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ABSTRACT: Amplicon sequencing from vinyl chloride degrading bioactive granular active carbon bioreactors

PROVIDER: PRJNA553156 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR9654570_1.fastq.gz	Fastqsanger.gz
	SRR9654570_2.fastq.gz	Fastqsanger.gz
	SRR9654571_1.fastq.gz	Fastqsanger.gz
	SRR9654571_2.fastq.gz	Fastqsanger.gz

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Microbial consortia driving lignocellulose transformation in agricultural woodchip bioreactors

Project description:Freshwater ecosystems can be largely affected by neighboring agriculture fields where potential fertilizer nitrate run-off may leach into surrounding water bodies. To counteract this eutrophic driver, farmers often utilize denitrifying woodchip bioreactors (WBRs) in which a consortium of microorganisms convert the nitrate into nitrogen-gases in anoxia, fueled by the degradation of lignocellulose. Polysaccharide-degrading strategies have been well-described for various aerobic and anaerobic systems, including the use of carbohydrate-active enzymes, utilization of lytic polysaccharide monooxygenases (LPMOs) and other redox enzymes, as well as the use of cellulosomes and polysaccharide utilization loci. However, for denitrifying microorganisms, the lignocellulose-degrading strategies remain largely unknown. Here, we have applied a combination of enrichment techniques, gas measurements, multi-omics approaches, and amplicon sequencing of fungal ITS and procaryotic 16S rRNA genes to highlight microbial drivers for lignocellulose transformation in woodchip bioreactors with the aim to provide an in-depth characterization of the indigenous microorganisms and their active enzymes. Our findings highlight a microbial community enriched for lignocellulose-degrading denitrifiers with key players from Giesbergeria, Cellulomonas, Azonexus, and UBA5070, including polysaccharide utilization loci from Bacteroidetes. A wide substrate specificity is observed among the many expressed carbohydrate active enzymes (CAZymes), evidencing a swift degradation of lignocellulose, including even enzymes with auxiliary activities whose functionality is still puzzling under strict anaerobic conditions.

2024-10-21 | PXD050137 | Pride

Nocardioides sp. JS614

Project description:A vinyl chloride assimilating bacteria

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Dehalococcoides mccartyi BAV1

Project description:Degrades dichloroethenes and vinyl chloride

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Dehalococcoides mccartyi VS strain:VS

Project description:A reductive dehalonater of vinyl chloride

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Part2: Dual element (C/Cl) isotope analysis indicates distinct mechanisms of reductive dehalogenation of chlorinated ethenes and dichloroethane in Dehalococcoides mccartyi strain BTF08 with defined reductive dehalogenase inventories

Project description:Dehalococcoides mccartyi strain BTF08 has the unique property to couple complete dechlorination of tetrachloroethene and 1,2-dichloroethane to ethene with growth by using the halogenated compounds as terminal electron acceptor. The genome of strain BTF08 encodes 20 genes for reductive dehalogenase homologous proteins (RdhA) including those described for dehalogenation of tetrachloroethene (PceA, PteA), trichloroethene (TceA) and vinyl chloride (VcrA). Thus far it is unknown under which conditions the different RdhAs are expressed, what their substrate specificity is and if different reaction mechanisms are employed. Here we found by proteomic analysis from differentially activated batches that PteA and VcrA were expressed during dechlorination of tetrachloroethene to ethene, while TceA was expressed during 1,2-dichloroethane dehalogenation. Carbon and chlorine compound-specific stable isotope analysis suggested distinct reaction mechanisms for the dechlorination of (i) cis-dichloroethene and vinyl chloride and (ii) tetrachloroethene. This differentiation was observed independent of the expressed RdhA proteins. Differently, two stable isotope fractionation patterns were observed for 1,2-dichloroethane transformation, for cells with distinct RdhA inventories. Conclusively, we could link specific RdhA expression with functions and provide an insight into the apparently substrate-specific reaction mechanisms in the pathway of reductive dehalogenation in D. mccartyi strain BTF08.

2020-06-25 | PXD018595 | Pride

Dual element (C/Cl) isotope analysis indicates distinct mechanisms of reductive dehalogenation of chlorinated ethenes and dichloroethane in Dehalococcoides mccartyi strain BTF08 with defined reductive dehalogenase inventories

2020-06-10 | PXD018558 | Pride

dechlorinating enrichment culture KB-1

Project description:Vinyl Chloride Degradation by Mixed Microbial Community KB1

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Genome-resolved meta-omics ties microbial dynamics to process performance in biotechnology for thiocyanate degradation

Project description:The work provides an organism-level framework describing the mechanisms underlying SCN- degradation, and opens possibilities for improving efficiency and nitrogen removal in SCN-degrading bioreactors for bioremediation of Industrial wastewater.

2016-08-29 | MSV000080104 | MassIVE

Genome-wide transcriptional changes induced by different carbon sources and carbon starvation in Aspergillus nidulans

Project description:Understanding the coordinated regulation of the hundreds of carbohydrate-active enzyme (CAZyme) genes occurring in the genomes of fungi has great practical importance. We recorded genome-wide transcriptional changes of Aspergillus nidulans cultivated on glucose, lactose or arabinogalactan as well as under carbon starved conditions. We determined both carbon stress specific changes (a carbon stress vs. glucose) and culture specific changes (a culture vs. all other cultures). Many CAZyme genes showed carbon stress specific and/or culture specific upregulation on arabinogalactan (138 and 62 genes, respectively). Besides galactosidase and arabinan degrading enzyme genes, enrichment of cellulolytic, pectinolytic, mannan and xylan degrading enzyme genes were observed in these gene sets. Less, 81 and 107 carbon stress specific as well as 6 and 16 culture specific upregulated genes were found on lactose and in carbon starved cultures, respectively. They were enriched only in galactosidase and xylosidase genes on lactose and rhamnogalacturonanase genes in both cultures. Some CAZyme genes (29 genes) showed culture specific upregulation on glucose and they were enriched in beta-1,4-glucanase genes. Behavioral ecological background of these characteristics was evaluated to organize comprehensively our knowledge on CAZyme production, which can lead to develop new strategies to produce enzymes for plant cell wall saccharification.

2022-01-26 | GSE189016 | GEO

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

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