Lignocellulose-degrading consortium
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ABSTRACT:
PROVIDER: PRJNA926365 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Draft Genome Sequence of Chitinophaga, isolated from degrading biomass lignocellulose consortium
| PRJEB15907 | ENA
Project description:Microbial communities that degrade lignocellulosic biomass are typified by high levels of species- and strain-level complexity, as well as synergistic interactions between both cellulolytic and non-cellulolytic microorganisms. Here we deconvoluted a highly efficient cellulose-degrading and methanogenic consortium (SEM1b) that is co-dominated by Clostridium (Ruminiclostridium) thermocellum and multiple heterogenic strains affiliated to C. proteolyticus. A time-series analysis was performed over the entire lifetime span of the microbial community and comprised of metagenomic, metatranscriptomic, metabolomics, metaproteomic and 16S rRNA gene analysis for 8 time points, in triplicate. Metagenomic analysis of SEM1b recovered metagenome-assembled genomes (MAGs) for each constituent population, whereas in parallel two novel strains of C. proteolyticus were isolated and sequenced. Both the recovered MAGs and the isolated strains were used as a database for further functional meta-omics. Absolute quantitative metatranscriptomics was performed thanks the spike-in of an in vitro transcribed RNA as an internal standard and label-free quantification was used for the metaproteomic analysis. The present dataset has been used for several publications. The first aim of the project was to characterize the interactions between uncultured populations in a lignocellulose-degrading community. Furthermore, because of the in-depth multi-omics characterization of the community, the dataset was used to develop new approaches for meta-omics integration as well as to assess the protein-to-RNA ratio of multiple microbial populations simultaneously. Modifications of multi-omics toolkits allowed us to assess the linearity between transcriptome and proteome for each population over time and reveal deeper functional-related trends and integrative co-dependent metabolisms that drive the overall phenotype of microbial communities.
2020-08-21 | PXD016242 | Pride
Project description:The genome of the lignocellulose-degrading, extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus encodes genes comprising clusters of glycoside hydrolases, ABC transporters and metabolic enzymes that are transcriptionally responsive to carbohydrates. Transcriptomic and biosolubilization analyses were used to determine if C. saccharolyticus could be deployed as a probe to assess the characteristics of plant biomass feedstocks and efficacy of pre-treatment methods, as these both relate to deconstruction strategies for biofuels production. Based on the response of C. saccharolyticus to plant cell wall polysaccharides, genomic loci were identified that reflected the availability of cellulose, glucomannan, pectin and xylan in biomass to microbial degradation. Furthermore, these loci were useful in assessing how various plant biomass feedstocks (genetically and chemically modified Populus sp., unpretreated Populus sp., and chemically modified switchgrass) were amenable C. saccharolyticus solubilization.
2016-11-23 | GSE90445 | GEO
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:A microbial consortium wsc-9 Metagenome
| PRJNA382431 | ENA
Project description:White-rot basidiomycete fungi are potent degraders of plant biomass with the ability to mineralize all lignocellulose components. Recent comparative genomics studies showed that these fungi use a wide diversity of enzymes for wood degradation. In order to improve our understanding on the enzymatic mechanisms leading to lignocellulose breakdown, we analysed the early response of the white-rot fungus Pycnoporus coccineus CIRM-BRFM310 to various lignocellulosic substrates at two time points; Day 3 and Day 7.
2017-05-21 | GSE94878 | GEO
Project description:lignocellulose-degrading enrichment culture Raw sequence reads
| PRJNA734132 | ENA
Project description:Lignocellulose fractionation by microbial consortia
| PRJEB26853 | ENA
Project description:Producing the fuels and chemicals from renewable plant biomass has been thought as a feasible way for global sustainable development. However, the economical efficiency of biorefinery remains challenges. Here a cellulolytic thermophilic fungus, Myceliophthora thermophila, was constructed into a platform through metabolic engineering, which can efficiently convert lignocellulose to important bulk chemicals for polymers, four carbon 1, 4-diacids (malic and succinic acid), directly from lignocellulose without any extra enzymes addition or complicated pretreatment, with titer of over 200 g/L on cellulose and 110 g/L on plant biomass (corncob) during fed-batch fermentation. Our study represents a milestone of consolidated bioprocessing technology (CBP) and offers a new promising system for cost-effectively production of biomass-based chemicals and potentially fuels.
2021-05-04 | GSE114057 | GEO
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 5‑hydroxymethylfurfural 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.
2014-07-18 | GSE58902 | GEO