Soil metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB19962 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR636340_1.fastq.gz | Fastqsanger.gz | |||
| DRR636340_2.fastq.gz | Fastqsanger.gz | |||
| DRR638528_1.fastq.gz | Fastqsanger.gz | |||
| DRR638528_2.fastq.gz | Fastqsanger.gz | |||
| DRR638529_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 148 |
Similar Datasets
Project description:Rice paddies contribute substantially to atmospheric methane (CH4) and these emissions are expected to increase as the need to feed the human population
grows. Here, we show that two independent rice genotypes overexpressing genes for PLANT PEPTIDES CONTAINING SULFATED TYROSINE (PSY) reduced cumulative CH4 emissions by 38% (PSY1) and 58% (PSY2) over the growth period compared with controls. Genome-resolved metatranscriptomic data from rhizosphere soils reveal lower ratios of gene activities for CH4 production versus consumption, decrease in activity of H2-producing genes, and increase in bacterial H2 oxidation pathways in the PSY genotypes. Metabolic modeling using metagenomic and metabolomic data predicts elevated levels of H2 oxidation and suppressed H2 production in the PSY rhizosphere. The H2- oxidizing bacteria have more genes for utilization of gluconeogenic acids than H2- producing counterparts, and their activities were likely stimulated by the observed enrichment of gluconeogenic acids (mostly amino acids) in PSY root exudates. Together these results suggest that decreased CH4 emission is due to the reduction of H2 available for hydrogenotrophic methanogenesis. The combination of rice phenotypic characterization, microbiome multi-omic analysis, and metabolic modeling described here provides a powerful strategy to discover the mechanisms by which specific plant genotypes can alter biogeochemical cycles to reduce CH4 emissions.
The work (proposal:https://doi.org/10.46936/10.25585/60008481) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.
2025-04-24 | MSV000097725 | MassIVE
Project description:Rice paddies contribute substantially to atmospheric methane (CH4) and these emissions are expected to increase as the need to feed the human populationgrows. Here, we show that two independent rice genotypes overexpressing genes for PLANT PEPTIDES CONTAINING SULFATED TYROSINE (PSY) reduced cumulative CH4 emissions by 38% (PSY1) and 58% (PSY2) over the growth period compared with controls. Genome-resolved metatranscriptomic data from rhizosphere soils reveal lower ratios of gene activities for CH4 production versus consumption, decrease in activity of H2-producing genes, and increase in bacterial H2 oxidation pathways in the PSY genotypes. Metabolic modeling using metagenomic and metabolomic data predicts elevated levels of H2 oxidation and suppressed H2 production in the PSY rhizosphere. The H2- oxidizing bacteria have more genes for utilization of gluconeogenic acids than H2- producing counterparts, and their activities were likely stimulated by the observed enrichment of gluconeogenic acids (mostly amino acids) in PSY root exudates. Together these results suggest that decreased CH4 emission is due to the reduction of H2 available for hydrogenotrophic methanogenesis. The combination of rice phenotypic characterization, microbiome multi-omic analysis, and metabolic modeling described here provides a powerful strategy to discover the mechanisms by which specific plant genotypes can alter biogeochemical cycles to reduce CH4 emissions.
The work (proposal:https://doi.org/10.46936/10.25585/60008481) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.
2024-11-06 | MSV000096316 | MassIVE
Project description:Here we present the assembled genome of the facultative methanotroph, Methylocystis strain SB2, along with assessment of its transcriptome when grown on methane vs. ethanol. As expected, transcriptomic analyses indicate methane is converted to carbon dioxide via the canonical methane oxidation pathway for energy generation, and that carbon is assimilated at the level of formaldehyde via the serine cycle. When grown on ethanol, it appears this strain converts ethanol to acetyl-CoA and then utilizes the TCA cycle for energy generation and the ethylmalonyl CoA pathway for the production of biomass. All cultures were grown in triplicates for subsequent DNA and RNA extraction as well as for subsequent sequencing using Illumina. Transcriptomic analysis results presented in this Series.
2014-03-20 | E-GEOD-51345 | biostudies-arrayexpress
Project description:Here we present the assembled genome of the facultative methanotroph, Methylocystis strain SB2, along with assessment of its transcriptome when grown on methane vs. ethanol. As expected, transcriptomic analyses indicate methane is converted to carbon dioxide via the canonical methane oxidation pathway for energy generation, and that carbon is assimilated at the level of formaldehyde via the serine cycle. When grown on ethanol, it appears this strain converts ethanol to acetyl-CoA and then utilizes the TCA cycle for energy generation and the ethylmalonyl CoA pathway for the production of biomass.
2014-03-20 | GSE51345 | GEO
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
Project description:Experiment to understand relationships between sheep rumen wall transcriptome and microbial methane emissions
2017-12-30 | GSE81847 | GEO
Project description:We established simple synthetic microbial communities in a microcosm model system to determine the mechanisms that underlay cross-feeding in microbial methane-consuming communities. Co-occurring strains from Lake Washington sediment were used that are involved in methane consumption, a methanotroph and two non-methanotrophic methylotrophs.
2016-12-26 | GSE85736 | GEO
Project description:We report here a methanotroph, Methylotuvimicrobium buryatense 5GB1C, that consumes methane at 500ppm at rates several times higher than any previously published. Analyses of bioreactor-based performance and RNAseq based transcriptomics suggest that this superior ability to utilize low methane is based at least in part on an extremely low non-growth associated maintenance energy and on a 5-fold higher methane specific affinity than previous reports.
2023-08-02 | GSE221011 | GEO
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: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