DENITRO_FDB
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB73557 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR13341308_1.fastq.gz | Fastqsanger.gz | |||
| ERR13341308_2.fastq.gz | Fastqsanger.gz | |||
| ERR13341309_1.fastq.gz | Fastqsanger.gz | |||
| ERR13341309_2.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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
Project description:Microbial communities in woodchip bioreactors
| PRJNA509197 | ENA
Project description:Woodchip bioreactors bioaugmentation
| PRJEB58151 | ENA
Project description:Lignocellulose fractionation by microbial consortia
| PRJEB26853 | ENA
Project description:In this study, microbial communities from triplicate leach-bed anaerobic bioreactors digesting grass were analysed. Each reactor comprised two microbial fractions, one immobilized on grass (biofilm) and the other in a planktonic state present in the leachate. Microbial communities from the two fractions were systematically investigated for community composition and function. This was carried out using DNA, RNA and protein co-extraction. The microbial structure of each fraction was examined using 16S rRNA deep sequencing, while the active members of the consortia were identified using the same approach on cDNA generated from co-extracted RNA samples. Microbial function was investigated using a metaproteomic workflow combining SDS-PAGE and LC-MS/MS analysis.
2018-10-23 | PXD007956 | Pride
Project description:Lignocellulose, the structural component of plant cells, is a major agricultural by-product and the most abundant terrestrial source of biopolymers on Earth. The complex and insoluble nature of lignocellulose limits its conversion into value-added commodities and, currently, efficient transformation requires expensive pre-treatments and high loadings of enzymes. Here we report on lignocellulolytic enzyme discovery from Parascedosporium putredinis NO1 during its deconstruction of wheat straw probing both the cultural supernatant and selecting for proteins bound to insoluble component of the growth culture.
2020-01-06 | MSV000084758 | MassIVE
Project description:Efficient microbial conversion of lignocellulosic hydrolysates to biofuels is a key barrier to the economically viable deployment of lignocellulosic biofuels. A chief contributor to this barrier is the impact on microbial processes and energy metabolism of lignocellulose-derived inhibitors, including phenolic carboxylates, phenolic amides (for ammonia-pretreated biomass), phenolic aldehydes, and furfurals. To understand the bacterial pathways induced by inhibitors present in ammonia-pretreated biomass hydrolysates, which are less well studied than acid-pretreated biomass hydrolysates, we developed and exploited synthetic mimics of ammonia-pretreated corn stover hydrolysate (ACSH). To determine regulatory responses to the inhibitors normally present in ACSH, we measured transcript and protein levels in an Escherichia coli ethanologen using RNA-seq and quantitative proteomics during fermentation to ethanol of synthetic hydrolysates containing or lacking the inhibitors. Our study identified four major regulators mediating these responses, the MarA/SoxS/Rob network, AaeR, FrmR, and YqhC. Induction of these regulons was correlated with a reduced rate of ethanol production, buildup of pyruvate, depletion of ATP and NAD(P)H, and an inhibition of xylose conversion. The aromatic aldehyde inhibitor 5M-bM-^@M-^Qhydroxymethylfurfural appeared to be reduced to its alcohol form by the ethanologen during fermentation, whereas phenolic acid and amide inhibitors were not metabolized. Together, our findings establish that the major regulatory responses to lignocellulose-derived inhibitors are mediated by transcriptional rather than translational regulators, suggest that energy consumed for inhibitor efflux and detoxification may limit biofuel production, and identify a network of regulators for future synthetic biology efforts. E.coli ethanologen strain GLBRCE1 or GLBRCE1 lacking the plasmid-borne PET cassette (GLBRCE1_pBBR) was grown in AFEX corn stover hydrolysate (ACSH) Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH, and cultures were diluted into ACSH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2. One biological replicate was grown in each medium. RNA samples were obtained at 3 time points, corresponding to exponential (Exp), transitional (Trans), and stationary (Stat) growth phases.
2014-07-18 | E-GEOD-58902 | biostudies-arrayexpress
Project description:Efficient microbial conversion of lignocellulosic hydrolysates to biofuels is a key barrier to the economically viable deployment of lignocellulosic biofuels. A chief contributor to this barrier is the impact on microbial processes and energy metabolism of lignocellulose-derived inhibitors, including phenolic carboxylates, phenolic amides (for ammonia-pretreated biomass), phenolic aldehydes, and furfurals. To understand the bacterial pathways induced by inhibitors present in ammonia-pretreated biomass hydrolysates, which are less well studied than acid-pretreated biomass hydrolysates, we developed and exploited synthetic mimics of ammonia-pretreated corn stover hydrolysate (ACSH). To determine regulatory responses to the inhibitors normally present in ACSH, we measured transcript and protein levels in an Escherichia coli ethanologen using RNA-seq and quantitative proteomics during fermentation to ethanol of synthetic hydrolysates containing or lacking the inhibitors. Our study identified four major regulators mediating these responses, the MarA/SoxS/Rob network, AaeR, FrmR, and YqhC. Induction of these regulons was correlated with a reduced rate of ethanol production, buildup of pyruvate, depletion of ATP and NAD(P)H, and an inhibition of xylose conversion. The aromatic aldehyde inhibitor 5M-bM-^@M-^Qhydroxymethylfurfural appeared to be reduced to its alcohol form by the ethanologen during fermentation, whereas phenolic acid and amide inhibitors were not metabolized. Together, our findings establish that the major regulatory responses to lignocellulose-derived inhibitors are mediated by transcriptional rather than translational regulators, suggest that energy consumed for inhibitor efflux and detoxification may limit biofuel production, and identify a network of regulators for future synthetic biology efforts. Fermentations were carried out in 0.5L bioreactors (Sartorius) containing 0.3L of SynH, SynH lacking osmoprotectants, SynH+LT, or SynH lacking osmoprotectants but containing lignotoxins and cultures were diluted into SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2. Two biological replicates (independent cultures) were grown in each medium. RNA samples were obtained at 4 time points, corresponding to exponential (Exp), transitional (Trans), early stationary (Stat1), and late stationary (Stat2) growth phases.
2014-07-18 | E-GEOD-58976 | biostudies-arrayexpress