, these trends were explored for two additional aerobic methanotroph pure cultures, Methylocystis parvus OBBP and Methylomicrobium album BG8. At steady-state conditions, per cell pmoA mRNA transcript levels strongly correlated with per cell methane oxidation across the three methanotrophs across many orders of magnitude of activity (R2 = 0.91). Additionally, genome-wide expression data (RNA-seq) were used to explore transcriptomic responses of steady state M. album BG8 cultures to short-term CH4 and O2 limitation. These limitations induced regulation of genes involved in central carbon metabolism (including carbon storage), cell motility, and stress response.
2021-11-17 | GSE188821 | GEO
Project description:Methane monooxygenases (MMOs) are enzymes that catalyze the oxidation of methane to methanol in methanotrophic bacteria. As potential targets for new gas-to-liquid methane bioconversion processes, MMOs have attracted intense attention in recent years. There are two distinct types of MMO, a soluble, cytoplasmic MMO (sMMO) and a membrane-bound, particulate MMO (pMMO). Both oxidize methane at metal centers within a complex, multisubunit scaffold, but the structures, active sites, and chemical mechanisms are completely different. This Current Topic review article focuses on the overall architectures, active site structures, substrate reactivities, protein-protein interactions, and chemical mechanisms of both MMOs, with an emphasis on fundamental aspects. In addition, recent advances, including new details of interactions between the sMMO components, characterization of sMMO intermediates, and progress toward understanding the pMMO metal centers are highlighted. The work summarized here provides a guide for those interested in exploiting MMOs for biotechnological applications.
| S-EPMC5257249 | biostudies-literature
Project description:Methane is a potent greenhouse gas that contributes significantly to climate change and is primarily regulated in Nature by methanotrophic bacteria, which consume methane gas as their source of energy and carbon, first by oxidizing it to methanol. The direct oxidation of methane to methanol is a chemically difficult transformation, accomplished in methanotrophs by complex methane monooxygenase (MMO) enzyme systems. These enzymes use iron or copper metallocofactors and have been the subject of detailed investigation. While the structure, function, and active site architecture of the copper-dependent particulate methane monooxygenase (pMMO) have been investigated extensively, its putative quaternary interactions, regulation, requisite cofactors, and mechanism remain enigmatic. The iron-dependent soluble methane monooxygenase (sMMO) has been characterized biochemically, structurally, spectroscopically, and, for the most part, mechanistically. Here, we review the history of MMO research, focusing on recent developments and providing an outlook for future directions of the field. Engineered biological catalysis systems and bioinspired synthetic catalysts may continue to emerge along with a deeper understanding of the molecular mechanisms of biological methane oxidation. Harnessing the power of these enzymes will necessitate combined efforts in biochemistry, structural biology, inorganic chemistry, microbiology, computational biology, and engineering.
| S-EPMC10923174 | biostudies-literature
Project description:sulfur driven denitrification methane oxidation Genome sequencing and assembly
| PRJNA766825 | ENA
Project description:Methanotrophic bacteria represent a potential route to methane utilization and mitigation of methane emissions. In the first step of their metabolic pathway, aerobic methanotrophs use methane monooxygenases (MMOs) to activate methane, oxidizing it to methanol. There are two types of MMOs: a particulate, membrane-bound enzyme (pMMO) and a soluble, cytoplasmic enzyme (sMMO). The two MMOs are completely unrelated, with different architectures, metal cofactors, and mechanisms. The more prevalent of the two, pMMO, is copper-dependent, but the identity of its copper active site remains unclear. By contrast, sMMO uses a diiron active site, the catalytic cycle of which is well understood. Here we review the current state of knowledge for both MMOs, with an emphasis on recent developments and emerging hypotheses. In addition, we discuss obstacles to developing expression systems, which are needed to address outstanding questions and to facilitate future protein engineering efforts.
| S-EPMC7965334 | biostudies-literature
Project description:Methane gas (CH4) has been identified as an important alternative source of carbon and energy in some freshwater food webs. CH4 is oxidized by methane oxidizing bacteria (MOB), and subsequently utilized by chironomid larvae, which may exhibit low ?(13)C values. This has been shown for chironomid larvae collected from lakes, streams and backwater pools. However, the relationship between CH4 concentrations and ?(13)C values of chironomid larvae for in-stream impoundments is unknown. CH4 concentrations were measured in eleven in-stream impoundments located in the Queich River catchment area, South-western Germany. Furthermore, the ?(13)C values of two subfamilies of chironomid larvae (i.e. Chironomini and Tanypodinae) were determined and correlated with CH4 concentrations. Chironomini larvae had lower mean ?(13)C values (-29.2 to -25.5 ‰), than Tanypodinae larvae (-26.9 to -25.3 ‰). No significant relationships were established between CH4 concentrations and ?(13)C values of chironomids (p>0.05). Mean ?(13)C values of chironomid larvae (mean: -26.8‰, range: -29.2‰ to -25.3‰) were similar to those of sedimentary organic matter (SOM) (mean: -28.4‰, range: -29.3‰ to -27.1‰) and tree leaf litter (mean: -29.8 ‰, range: -30.5‰ to -29.1‰). We suggest that CH4 concentration has limited influence on the benthic food web in stream impoundments.
| S-EPMC4216073 | biostudies-literature
Project description:Lakes are a natural source of methane to the atmosphere and contribute significantly to total emissions compared to the oceans. Controls on methane emissions from lake surfaces, particularly biotic processes within anoxic hypolimnia, are only partially understood. Here we investigated biological methane oxidation in the water column of the seasonally stratified Lake Rotsee. A zone of methane oxidation extending from the oxic/anoxic interface into anoxic waters was identified by chemical profiling of oxygen, methane and ?13C of methane. Incubation experiments with 13C-methane yielded highest oxidation rates within the oxycline, and comparable rates were measured in anoxic waters. Despite predominantly anoxic conditions within the zone of methane oxidation, known groups of anaerobic methanotrophic archaea were conspicuously absent. Instead, aerobic gammaproteobacterial methanotrophs were identified as the active methane oxidizers. In addition, continuous oxidation and maximum rates always occurred under light conditions. These findings, along with the detection of chlorophyll a, suggest that aerobic methane oxidation is tightly coupled to light-dependent photosynthetic oxygen production both at the oxycline and in the anoxic bottom layer. It is likely that this interaction between oxygenic phototrophs and aerobic methanotrophs represents a widespread mechanism by which methane is oxidized in lake water, thus diminishing its release into the atmosphere.
| S-EPMC4508055 | biostudies-literature
Project description:Organic crusts on liquid manure storage tanks harbor ammonia- and nitrite-resistant methane oxidizers and may significantly reduce methane emissions. Methane oxidation potential (0.6 mol CH(4) m(-2) day(-1)) peaked during fall and winter, after 4 months of crust development. Consequences for methane mitigation potential of crusts are discussed.
| S-EPMC3536077 | biostudies-literature
Project description:Methane inhibited NH4+ utilization by Nitrosomonas europaea with a Ki of 2mM. O2 consumption was not inhibited. In the absence of NH4+, or with hydrazine as reductant, methane caused nearly a doubling in the rate of O2 uptake. The stimulation was abolished by allylthiourea, a sensitive inhibitor of the oxidation of NH4+. Analysis revealed that methanol was being formed in these experiments, with yields approaching 1 mol of methanol per mol of O2 consumed under certain conditions. When cells were incubated with NH4+ under an atmosphere of 50% methane, 50 microM-methanol was generated in 1 h. It is concluded that methane is an alternative substrate for the NH3-oxidizing enzyme (ammonia mono-oxygenase),m albeit with a much lower affinity than for methane mono-oxygenase of methanotrophs.
| S-EPMC1152006 | biostudies-other
Project description:Transcriptional profiling of methanotrophic bacteria (pmoA gene) in methane oxidation biocover soil by depth
2013-09-28 | GSE51235 | GEO