Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Straw-decomposing bacterial community

ABSTRACT: Dynamic variation of bacterial community assemblage and functional profiles during rice straw degradation

PROVIDER: PRJEB60739 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR11020855.fastq.gz	Fastqsanger.gz
	ERR11020856.fastq.gz	Fastqsanger.gz
	ERR11020857.fastq.gz	Fastqsanger.gz
	ERR11020858.fastq.gz	Fastqsanger.gz
	ERR11020859.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Integrated proteomics and metabolomics analysis of rice leaves in response to rice straw return

Project description:Straw return is crucial for the sustainable development of rice planting. To investigate the response of rice leaves to rice straw return, we analyzed the physiological index of rice leaves and measured differentially expressed protein (DEPs) and differentially expressed metabolites (DEMs) levels in rice leaves by the use of proteomics and metabolomics approaches. The results showed that, compared with no rice straw return, rice straw return significantly decreased the dry weight of rice plants and nonstructural carbohydrate contents and destroyed the chloroplast ultrastructure. In rice leaves under rice straw return, 329 DEPs were upregulated, 303 DEPs were downregulated, 44 DEMs were upregulated, and 71 DEMs were downregulated. These DEPs and DEMs were mainly involved in various molecular processes, including photosynthesis, carbon fixation in photosynthetic organisms, glycolysis, and the citric acid cycle. Rice straw return promoted the accumulation of osmotic adjustment substances, such as organic acids, amino acids, and other substances, and reduced the material supply and energy production of carbon metabolism, thus inhibiting the growth of rice.

2022-09-12 | PXD035835 | Pride

Decomposing wheat straw

Project description:Future climate conditions accelerate wheat straw decomposition alongside altered microbial community composition, assembly patterns, and interaction networks

| PRJNA807133 | ENA

Screening of fiber-degrading bacteria and metabolic utilization rice straw

Project description:To increase the utilization rate of straw, the purpose of this study screened cellulose-degrading bacteria from the intestinal tract of termites by Congo red primary screening and filter paper degradation re-screening test, which was Cellulomonas iranensis (CE). The enzyme activities of endoglucanase, exoglucose and β glucosidase of them were measured at 0.097 U/mL, 0.316 U/mL, 0.110 U/mL. PS was also inoculated in the liquid medium with rice straw or glucose as the sole carbon source for14 days fermentation. Further transcriptomic and proteomic analyses revealed that rice straw cultured CE an upregulation of genes and a downregulation of genes, compared with glucose cultured PS.

2025-06-18 | PXD065194 |

Procambarus clarkii digests rice straw

Project description:The types and sources of digestive enzymes during the process of rice straw digestion in Procambarus clarkii.

2025-07-02 | PXD065681 |

Transcriptomes of Aspergillus fumigatus Z5 induced by different carbon sources

Project description:Various saprotrophic microorganisms, especially filamentous fungi, can efficiently degrade lignocellulose that is one of the most abundant natural material on earth. It consists of complex carbohydrates and aromatic polymers found in plant cell wall and thus in plant debris. Aspergillus fumigatus Z5 was isolated from compost heaps and showed highly efficient plant biomass-degradation capability.Genome analysis revealed an impressive array of genes encoding cellulases, hemicellulases, and pectinases involved in lignocellulosic biomass degradation. We sequenced the transcriptomes of Aspergillus fumigatus Z5 induced by sucrose, xylan, cellulose and rice straw, respectively. There were 444, 1711 and 1386 significantly differently (q-value â¤ 0.0001 and |log2 of the ratio of the RPM values| â¥ 2) expressed genes in xylan, cellulose and rice straw,respectively, relative to sucrose control. After incubation at 45 â, 145rpm for 20 hours with sucrose as the carbon source, mycelia were induced for 16 hours using xylan, cellulose and rice straw, respectively. Transcriptome induced by sucrose was used as the control when comparing the differences between other three transcriptomes (induced by xylan, cellulose and rice straw, respectively).

2015-11-22 | E-GEOD-55086 | biostudies-arrayexpress

GeoChip 5.0 microarray of the active bacterial community from both warming and control soil samples

Project description:To determine whether and how warming affects the functional capacities of the active microbial communities, GeoChip 5.0 microarray was used. Briefly, four fractions of each 13C-straw sample were selected and regarded as representative for the active bacterial community if 16S rRNA genes of the corresponding 12C-straw samples at the same density fraction were close to zero.

2023-12-30 | E-MTAB-13326 | biostudies-arrayexpress

Rice straw composting

Project description:Rice straw composting Raw sequence reads

| PRJNA748508 | ENA

Nitrogen source-driven regulation of Irpex lacteus for enhanced lignocellulose degradation and microbial protein production in wheat straw

Project description:White rot fungi, such as Irpex lacteus, offer significant potential for lignocellulose degradation and protein synthesis in sustainable biofuel and animal feed production,but optimizing nitrogen sources to balance fungal growth, lignin degradation, and protein synthesis remains a critical challenge.This study investigated the effects of ammonium chloride (NH₄Cl) and sodium nitrate (NaNO₃) on I. lacteus fermentation in wheat straw, with a focus on the regulation of nitrogen source.Transcriptomic analysis revealed that NaNO₃ upregulated genes associated with nitrogen uptake and cellulose/hemicellulose degradation,while exerting less repression on key ligninolytic enzymes, such as manganese peroxidase and cytochrome P450, compared to NH₄Cl.These findings suggest that NaNO₃ enhances I. lacteus metabolism by harmonizing lignin degradation with efficient nitrogen conversion.

2025-05-21 | GSE297384 | GEO

Transcriptomes of Aspergillus fumigatus Z5 induced by different carbon sources

Project description:Various saprotrophic microorganisms, especially filamentous fungi, can efficiently degrade lignocellulose that is one of the most abundant natural material on earth. It consists of complex carbohydrates and aromatic polymers found in plant cell wall and thus in plant debris. Aspergillus fumigatus Z5 was isolated from compost heaps and showed highly efficient plant biomass-degradation capability.Genome analysis revealed an impressive array of genes encoding cellulases, hemicellulases, and pectinases involved in lignocellulosic biomass degradation. We sequenced the transcriptomes of Aspergillus fumigatus Z5 induced by sucrose, xylan, cellulose and rice straw, respectively. There were 444, 1711 and 1386 significantly differently (q-value ≤ 0.0001 and |log2 of the ratio of the RPM values| ≥ 2) expressed genes in xylan, cellulose and rice straw,respectively, relative to sucrose control.

2015-11-22 | GSE55086 | GEO

Comparative analysis of the Trichoderma reesei transcriptome during growth on the cellulase inducing substrates wheat straw and lactose

Project description:We have examined and compared the transcriptome of T. reesei growing on wheat straw and lactose as carbon sources under otherwise similar conditions. Gene expression on wheat straw exceeded that on lactose, and 1619 genes were found to be only induced on wheat straw but not on lactose. They comprised 30 % of the CAZome, but were also enriched in genes associated with phospholipid metabolism, DNA synthesis and repair and iron homeostatis. Two thirds of the CAZome was expressed both on wheat straw as well as on lactose, but 60 % of it at least >2-fold higher on the former. Major wheat straw specific genes comprised xylanases, chitinases and ß-mannosidases. Interestingly, the latter two CAZyme families were significantly higher expressed in a strain in which xyr1 encoding the major regulator of cellulase and hemicellulase biosynthesis is non-functional, demonstrating that XYR1 is a repressor of these genes.

2013-09-17 | GSE46155 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data