Deep subsurface sample
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA642293 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14866092.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 1 of 1 |
Similar Datasets
Project description:Bicarbonate metabolising microorganisms from deep granitic subsurface through selective enrichment
| PRJNA643233 | ENA
Project description:Organic carbon metabolising microorganisms from deep granitic subsurface through selective enrichment
| PRJNA644301 | ENA
Project description:Subsurface weathering of granitic minerals by microorganisms
| PRJNA523798 | ENA
Project description:Members of the bacterial phylum Spirochaetes are primarily studied for their commensal and pathogenic roles in animal hosts. However, Spirochaetes are also frequently detected in anoxic hydrocarbon-contaminated environments but their ecological role in such ecosystems has so far remained unclear. Here we provide a functional trait to these frequently detected organisms with an example of a sulfate-reducing, naphthalene-degrading enrichment culture consisting of a sulfate-reducing deltaproteobacterium Desulfobacterium naphthalenivorans and a novel spirochete Rectinema cohabitans. Using a combination of genomic, proteomic, and physiological studies we show that R. cohabitans grows by fermentation of organic compounds derived from biomass from dead cells (necromass). It recycles the derived electrons in the form of H2 to the sulfate-reducing D. naphthalenivorans, thereby supporting naphthalene degradation and forming a simple microbial loop. We provide metagenomic evidence that equivalent associations between Spirochaetes and hydrocarbon-degrading microorganisms are of general importance in hydrocarbon- and organohalide-contaminated ecosystems. We propose that environmental Spirochaetes form a critical component of a microbial loop central to nutrient cycling in subsurface environments. This emphasizes the importance of necromass and H2-cycling in highly toxic contaminated subsurface habitats such as hydrocarbon-polluted aquifers.
2018-05-17 | PXD005624 | Pride
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:Terrestrial deep subsurface Raw sequence reads
| PRJNA482760 | ENA
Project description:Olkiluoto deep subsurface groundwater activations
| PRJEB28560 | ENA
Project description:Genetic diversity in terrestrial subsurface ecosystems impacted by geological degassing
| PRJNA767587 | ENA
Project description:The unique capability of acetogens to ferment a broad range of substrates renders them ideal candidates for the biotechnological production of commodity chemicals. In particular the ability to grow with H2:CO2 or syngas (a mixture of H2/CO/CO2) makes these microorganisms ideal chassis for sustainable bioproduction. However, advanced design strategies for acetogens are currently hampered by incomplete knowledge about their physiology and our inability to accurately predict phenotypes. Here we describe the reconstruction of a novel genome-scale model of metabolism and macromolecular synthesis (ME-model) to gain new insights into the biology of the model acetogen Clostridium ljungdahlii. The model represents the first ME-model of a Gram-positive bacterium and captures all major central metabolic, amino acid, nucleotide, lipid, major cofactors, and vitamin synthesis pathways as well as pathways to synthesis RNA and protein molecules necessary to catalyze these reactions, thus significantly broadens the scope and predictability. Use of the model revealed how protein allocation and media composition influence metabolic pathways and energy conservation in acetogens and accurately predicted secretion of multiple fermentation products. Predicting overflow metabolism is of particular interest since it enables new design strategies, e.g. the formation of glycerol, a novel product for C. ljungdahlii, thus broadening the metabolic capability for this model microbe. Furthermore, prediction and experimental validation of changing secretion rates based on different metal availability opens the window into fermentation optimization and provides new knowledge about the proteome utilization and carbon flux in acetogens.
2024-01-11 | MODEL2204200003 | BioModels
Project description:Acetate is a simple carboxylic acid that is synthesized in various microorganisms. Although acetate toxicity and tolerance have been studied in many microorganisms, little is known about the effects of exogenous acetate on the cell growth of acetogenic bacteria. In this study, we report the phenotypic changes that occurred in the acetogenic bacterium Clostridium sp. AWRP as a result of an adaptive laboratory evolution under acetate challenge. When compared with the wild-type strain, the acetate-adapted strain displayed a tolerance to acetate up to 10 g L-1 and higher biomass yields in batch cultures, although the metabolite profiles greatly varied depending on culture conditions. Interestingly, genome sequencing revealed that the adapted strain harbored three point mutations in the genes encoding an electron-bifurcating hydrogenase, which is crucial to its autotrophic growth on CO2 + H2, in addition to one in the dnaK gene. Transcriptome analysis revealed the global change in the gene expression profile of the acetate-adapted strain. Strikingly, most genes involved in CO2-fixing Wood-Ljungdahl pathway and auxiliary pathways for energy conservation (e.g., Rnf complex, Nfn, etc.) were significantly down-regulated. In addition, we observed that a couple of metabolic pathways associated with dissimilation of nucleosides and carbohydrates were significantly up-regulated in the acetate-adapted strain as well as several amino acid biosynthetic pathways, indicating that the strain might increase its fitness by utilizing organic substrates in response to the down-regulation of carbon fixation. Further investigation into the carbon fixation degeneration of the acetate-adapted strain will provide practical implications in CO2 + H2 fermentation using acetogenic bacteria for long-term continuous fermentation. The transcriptome profiles of the wild-type Clostridium sp. AWRP and its acetate-tolerant derivative 46T-a were compared.
2022-06-26 | GSE206757 | GEO