Nitrate reduction & Fe(II) oxidation in paddy soil
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ABSTRACT:
PROVIDER: PRJEB11487 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Investigation of whole genome gene expression level changes in anaerobic, nitrate-dependent Fe(II) oxidation in the chemolithoautotrophic bacterium Thiobacillus denitrificans
2013-08-15 | GSE46339 | GEO
Project description:Investigation of whole genome gene expression level changes in anaerobic, nitrate-dependent Fe(II) oxidation in the chemolithoautotrophic bacterium Thiobacillus denitrificans Here we report on a study to identify genes associated with nitrate-dependent Fe(II) oxidation by whole-genome transcriptional (microarray) assays including the use of FeCO3, Fe2+, and U(IV) oxides as electron donors under denitrifying conditions. A 25 chip study using total RNA recovered from wild-type T. denitrificans was cultivated at 30oC under strictly anaerobic conditions with growth medium that contained 20 mM thiosulfate, 20 mM nitrate, and 30 mM bicarbonate (pH ~7) and exposed to 8 treatments. Each chip measures the expression level of 2832 ORFs with N 24-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.
2013-08-15 | E-GEOD-46339 | biostudies-arrayexpress
Project description:Fe(II) can be oxidized by mixotrophic nitrate-reducing Fe(II)-oxidizing bacteria to Fe(III), leading to mineral precipitation. However, the effects of this process on the metabolism and reproduction ability of the Fe(II)-oxidizing bacterial cells have not yet been quantified. In this study, we investigated the effects of Fe(II) on the mixotrophic nitrate-reducing Fe(II)-oxidizing bacteria Acidovorax sp. BoFeN1 by performing cell plate counts, chemical analyses, and scanning electron microscopy (SEM) imaging. The result showed that nitrate-reducing Fe(II)-oxidizing bacteria Acidovorax sp. BoFeN1 undergoes a striking physiological state in which respiration persists while cell reproduction collapses after their oxidation of Fe(II). Across 0.1–10 mM Fe(II), colony-forming units dropped by up to 103-fold, yet acetate consumption remained largely unaffected and nitrate reduction was even slightly promoted. SEM-EDS reveals extensive Fe(III) encrustation on cells. Adding an Fe(III) chelator, citrate, restored reproductive capacity without notably changes in Fe(II) oxidation or nitrate reduction, indicating that it was the products of Fe(II) oxidation, the secondary Fe(III) minerals, that impaired cell reproduction. These findings uncover a mineral encrustation-driven uncoupling between respiration and reproduction, suggest how natural organic ligands may buffer NRFeOx bacterial communities in Fe-rich anoxic environments, and point to cellular-level levers for mitigating denitrification failures and N2O risks in engineered and natural systems.
2026-01-01 | PXD072688 |
Project description:Pelobacter carbinolicus is phylogenetically intertwined with the Geobacteraceae, a family of deltaproteobacteria which couple oxidation of organic compounds to Fe(III) reduction. Whereas Geobacter species completely oxidize organic compounds to CO2, Pelobacter species either ferment or oxidize short chain alcohols to acetate. Pelobacter species also contain far fewer c-type cytochromes, proteins which play a role in electron transfer during Fe(III) respiration, compared to their Geobacter counterparts. Keywords: two-condition comparison
2008-05-22 | GSE8338 | GEO
Project description:Pelobacter carbinolicus is phylogenetically intertwined with the Geobacteraceae, a family of deltaproteobacteria which couple oxidation of organic compounds to Fe(III) reduction. Whereas Geobacter species completely oxidize organic compounds to CO2, Pelobacter species either ferment or oxidize short chain alcohols to acetate. Pelobacter species also contain far fewer c-type cytochromes, proteins which play a role in electron transfer during Fe(III) respiration, compared to their Geobacter counterparts. Keywords: two-condition comparison Three biological replicates were hybridized in duplicate. Experimental (FeIII) was labeled with cy5, control (acetoin) was labeled with cy3.
2008-05-21 | E-GEOD-8338 | biostudies-arrayexpress
Project description:Nitrate-reducing iron(II)-oxidizing bacteria are widespread in the environment contribute to nitrate removal and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and poorly understood. The most prominent model system for this type of studies is enrichment culture KS, which originates from a freshwater sediment in Bremen, Germany. To gain insights in the metabolism of nitrate reduction coupled to iron(II) oxidation under in the absence of organic carbon and oxygen limited conditions, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture KS. Raw sequencing data of 16S rRNA amplicon sequencing, shotgun metagenomics (short reads: Illumina; long reads: Oxford Nanopore Technologies), metagenome assembly, raw sequencing data of shotgun metatranscriptomes (2 conditions, triplicates) can be found at SRA in https://www.ncbi.nlm.nih.gov/bioproject/PRJNA682552. This dataset contains proteomics data for 2 conditions (heterotrophic and autotrophic growth conditions) in triplicates.
2021-05-17 | PXD023186 | Pride
Project description:Nitrate-reducing iron(II)-oxidizing (NDFO) bacteria are widespread in the environment contribute to nitrate removal and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and poorly understood. The most prominent model system for this type of studies is enrichment culture KS, which originates from a freshwater sediment in Bremen, Germany. A second NDFO culture, culture BP, was obtained with a sample taken in 2015 at the same pond and cultured in a similar way. To gain insights in the metabolism of nitrate reduction coupled to iron(II) oxidation under in the absence of organic carbon and oxygen limited conditions, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture BP. Raw sequencing data of 16S rRNA amplicon sequencing (V4 region with Illumina and near full-length with PacBio), shotgun metagenomics, metagenome assembly, raw sequencing data of shotgun metatranscriptomes (2 conditions, triplicates) can be found at SRA in https://www.ncbi.nlm.nih.gov/bioproject/PRJNA693457. This dataset contains proteomics data for 2 conditions in triplicates. Samples R23, R24, and R25 are grown in autotrophic conditions, samples R26, R27, and R28 in heterotrophic conditions.
2021-05-17 | PXD023710 | Pride
Project description:Geobacter sulfurreducens is a widely explored microorganism recognized by its metabolic versatility able to reduce a number of external electron acceptors. In the present study the capacity of this strain to reduce nitrate was evaluated along with its transcriptomic profile under nitrate-reducing conditions and the catalytic role of Pd nanoparticles on the reductive pathway. Results demonstrated that G. sulfurreducens was able to reduce nitrate and important kinetic differences related to the time response were found among the electron donors used (acetate and hydrogen). When using acetate, a delay response on nitrate reduction of 4 days and reduction of 94% of nitrate was achieved, while nitrite was not detected, and all the nitrogen was recovered as ammonium (79.6 ± 5.7 %). The use of hydrogen as electron donor increased 2-fold the maximum rate of nitrate reduction, leading to 93% reduction of nitrate during the first 20 h with recovery of 45% as ammonium, while nitrite was not detected. In addition, transcriptome profiling analysis of G. sulfurreducens under nitrate-reducing conditions using hydrogen or acetate as an electron donor at 2 and 6 days reveals that a core of 146 genes (69 upregulated and 77 downregulated) are differentially expressed in all conditions. Genes related to nitrogen metabolism, such as nrfA and nrfH, gdhA, and amtB, were upregulated in the incubations and RT-qPCR data confirmed upregulations of these genes. Experiments performed with biologically synthesized Pd (Bio-Pd) + G. sulfurreducens cells demonstrated synergistic input of Bio-Pd and the metabolic capacity of G. sulfurreducens. These results expand the metabolic versatility of G. sulfurreducens, which may have important implications in nitrogen cycling in natural environments and engineered systems.
2023-06-01 | GSE179298 | GEO
Project description:Nitrate-dependent anaerobic propane and butane oxidation coupled to anaerobic ammonium oxidation
2024-05-24 | PXD039266 | Pride
Project description:AOM coupled to nitrate reduction reactor Genome sequencing and assembly
| PRJNA836951 | ENA