Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1064244 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27543161_1.fastq.gz | Fastqsanger.gz | |||
| SRR27543161_2.fastq.gz | Fastqsanger.gz | |||
| SRR27543162_1.fastq.gz | Fastqsanger.gz | |||
| SRR27543162_2.fastq.gz | Fastqsanger.gz | |||
| SRR27543163_1.fastq.gz | Fastqsanger.gz |
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Project description:RNA-Seq profiling of Methylomicrobium alcaliphilum strain 20Z grown in batch on methane. The RNA-Seq work is one part of a systems approach to characterizing metabolism of 20Z during growth on methane. We demonstrate that methane assimilation is coupled with a highly efficient pyrophosphate-mediated glycolytic pathway, which under O2 limitation participates in a novel form of fermentation-based methanotrophy. This surprising discovery suggests a novel mode of methane utilization in oxygen-limited environments, and opens new opportunities for a modular approach towards producing a variety of excreted chemical products using methane as a feedstock.
2013-09-25 | GSE51145 | GEO
Project description:RNA-Seq profiling of Methylomicrobium alcaliphilum strain 20Z grown in batch on methane. The RNA-Seq work is one part of a systems approach to characterizing metabolism of 20Z during growth on methane. We demonstrate that methane assimilation is coupled with a highly efficient pyrophosphate-mediated glycolytic pathway, which under O2 limitation participates in a novel form of fermentation-based methanotrophy. This surprising discovery suggests a novel mode of methane utilization in oxygen-limited environments, and opens new opportunities for a modular approach towards producing a variety of excreted chemical products using methane as a feedstock. Four replicates of batch growth
2013-09-25 | E-GEOD-51145 | biostudies-arrayexpress
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:Alaska methane cycling microbiome
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Project description:Disko methane-cycling microbiome
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Project description:Aerobic methanotrophic bacteria use methane as their sole source of carbon and energy and serve as a major sink for the potent greenhouse gas methane in freshwater ecosystems. Despite this important environmental role, little is known about the molecular details of how these organisms interact in the environment. Many bacterial species use quorum sensing systems to regulate gene expression in a density-dependent manner. We have identified a quorum sensing system in the genome of Methylobacter tundripaludum, a dominant methane-oxidizer in methane enrichments of sediment from Lake Washington (Seattle, WA, USA). We determined that M. tundripaludum primarily produces N-3-hydroxydecanoyl-L-homoserine lactone (3-OH-C10-HSL) and that production is governed by a positive feedback loop. We then further characterized this system by determining which genes are regulated by quorum sensing in this methane-oxidizer using RNA-seq, and discovered this system regulates the expression of a novel nonribosomal peptide synthetase biosynthetic gene cluster. These results identify and characterize a mode of cellular communication in an aerobic methane-oxidizing bacterium.
2016-08-16 | GSE85617 | GEO
Project description:Aerobic methanotrophic bacteria use methane as their sole source of carbon and energy and serve as a major sink for the potent greenhouse gas methane in freshwater ecosystems. Despite this important environmental role, little is known about the molecular details of how these organisms interact in the environment. Many bacterial species use quorum sensing systems to regulate gene expression in a density-dependent manner. We have identified a quorum sensing system in the genome of Methylobacter tundripaludum, a dominant methane-oxidizer in methane enrichments of sediment from Lake Washington (Seattle, WA, USA). We determined that M. tundripaludum primarily produces N-3-hydroxydecanoyl-L-homoserine lactone (3-OH-CÂ10-HSL) and that production is governed by a positive feedback loop. We then further characterized this system by determining which genes are regulated by quorum sensing in this methane-oxidizer using RNA-seq, and discovered this system regulates the expression of a novel nonribosomal peptide synthetase biosynthetic gene cluster. These results identify and characterize a mode of cellular communication in an aerobic methane-oxidizing bacterium. Samples are 2 sets of biological replicates of a Methylobacter tundripaludum strain 21/22 mutant where the acyl-homoserine lactone (AHL) synthase gene mbaI (T451DRAFT_0796) has been deleted. The mutant strain was grown to log (48 hours) or stationary (68 hours) phase in the absence or presence of the AHL 3-OH-C10-HSL.
2016-08-16 | E-GEOD-85617 | biostudies-arrayexpress
Project description:To obtain deeper understanding of atmospheric dynamics of the potent greenhouse gas methane, controlling factors of methanotrophs, as the sole biological methane sink, is necessary. Recent research has revealed complex interactions between methanotrophs and heterotrophs, involving volatile organic compounds (VOCs). In environments with high methane concentrations VOC-mediated interactions significantly influence methane cycling and emissions. Here, we employed a multidisciplinary approach, utilizing proteomics, volatile analysis, and measurements of bacterial growth and methane oxidation to elucidate underlying mechanisms of VOC-mediated interactions between heterotrophs and methanotrophs. The results demonstrate that specific VOCs, like dimethylpolysulfides, released by heterotrophic bacteria can inhibit growth and methane uptake of methanotrophs, while other VOCs had the opposite effect. Proteomics analysis revealed differential protein expression patterns depending on exposure to the volatolome of a heterotrophic bacterium or with CO2 added, which was most pronounced with the particulate and soluble methane monooxygenase. The current study demonstrated potential biotic modulation of methanotrophy without direct contact, caused by VOC or CO2 from respiration, or both, with a proteomic response. Although further research is needed to elucidate the specific mechanisms involved, it is clear that methanotroph-heterotroph interactions need to be investigated closer to informs strategies for mitigating emission of the greenhouse gas methane.
2024-08-08 | PXD051964 | Pride
Project description:Natural and anthropogenic wetlands are main sources of the atmospheric greenhouse gas methane. Methane emissions from wetlands are mitigated by methanotrophic microorganisms and by processes at the oxic-anoxic interface, such as sulfur cycling, that reduce the activity of methanogens. In this study, we obtained a pure culture (strain HY1) of a versatile wetland methanotroph that oxidizes various organic and inorganic compounds. This strain represents (i) the first isolate that can aerobically oxidize both methane and reduced sulfur compounds and (ii) a new alphapoteobacterial species, named Candidatus Methylovirgula thiovorans. Genomic and proteomic analyses showed that soluble methane monooxygenase and XoxF-type alcohol dehydrogenases are the only enzymes for methane and methanol oxidation, respectively. Unexpectedly, strain HY1 harbors various pathways for respiratory sulfur oxidation and oxidized reduced sulfur compounds to sulfate using the Sox-rDsr pathway (without SoxCD) and the S4I system. It employed the Calvin-Benson-Bassham cycle for CO2 fixation during chemolithoautotrophic growth on the reduced sulfur compounds. Methane and thiosulfate were independently and simultaneously oxidized by strain HY1 for growth. Proteomic and microrespiratory analyses showed that the metabolic pathways for methane and thiosulfate oxidation were induced in the presence of their substrates. The discovery of this versatile methanotroph demonstrates that methanotrophy and thiotrophy is compatible in a single bacterium and adds a new aspect to interactions of methane and sulfur cycles in oxic-anoxic interface environments.
2022-07-11 | PXD025979 | Pride