Ontology highlight
ABSTRACT:
PROVIDER: PRJNA934860 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR23455085_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR24914124_1.fastq.gz | Fastqsanger.gz | |||
| SRR24914124_2.fastq.gz | Fastqsanger.gz |
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Project description:<p>Abstract This study focused on elucidating the lignocellulose degradation mechanism of Pholiota adiposa strain YAHS, aiming to provide theoretical basis and microbial resources for straw biorefining. Using the aniline blue-guaiacol plate screening method, 11 fungal strains were isolated from the Loess Plateau of northern Shaanxi. The highly efficient degrading strain P. adiposa YAHS was identified through DNS-based enzyme activity assays for cellulase and ligninase, combined with ITS sequence analysis. Whole-genome sequencing was performed using a hybrid approach integrating Illumina NovaSeq and Nanopore MinION platforms. Transcriptome-wide differential gene expression analysis was conducted via DESeq2, and untargeted metabolomics was carried out using UPLC-QTOF-MS. Multi-omics data were integrated to dissect the degradation pathways. Results showed that the genome of P. adiposa YAHS is 55.2 Mb in size, encoding 719 carbohydrate-active enzymes (CAZymes), with glycoside hydrolases (GHs) accounting for 37.4%. Multi-omics analysis revealed that this strain degrades lignocellulose into carbohydrates such as monosaccharides, oligosaccharides, and sugar alcohols through key enzymatic genes (e.g., exoglucanase, β-glucosidase, β-xylosidase, β-mannanase, monooxygenase) and metabolic pathways (e.g., sucrose/starch metabolism, fructose/mannose metabolism, anthranilate degradation). we preliminarily elucidated the lignocellulose degradation mechanism of fungi in the genus Pholiota through integrated multi-omics analysis, revealed the critical roles of key cellulolytic enzymes in this process, and provided important microbial resources and theoretical support for the development of novel biorefining technologies.</p>
2025-10-12 | MTBLS13121 | MetaboLights
Project description:The induction of genes in response to exposure of T. reesei to wheat straw was explored using genome-wide RNA-seq and compared to published RNA-seq data and model of how A. niger senses and responds to the lignocellulose. After 24 h of exposure to straw, transcript levels of known and predicted lignocellulose-degrading enzymes increased to around 8% of total cellular mRNA in T. reesei, which was much less when compared to A. niger. The bulk of enzymes used to deconstruct wheat straw is similar in both fungi. Other, non-plant cell wall-degrading enzymes which may aid in lignocellulose degradation were also uncovered in T. reesei and similar to those described in A. niger. Antisense transcripts were also shown to be present in T. reesei and their expession can be regulated by the respective growth condition.
2013-04-01 | GSE44648 | GEO
Project description:Evidence shows that bacteria contribute actively to the decomposition of cellulose and hemicellulose in forest soil; however, their role in this process is still unclear. Here we performed the screening and identification of bacteria showing potential cellulolytic activity from litter and organic soil of a temperate oak forest. The genomes of three cellulolytic isolates previously described as abundant in this ecosystem were sequenced and their proteomes were characterized during the growth on plant biomass and on microcrystalline cellulose. Pedobacter and Mucilaginibacter showed complex enzymatic systems containing highly diverse carbohydrate-active enzymes for the degradation of cellulose and hemicellulose, which were functionally redundant for endoglucanases, -glucosidases, endoxylanases, -xylosidases, mannosidases and carbohydrate-binding modules. Luteibacter did not express any glycosyl hydrolases traditionally recognized as cellulases. Instead, cellulose decomposition was likely performed by an expressed GH23 family protein containing a cellulose-binding domain. Interestingly, the presence of plant lignocellulose as well as crystalline cellulose both trigger the production of a wide set of hydrolytic proteins including cellulases, hemicellulases and other glycosyl hydrolases. Our findings highlight the extensive and unexplored structural diversity of enzymatic systems in cellulolytic soil bacteria and indicate the roles of multiple abundant bacterial taxa in the decomposition of cellulose and other plant polysaccharides.
2016-05-02 | PXD003844 | Pride
Project description:Soil humic substances are known to positively influence plant growth and nutrition. In particular, low-molecular fractions have been shown to increase NO3- uptake and PM H+-ATPase activity and alter expression of related genes. Changes in maize root transcriptome due to treatment with nitrate (NO3-), Water-Extractable Humic Substances (WEHS) and NO3-+WEHS were analyzed.
2018-07-30 | GSE103184 | GEO
Project description:The induction of genes in response to exposure of T. reesei to wheat straw was explored using genome-wide RNA-seq and compared to published RNA-seq data and model of how A. niger senses and responds to the lignocellulose. After 24 h of exposure to straw, transcript levels of known and predicted lignocellulose-degrading enzymes increased to around 8% of total cellular mRNA in T. reesei, which was much less when compared to A. niger. The bulk of enzymes used to deconstruct wheat straw is similar in both fungi. Other, non-plant cell wall-degrading enzymes which may aid in lignocellulose degradation were also uncovered in T. reesei and similar to those described in A. niger. Antisense transcripts were also shown to be present in T. reesei and their expession can be regulated by the respective growth condition. Triplicate samples of T. reesei cultivated in each of the three following conditions were taken: 1) After 48 h growth in glucose-based minimal media; 2) After transfer of mycelia from glucose-based media into media containing wheat straw as a sole carbon source and 3) 5 h after addition of glucose to straw cultures.
2013-04-01 | E-GEOD-44648 | biostudies-arrayexpress
Project description:Arthrobacter chlorophenolicus A6 is a 4-chlorophenol degrading soil bacterium with high phyllosphere colonization capacity. Till now the genetic basis for the phyllosphere competency of Arthrobacter or other pollutant-degrading bacteria is uncertain. We investigated global gene expression profile of A. chlorophenolicus grown in the phyllosphere of common bean (Phaseolus vulgaris) compared to growth on agar surfaces.
2013-06-21 | GSE48198 | GEO
Project description:Genome-wide scanning of gene expression by microarray techniques was successfully performed on RNA extracted from a sterilized soil inoculated with Pseudomonas putida KT2440/pSL1, which contains a chloroaromatic degrading plasmid, in the presence or absence of 3-chlorobenzoic acid (3CB). The genes showing significant changes in their expression in both triplicate microarray analyses using amplified RNA and single microarray analysis using unamplified RNA were investigated. Pathway analysis revealed that the benzoate degradation pathway underwent the most significant changes following treatment with 3CB. Analysis based on categorization of differentially expressed genes against 3CB revealed new findings about the cellular responses of the bacteria to 3CB, including upregulation of the genes specifically involved in transport of 3CB, and induction of a K+/H+ antiporter complex, an universal stress protein, two cytochrome P450 proteins and an efflux transporter. Downregulated expression of some genes involved in carbon metabolism and the genes belong to a prophage in the presence of 3CB was observed. This study demonstrated the applicability of the method of soil RNA extraction for microarray analysis through a proof-of-concept experiment using a sterilized soil inoculated with Pseudomonas putida KT2440/pSL1.
2011-03-29 | GSE28215 | GEO
Project description:Genome-wide scanning of gene expression by microarray techniques was successfully performed on RNA extracted from a sterilized soil inoculated with Pseudomonas putida KT2440/pSL1, which contains a chloroaromatic degrading plasmid, in the presence or absence of 3-chlorobenzoic acid (3CB). The genes showing significant changes in their expression in both triplicate microarray analyses using amplified RNA and single microarray analysis using unamplified RNA were investigated. Pathway analysis revealed that the benzoate degradation pathway underwent the most significant changes following treatment with 3CB. Analysis based on categorization of differentially expressed genes against 3CB revealed new findings about the cellular responses of the bacteria to 3CB, including upregulation of the genes specifically involved in transport of 3CB, and induction of a K+/H+ antiporter complex, an universal stress protein, two cytochrome P450 proteins and an efflux transporter. Downregulated expression of some genes involved in carbon metabolism and the genes belong to a prophage in the presence of 3CB was observed. This study demonstrated the applicability of the method of soil RNA extraction for microarray analysis through a proof-of-concept experiment using a sterilized soil inoculated with Pseudomonas putida KT2440/pSL1. A study using total RNA extracted from soil cultures of Pseudomonas putida KT2440/pSL1. Each chip measures the expression level of 5,341 genes from the Pseudomonas putida KT2440 genome with two sets of six 60-mer probes per gene.
2011-03-29 | E-GEOD-28215 | biostudies-arrayexpress
Project description:<p>Background:</p><p>Lignocellulose represents a primary input of organic carbon (C) into soils, yet the identity of specific microorganisms and genes which drive lignocellulose turnover in soils remain poorly understood. To address this knowledge gap, we used a 10-year grassland plant-exclusion experiment to investigate how reduced plant C inputs affects microbial communities and their lignocellulolytic potential using a combination of metagenomic sequencing and untargeted metabolomics. We specifically tested the hypothesis that microbial community function in bare fallow plots would transition towards microbiota with genes for recalcitrant biomass degradation (i.e., lignocellulose), when compared to grassland plots with high labile C inputs. </p><p>Results:</p><p>Long term plant exclusion lowered soil C and N and reduced cellulose content, whilst hemicellulose and lignin were unchanged. Similarly soil microbiomes were highly distinct in long-term bare soils, along with soil extracellular enzyme profiles, though short term plant-removal effects were less apparent. Plant exclusion resulted in a general enrichment of Firmicutes, Thaumarchaeota, Acidobacteria, Fusobacteria, and Ascomycota, with a general reduction in Actinobacteria. However, changes in bare soil lignocellulose degradation genes were more associated with discrete taxa from diverse lineages, particularly the Proteobacteria. Grouping of lignocellulose-degrading genes into broad substrate classes (cellulases, hemicellulases and lignases) revealed a possible increase in lignin degradation genes under plant exclusion confirming our hypothesis, although all other changes were at the level of the CAZy family. Intriguingly, untargeted metabolome profiles were highly responsive to plant exclusion, even after only one year. Bare soils were depleted in oligosaccharides and enriched in monosaccharides, fatty and carboxylic acids, supporting emerging evidence of long-term persistent C being within simple compounds. </p><p>Conclusions:</p><p>Together our data show that extracellular lignin degrading enzymes increase under long term plant exclusion. There is now a need for increased focus on the microbial metabolic mechanisms which regulate the processing and persistence of enzymatically released compounds, particularly in energy limited soils.</p>
2025-07-16 | MTBLS12728 | MetaboLights