Similar Datasets
Project description:This study examines the transcriptomic response of biofilms of the PAH-degrading Sphingomonas sp. LH128 on solute stress when actively degrading and growing on the PAH compound. To address the effect of solute stress on bacterial physiology and transcriptomic response, NaCl was used as osmolyte. Both acute and chronic solute stress was invoked to assess differences in short-term and long-term responses.
2012-06-18 | GSE38296 | GEO
Project description:We report the differential expression of a PAH degrading bacterium in different states of substrate induction.
2013-02-22 | GSE44536 | GEO
Project description:We report the differential expression of a PAH degrading bacterium in different states of substrate induction. Separate substrate cultivation of the same batch of bacterial isolates; total RNA extraction, processing and sequencing; gene expression analysis using bioinformatics softwares and experimental validation using qRT-PCR.
2013-02-22 | E-GEOD-44536 | biostudies-arrayexpress
Project description:This study examines the transcriptomic response of biofilms of the PAH-degrading Sphingomonas sp. LH128 on solute stress when actively degrading and growing on the PAH compound. To address the effect of solute stress on bacterial physiology and transcriptomic response, NaCl was used as osmolyte. Both acute and chronic solute stress was invoked to assess differences in short-term and long-term responses. Transcriptomic response of phenanthrene degrading Sphingomonas sp. LH128 biofilms as a response to short-term and long-term solute (NaCl) stress was studied using genome-wide gene expression analysis. For this purpose, the strain was grown in customized continuous glass flow chambers that contain solid phenanthrene as a sole carbon source and that allow easy recovery of biofilm cells for transcriptomic and physiological analysis. A NaCl stress of 450 mM was imposed on LH128 biofilms growing on phenanthrene crystals coated on glass slides either for 4 hours (acute stress) or for 3 days (chronic stress). RNA was extracted from the biofilm and cDNA was synthesized and labeled with Cy3. Transcriptomic response in the stressed biofilms of three replicates per conditions were analyzed and compared with non-stressed
2012-06-18 | E-GEOD-38296 | biostudies-arrayexpress
Project description:Filamentous fungi are widely used in the production of biomass degrading enzymes, e.g. cellulases and pectinases. In order to study the secretome of biomass degrading fungi, proteomics studies were carried out on the extracellular proteins of fungal strains.
2024-01-03 | PXD048232 | iProX
Project description:Wood-degrading fungi play a critical role in global carbon cycling, and their varied mechanisms for deconstruction offer pathways for industrial bioconversion. In this study, we used comparative genomics to isolate upregulation patterns among fungi with brown rot (carbohydrate-selective) or white rot (lignin-degrading) nutritional modes. Specifically, we used whole-transcriptome profiling to compare early, middle, and late decay stages on wood wafers, matching differentially-expressed gene (DEG) patterns with fungal growth and enzyme activities. This approach highlighted 34 genes uniquely upregulated in early brown rot stages, with notable candidates involved in generating reactive oxygen species (ROS) as a pretreatment mechanism during brown rot. This approach further isolated 18 genes in late brown rot stages that may be adapted to handle oxidatively-reacted lignocellulose components. By summing gene expression levels in functional classes, we also identified a broad and reliable distinction in glycoside hydrolase (GH) versus lignocellulose oxidative (LOX) transcript counts that may reflect the energy investment burden of lignin-degrading machinery among white rot fungi.
2018-01-05 | GSE108189 | GEO
Project description:Decomposition of soil organic matter in forest soils is thought to be controlled by the activity of saprotrophic fungi, while biotrophic fungi including ectomycorrhizal fungi act as vectors for input of plant carbon. The limited decomposing ability of ectomycorrhizal fungi is supported by recent findings showing that they have lost many of the genes that encode hydrolytic plant cell-wall degrading enzymes in their saprophytic ancestors. Nevertheless, here we demonstrate that ectomycorrhizal fungi representing at least four origins of symbiosis have retained significant capacity to degrade humus-rich litter amended with glucose. Spectroscopy showed that this decomposition involves an oxidative mechanism and that the extent of oxidation varies with the phylogeny and ecology of the species. RNA-Seq analyses revealed that the genome-wide set of expressed transcripts during litter decomposition has diverged over evolutionary time. Each species expressed a unique set of enzymes that are involved in oxidative lignocellulose degradation by saprotrophic fungi. A comparison of closely related species within the Boletales showed that ectomycorrhizal fungi oxidized litter material as efficiently as brown-rot saprotrophs. The ectomycorrhizal species within this clade exhibited more similar decomposing mechanisms than expected from the species phylogeny in concordance with adaptive evolution occurring as a result of similar selection pressures. Our data shows that ectomycorrhizal fungi are potential organic matter decomposers, yet not saprotrophs. We suggest that the primary function of this decomposing activity is to mobilize nutrients embedded in organic matter complexes and that the activity is driven by host carbon supply. Comparative transcriptomics of ectomycorrhizal (ECM) versus brown-rot (BR) fungi while degrading soil-organic matter
2015-09-24 | E-GEOD-64897 | biostudies-arrayexpress
Project description:Metagenome diversity in polyaromatic hydrocarbon (PAH) degrading consortium (NS-PAH-2015-HSR-4)
| PRJNA587568 | ENA