Ontology highlight
ABSTRACT:
PROVIDER: PRJNA667171 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Deciphering the in situ activities of microorganisms is essential for understanding the biogeochemical processes occurring in complex environments. Here we used environmental metaproteomics to obtain information about the identity and activity of subsurface microbial populations in coal-tar-contaminated groundwater. The present study reports metaproteomic data showing high representation of Candidatus Methylomirabilis oxyfera in our study site’s subsurface microbial community. In addition, eight of the nine proteins of the n-damo pathway were identified—indicating that n-damo is an active process occurring in situ in this habitat.
2022-02-22 | PXD001035 | Pride
Project description:Deciphering the in situ activities of microorganisms is essential for understanding the biogeochemical processes occurring in complex environments. Here we used environmental metaproteomics to obtain information about the identity and activity of subsurface microbial populations in coal-tar-contaminated groundwater. The present study reports metaproteomic data showing high representation of Candidatus Methylomirabilis oxyfera in our study site’s subsurface microbial community. In addition, eight of the nine proteins of the n-damo pathway were identified—indicating that n-damo is an active process occurring in situ in this habitat.
2022-02-22 | PXD001036 | Pride
Project description:Deciphering the in situ activities of microorganisms is essential for understanding the biogeochemical processes occurring in complex environments. Here we used environmental metaproteomics to obtain information about the identity and activity of subsurface microbial populations in coal-tar-contaminated groundwater. The present study reports metaproteomic data showing high representation of Candidatus Methylomirabilis oxyfera in our study site’s subsurface microbial community. In addition, eight of the nine proteins of the n-damo pathway were identified—indicating that n-damo is an active process occurring in situ in this habitat.
2022-02-22 | PXD001037 | Pride
Project description:Terrestrial deep subsurface Raw sequence reads
| PRJNA482760 | ENA
Project description:This project aims to investigate the metabolic pathways expressed by the active microbial community occurring at the deep continental subsurface. Subsurface chemoLithoautotrophic Microbial Ecosystems (SLiMEs) under oligotrophic conditions are supported by H2; however, the overall ecological trophic structures of these communities are poorly understood. Some deep, fluid-filled fractures in the Witwatersrand Basin, South Africa appear to support inverted trophic pyramids wherein methanogens contributing <5% of the total DNA apparently produce CH4 that supports the rest of the community. Here we show the active metabolic relationships of one such trophic structure by combining metatranscriptomic assemblies, metaproteomic and stable isotopic data, and thermodynamic modeling. Four autotrophic β-proteobacteria genera that are capable of oxidizing sulfur by denitrification dominate. They co-occur with sulfate reducers, anaerobic methane oxidizers and methanogens, which each comprises <5% of the total community. Defining trophic levels of microbial chemolithoautotrophs by the number of transfers from the initial abiotic H2-driven CO2 fixation, we propose a top-down cascade influence of the metabolic consumers that enhances the fitness of the metabolic producers to explain the inverted biomass pyramid of a multitrophic SLiME. Symbiotic partnerships are pivotal in the deep biosphere on and potentially beyond the Earth.
2018-10-27 | PXD004634 | Pride
Project description:Hydrogen can be an important source of energy for chemolithotrophic acidophiles, especially in the deep terrestrial subsurface. Nevertheless, the current knowledge of microbial hydrogen utilization in acidic environments is minimal. A multi-omics analysis was applied on Acidithiobacillus ferrooxidans growing aerobically and anaerobically (with ferric iron) on hydrogen as an electron donor, and a respiratory model proposed from the results obtained. In this model, both [NiFe] hydrogenases, cytoplasmic uptake and membrane-bound respiratory, oxidize molecular hydrogen to two protons and two electrons. The electrons are used to reduce membrane-soluble ubiquinone to ubiquinol. Genetically associated [FeS]-binding proteins mediate electron relay from the hydrogenases to the ubiquinone pool. Under aerobic conditions, reduced ubiquinol transfers electrons to either cytochrome aa3 oxidase via cytochrome bc1 complex and cytochrome c4 or the alternate directly to cytochrome bd oxidase, resulting in proton efflux together with the reduction of molecular oxygen to water. Under anaerobic conditions, reduced ubiquinol transfers electrons to outer membrane cytochrome c (ferric iron reductase) via cytochrome bc1 complex and a cascade of electron transporters (cytochrome c4, cytochrome c552, rusticyanin, and high potential iron-sulfur protein), resulting in proton efflux together with the reduction of ferric iron to ferrous iron. The proton gradient generated by molecular hydrogen oxidation maintains the membrane potential and allows the generation of ATP via ATP synthase and NADH via NADH-ubiquinone oxidoreductase. To a lesser extent, NADH can also be generated by another bidirectional cytoplasmic hydrogenase. ATP and NADH are further utilized in the Calvin–Benson–Bassham cycle for inorganic carbon uptake and assimilation. These results further clarify the role of extremophiles in biogeochemical processes and their impact on the composition and features of the deep terrestrial subsurface from the distant past to the present.
2020-11-24 | PXD020361 | Pride
Project description:Biofilm metagenome from the deep terrestrial subsurface Raw sequence reads
| PRJNA295907 | ENA
Project description:G. uraniireducens was isolated from a subsurface site in Rifle, CO undergoing in situ uranium bioremediation. Sediments from the Rifle site were heat-sterilized, amended with acetate to simulate in situ bioremediation conditions, and inoculated with G. uraniireducens. Gene transcript abundance in these cells using sediment Fe(III) and Mn(IV) oxides as the electron acceptor were compared with transcript levels in cells grown with fumarate as the electron acceptor. Additional comparisons were made between cells grown on synthetic Fe(III) or Mn(IV) oxides and cells grown on fumarate. 3 biological replicates hybridized in duplicate
2010-07-21 | E-GEOD-12874 | biostudies-arrayexpress