Ontology highlight
ABSTRACT:
PROVIDER: PRJNA473250 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7223680_1.fastq.gz | Fastqsanger.gz | |||
| SRR7223680_2.fastq.gz | Fastqsanger.gz | |||
| SRR7223673_1.fastq.gz | Fastqsanger.gz | |||
| SRR7223673_2.fastq.gz | Fastqsanger.gz | |||
| SRR7223674_1.fastq.gz | Fastqsanger.gz |
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Project description:The fate of the carbon stocked in permafrost soils following global warming and permafrost thaw is of major concern in view of the potential for increased CH4 and CO2 emissions from these soils. Complex carbon compound degradation and greenhouse gas emissions are due to soil microbial communities, but their composition and functional potential in permafrost soils are largely unknown. Here, a 2 m deep permafrost and its overlying active layer soil were subjected to metagenome sequencing, quantitative PCR, and microarray analyses. The active layer soil and 2 m permafrost soil microbial community structures were very similar, with Actinobacteria being the dominant phylum. The two soils also possessed a highly similar spectrum of functional genes, especially when compared to other already published metagenomes. Key genes related to methane generation, methane oxidation and organic matter degradation were highly diverse for both soils in the metagenomic libraries and some (e.g. pmoA) showed relatively high abundance in qPCR assays. Genes related to nitrogen fixation and ammonia oxidation, which could have important roles following climatic change in these nitrogen-limited environments, showed low diversity but high abundance. The 2 m permafrost soil showed lower abundance and diversity for all the assessed genes and taxa. Experimental biases were also evaluated and showed that the whole community genome amplification technique used caused large representational biases in the metagenomic libraries. This study described for the first time the detailed functional potential of permafrost-affected soils and detected several genes and microorganisms that could have crucial importance following permafrost thaw.
2010-03-08 | GSE20073 | GEO
Project description:The fate of the carbon stocked in permafrost soils following global warming and permafrost thaw is of major concern in view of the potential for increased CH4 and CO2 emissions from these soils. Complex carbon compound degradation and greenhouse gas emissions are due to soil microbial communities, but their composition and functional potential in permafrost soils are largely unknown. Here, a 2 m deep permafrost and its overlying active layer soil were subjected to metagenome sequencing, quantitative PCR, and microarray analyses. The active layer soil and 2 m permafrost soil microbial community structures were very similar, with Actinobacteria being the dominant phylum. The two soils also possessed a highly similar spectrum of functional genes, especially when compared to other already published metagenomes. Key genes related to methane generation, methane oxidation and organic matter degradation were highly diverse for both soils in the metagenomic libraries and some (e.g. pmoA) showed relatively high abundance in qPCR assays. Genes related to nitrogen fixation and ammonia oxidation, which could have important roles following climatic change in these nitrogen-limited environments, showed low diversity but high abundance. The 2 m permafrost soil showed lower abundance and diversity for all the assessed genes and taxa. Experimental biases were also evaluated and showed that the whole community genome amplification technique used caused large representational biases in the metagenomic libraries. This study described for the first time the detailed functional potential of permafrost-affected soils and detected several genes and microorganisms that could have crucial importance following permafrost thaw. A 2m deep permafrost sample and it overlying active layer were sampled and their metagenome analysed. For microarray analyses, 8 other soil samples from the same region were used for comparison purposes.
2010-05-06 | E-GEOD-20073 | biostudies-arrayexpress
Project description:To investigate the effect that biological nitrogen fixation will have on plant responses to nitrogen dose at elevated CO2, alfalfa (Medicago sativa) lines were grown at three nitrogen doses and ambient or elevated CO2. Four lines were used in the study, two lines that can form nodules capable of fixing nitrogen (effective lines) and two lines that can not form nodules capable of nitrogen fixation (ineffective lines). The ineffective lines are the result of a complementary mutation in the same gene.
2024-02-26 | GSE244008 | GEO
Project description:Diatoms are a major primary producer accounting for 20% of the global primary production. Their massive carbon fixation is driven by the CO2-concentrating mechanisms (CCM), in which CO2 is actively supplied to the Rubisco localized in the pyrenoid, a membrane-less organelle of the plastid. To promote CO2 fixation, CO2 concentration in the pyrenoid matrix is assumed to be elevated while leakage of CO2 is minimized. However, due to the lack of information on the structural basis of diatom pyrenoid, the mechanism allowing efficient CO2 supply in conjunction with pyrenoid structure remains to be elucidated. While isolation of diatom pyrenoid is technically difficult due to structural instability, here we applied in vivo crosslinking using photo amino acids (pAA) which enabled us to obtain Rubisco enriched fractions. Based on LC-MS/MS analysis of the RbcL-enriched fraction, we identified a novel protein that surrounds the pyrenoid like a shell and hence named a Pyshell (Pyrenoid shell). Using genome-edited mutants, Pyshell was demonstrated to be a critical component required for growth under CO2-limiting conditions. The comprehensive analysis and identification of the pyrenoid component gave an important insight into the molecular basis driving the oceanic primary production.
2024-05-04 | PXD041920 | JPOST Repository
Project description:Carbon fixation plays a central role in determining cellular redox poise, increasingly understood to be a key parameter in cyanobacterial physiology. In the cyanobacterium Prochlorococcus--—the most abundant phototroph in the oligotrophic oceans--—the carbon-concentrating mechanism (CCM) is reduced to the bare essentials. Given the ability of Prochlorococcus populations to grow under a wide range of oxygen concentrations in the ocean, we wondered how carbon and oxygen physiology intersect in this minimal phototroph. We monitored genome-wide transcription in cells shocked with acute limitation of CO2, O2, or both. O2 limitation produced much smaller transcriptional changes than the broad suppression seen under CO2 limitation and CO2/O2 co-limitation. Strikingly, the transcriptional responses evoked by both CO2 limitation conditions were initially similar to that previously seen in high light stress, but at later timepoints we observed O2-dependent recovery of photosynthesis-related transcripts. These results suggest that oxygen plays a protective role in Prochlorococcus when carbon fixation is not a sufficient sink for light energy.
2015-04-15 | GSE65684 | GEO
Project description:Regulation of CO2 fixation in cyanobacteria is important both for the organism and the global carbon balance. Here we show that phosphoketolase in Synechococcus elongatus PCC7942 (SeXPK) possesses a distinct ATP sensing mechanism, which upon ATP drops, allows SeXPK to divert precursors of the RuBisCO substrate away from the Calvin-Benson-Bassham (CBB) cycle. Deleting the SeXPK gene increased CO2 fixation particularly during light-dark transitions. In high-density cultures, the xpk strain showed a 60% increase in carbon fixation, and unexpectedly resulted in sucrose secretion without any pathway engineering. Using cryo-EM analysis, we discovered that these functions were enabled by a unique allosteric regulatory site involving two subunits jointly binding two ATP, which constantly suppresses the activity of SeXPK until the ATP level drops. This magnesium-independent ATP allosteric site is present in many species across all three domains of life, where it may also play important regulatory functions.
2023-08-08 | GSE227397 | GEO
Project description:The pyrenoid, a single microcompartment of the chloroplasts of most algae and hornworts, is the major site of CO2 fixation. To compensate the limited availability of CO2 in aquatic environments due to slower CO2 diffusion in water than air, the RubisCO-containing pyrenoid is involved in a carbon concentrating mechanism (CCM) and promotes the carboxylase activity rather than the oxygenase activity of RubisCO, the Calvin-Benson cycle enzyme catalyzing the first step of CO2 fixation. Data in the literature suggest that pyrenoid can have other functions in addition to CO2 fixation. To decipher its functions, the characterization of the pyrenoid proteome in the microalga Chlamydomonas reinhardtii was undertaken. Pyrenoid-enriched fractions from two independent biological cultures (sample1 and sample2) were obtained from cells (WT-cell) or isolated chloroplasts (WT-cp) either from the wild-type (WT) strain or from pyrenoid-deficient Chlamydomonas strains (MX-CW15 and SS-AT) and analyzed by nLC-MS/MS. Substractive proteomic analysis allowed the identification of contaminant proteins and the characterization of the pyrenoid proteome.
2018-02-28 | PXD004509 | Pride