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ABSTRACT: composition and diversity of nitrate-reducing Fe(II)-oxidizing (NRFeOx) microorganisms

PROVIDER: PRJNA769796 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16267500_1.fastq.gz	Fastqsanger.gz
	SRR16267500_2.fastq.gz	Fastqsanger.gz
	SRR16267489_1.fastq.gz	Fastqsanger.gz
	SRR16267489_2.fastq.gz	Fastqsanger.gz
	SRR16267490_1.fastq.gz	Fastqsanger.gz

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Project description:Diversity of the autotrophic, nitrate-reducing, Fe(II)-oxidizing enrichment culture KS

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LC-MS/MS of autotrophic culture KS, that performs nitrate reduction coupled to iron(II) oxidation (NDFO)

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

LC-MS/MS of autotrophic culture BP, that performs nitrate reduction coupled to iron(II) oxidation (NDFO)

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

freshwater sediment metagenome

Project description:Multi-omics of the nitrate-reducing iron(II)-oxidizing culture BP

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Project description:Multi-omics of the nitrate-reducing iron(II)-oxidizing culture KS

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[Acidovorax] ebreus strain:LS-1

Project description:Transcriptome analysis of Nitrate-reducing Fe(II)-oxidizing bacteria Acidovorax ebreus LS-1 isolated from a Paddy Soil Field

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Rhodopseudomonas palustris TIE-1

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Genome-enabled studies of anaerobic, nitrate-dependent Fe(II) oxidation in the chemolithoautotrophic bacterium Thiobacillus denitrificans

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

Transcription profiling of wild type G. sulfurreducens DL1 strain and mutant DLCN16 (delta-rpoS::Km) using ferric citrate as an electron acceptor

Project description:Wild type G. sulfurreducens DL1 strain (see Caccavo, F., Jr., D. J. Lonergan, D. R. Lovley, M. Davis, J. F. Stolz, and M. J. McInerney. 1994. Geobacter sulfurreducens sp. nov., a hydrogen- and acetate-oxidizing dissimilatory metal-reducing microorganism. Appl Environ Microbiol 60:3752-9. see also Coppi, M. V., C. Leang, S. J. Sandler, and D. R. Lovley. 2001. Development of a genetic system for Geobacter sulfurreducens. Appl Environ Microbiol 67:3180-7.) and DLCN16 mutant (.rpoS::Km) (see Nuñez, C., L. Adams, S. Childers, and D. R. Lovley. 2004. The RpoS sigma factor in the dissimilatory Fe(III)-reducing bacterium Geobacter sulfurreducens. J Bacteriol 186:5543-6.) were grown under anaerobic conditions at 30 °C in continuous culture with a 200 ml working volume as previously described (see Esteve-Nunez, A., M. Rothermich, M. Sharma, and D. Lovley. 2005. Growth of Geobacter sulfurreducens under nutrient-limiting conditions in continuous culture. Environ Microbiol 7:641-8.). Cells were cultured at a growth rate of 0.05 h-1, steady-state cell growth was obtained after 5 volume refills and was confirmed by a constant cell density and concentrations of Fe(II). Acetate (5.5 mM) was the electron donor and the limiting substrate. The electron acceptor was Fe(III)-citrate (60mM). Two biological replicates of control and treatment cells were obtained to produce hybridizations for this experiment.

2005-01-01 | E-TIGR-123 | biostudies-arrayexpress

Genome-enabled studies of anaerobic, nitrate-dependent Fe(II) oxidation in the chemolithoautotrophic bacterium Thiobacillus denitrificans

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

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