Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Extraction of soil microbiome

ABSTRACT: A comparative study of several methods for extraction of soil microbiome

PROVIDER: PRJEB20467 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR1938220_1.fastq.gz	Fastqsanger.gz
	ERR1938220_2.fastq.gz	Fastqsanger.gz
	ERR1938221_1.fastq.gz	Fastqsanger.gz
	ERR1938221_2.fastq.gz	Fastqsanger.gz
	ERR1938222_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

extraction of soil microbiome

Project description:A comparative study of several methods for extraction of soil microbiome

| PRJEB20466 | ENA

soil microbiome

Project description:A comparative study of several methods for extraction of soil microbiome

| PRJEB20469 | ENA

soil microbiome

Project description:A comparative study of several methods for extraction of soil microbiome

| PRJEB20470 | ENA

Environmental soil gDNA extraction

Project description:Environmental soil gDNA extraction

| PRJEB37921 | ENA

Metaproteome analysis of different soil types

Project description:Metaproteome analysis of a forest soil and a potting soil. Different protein extraction methods were compared to investigate protein extraction efficiency and compatibility with sample downstream processing.

2015-03-26 | PRD000542 | Pride

Soil metaproteomics using DNA RNA protein co-extraction method

Project description:Soil is an inherently complex matrix and as such, we believe when performing culture-independent microbial community analyses using the 'omics' suite of tools, all biomolecules investigated should be co-extracted from the same biological sample. To this end, we developed a robust, cost-effective DNA, RNA and protein co-extraction method for soil. The samples deposited here represent 3 biological replicates from one of eight soil types tested in this work.

2019-07-15 | PXD007077 | Pride

The soil microbiome reduces Striga infection in sorghum by modulation of host-derived signaling molecules and root development

Project description:Sorghum bicolor is one of the most important cereal crops in the world, predominantly grown in sub‑Saharan Africa by smallholder farmers. Despite its outstanding resilience to abiotic stresses, approximately 20% of sorghum yield is annually lost on the African continent due to infestation with the parasitic weed Striga hermonthica. Existing Striga management strategies to decrease Striga infestation often show low efficiency and are not easily integrated into current agricultural practices. Microbial-based solutions may prove an effective, low-cost mode for reducing Striga parasitism in sub-Saharan Africa. Here, we demonstrate that the microbiome component of a field soil suppresses Striga infection of sorghum. Potential mechanisms underlying the soil microbiome’s influence on the host plant include root endodermal suberization and aerenchyma formation. Moreover, we observed a depletion of haustorium inducing factors, compounds essential for Striga to establish the host-parasite association, in root exudates collected from sorghum grown in the presence of the soil microbiome as compared to sterile conditions. We further identified individual microbial taxa associated with reduced Striga infection via changes in root cellular anatomy and differentiation as well as in exudate composition. Our study identifies a suite of traits that can be harnessed by individual microbial isolates or their consortia to induce Striga resistance. Combining microbes that elicit Striga resistance directly (affecting the parasite) via repression of haustorium formation with those that act indirectly (affecting the host), by reducing of Striga penetration through root tissue, can broaden the effectiveness of microbe-induced protection from Striga.

2022-10-31 | GSE216351 | GEO

Parallel protein extraction methods increase the diversity of protein identification in Park Grass Experiment soil

Project description:We have combined a modified protein extraction method, heat/thaw/phenol/chloroform (HTPC), with the established Surfactant extraction method to identify proteins from Park Grass Experiment (PGE) soil, which has an extensively sequenced microbial database.

2022-09-20 | PXD017392 | Pride

The preceding root system drives the rhizosphere microbiome

Project description:Background: The soil environment is responsible for sustaining most terrestrial plant life on earth, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. Understanding the microbial metagenome of the detritusphere and how it responds to agricultural management such as crop rotations and soil tillage will be vital for improving global food production. Methods: The rhizosphere soils of wheat and chickpea growing under + and - decaying root were collected for metagenomics sequencing. A gene catalogue was established by de novo assembling metagenomic sequencing. Genes abundance was compared between bulk soil and rhizosphere soils under different treatments. Conclusions: The study describes the diversity and functional capacity of a high-quality soil microbial metagenome. The results demonstrate the contribution of the microbiome from decaying root in determining the metagenome of developing root systems, which is fundamental to plant growth, since roots preferentially inhabit previous root channels. Modifications in root microbial function through soil management, can ultimately govern plant health, productivity and food security.

2020-03-06 | GSE146427 | GEO

rs11-07_opine2 - septante soil - Transcriptomic changes induced by opine production in Arabidopsis thaliana grown in natural soil

Project description:rs11-07_opine2 - septante soil - Transcriptomic changes induced by opine production in Arabidopsis thaliana grown in natural soil - Arabidopsis thalian Col- line was transformed in order to obtain transgenic lines that produce opine compound (octopine and mannopine). Transgenic lines producing respectively octopine and mannopine and the WT line were grown in greenhouse under long-day condition in pots containing half commercial compost and half soil of la Mérantaise and watered with water. Whole plant aged of one month were harvested and frozen in liquid nitrogen. The plants were ground with a mortar an pestls and RNA extraction was performed with the RNeasy extraction kit (QIAGEN) with cristal of PVP. The RNA concentration was measured on a NANODrop spectrophotometer.

2017-01-05 | GSE93121 | 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