CO2-fixation bacterial
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA757792 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:Seven carbon autotrophic fixation pathways were described so far. However, it is not common to find the co-existence of more than one cycle in a single cell. Here, we describe a thermophilic bacterium Carbonactinospora thermoautotrophica StC with a unique and versatile carbon metabolism. StC was isolated from a consortium found in a burning organic pile that exhibits an optimal growth temperature between 55° and 65° C. The genome analyses suggested that the strain StC potentially performs two-carbon fixation pathways, Calvin-Benson-Bassham (CBB) cycle and the Reductive citrate cycle (rTCA) and preserve a microcompartment related with CO2 concentration. To better understand the carbon fixation in StC strain, the expression of the genes of bacterial cells grown autotrophically and heterotrophically were analyzed. For our surprise the data showed the co-existing of the both carbon fixation pathways - CBB and rTCA cycles - in a cultivable thermophilic chemoautotrophic bacterium Carbonactinospora thermoautotrophica strain StC, based on integrated omics of genomics, transcriptomics, and proteomics. These two cycles working together may help microorganisms to improve the CO2 fixation. The knowledge about the co-occurrence of carbon cycle in a single cell leads open a question ‘why microorganisms use multiple pathways to fix carbon and what the advantage for this strategy?’. Advancing on this is a key to better understand the biological carbon fixation mechanism in thermophiles and prospecting the repurposing of enzymes in synthetic biology for biotechnological applications.
2024-04-09 | GSE263135 | 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: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:The melting of permafrost and its potential impact on greenhouse gas emissions is a major concern in the context of global warming. The fate of the carbon trapped in permafrost will largely depend on soil physico-chemical characteristics, among which are the quality and quantity of organic matter, pH and water content, and on microbial community composition. In this study, we used microarrays and real-time PCR (qPCR) targeting 16S rRNA genes to characterize the bacterial communities in three different soil types representative of various Arctic settings. The microbiological data were linked to soil physico-chemical characteristics and CO2 production rates. Microarray results indicated that soil characteristics, and especially the soil pH, were important parameters in structuring the bacterial communities at the genera/species levels. Shifts in community structure were also visible at the phyla/class levels, with the soil CO2 production rate being positively correlated to the relative abundance of the Alphaproteobacteria, Bacteroidetes, and Betaproteobacteria. These results indicate that CO2 production in Arctic soils does not only depend on the environmental conditions, but also on the presence of specific groups of bacteria that have the capacity to actively degrade soil carbon.
2011-01-01 | GSE24800 | GEO
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. Two biological replicates of timecourses under four conditions: medium bubbled with air (control) or three experimental gases (low CO2; low O2; or low CO2 and low O2)
2015-04-15 | E-GEOD-65684 | biostudies-arrayexpress
Project description:The melting of permafrost and its potential impact on greenhouse gas emissions is a major concern in the context of global warming. The fate of the carbon trapped in permafrost will largely depend on soil physico-chemical characteristics, among which are the quality and quantity of organic matter, pH and water content, and on microbial community composition. In this study, we used microarrays and real-time PCR (qPCR) targeting 16S rRNA genes to characterize the bacterial communities in three different soil types representative of various Arctic settings. The microbiological data were linked to soil physico-chemical characteristics and CO2 production rates. Microarray results indicated that soil characteristics, and especially the soil pH, were important parameters in structuring the bacterial communities at the genera/species levels. Shifts in community structure were also visible at the phyla/class levels, with the soil CO2 production rate being positively correlated to the relative abundance of the Alphaproteobacteria, Bacteroidetes, and Betaproteobacteria. These results indicate that CO2 production in Arctic soils does not only depend on the environmental conditions, but also on the presence of specific groups of bacteria that have the capacity to actively degrade soil carbon. Three different soil types from the Canadian high Arctic were sampled at two depths within the active layer of soil and at two sampling dates (winter and summer conditions), for a total of 20 samples.
2011-01-01 | E-GEOD-24800 | biostudies-arrayexpress
Project description:Cyanobacteria are oxygenic photoautotrophs notable for their ability to utilize atmospheric CO2 as the major source of carbon. The prospect of using cyanobacteria in converting solar energy and high concentrations of CO2 (e.g. flue gas from coal power plants) efficiently into biomass and renewable energy sources is of interest to many research fields. In order to guide further advances in this area, a better understanding about the metabolic changes that occur under conditions of high CO2 is important. The objective of this study is to utilize genome-wide microarray expression profiling in the unicellular diazotrophic cyanobacterium Cyanothece 51142 grown in 8% CO2-enriched air and to determined the impact of high CO2 on cyanobacterial cell physiology and growth.
2012-10-30 | GSE37621 | GEO
Project description:Bacterial community in nanoparticle-polluted soils under elevated CO2 Raw sequence reads
| PRJNA700848 | ENA
Project description:RECIRCULATION OF H2, CO2, AND ETHYLENE IMPROVES YIELDS AND CARBON FIXATION OF ANAEROBIC FERMENTATION
| PRJEB41050 | ENA