Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Rhizosphere metagenome

ABSTRACT: Rice rhizosphere metagenome

PROVIDER: PRJDA61421 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	DRR000836.fastq.gz	Fastqsanger.gz
	DRR000837.fastq.gz	Fastqsanger.gz
	DRR000838.fastq.gz	Fastqsanger.gz
	DRR000839.fastq.gz	Fastqsanger.gz
	DRR000840.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 5

Similar Datasets

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

Niche differentiation of arsenic-transforming microbial groups in rice rhizosphere compartments as impacted by water management and soil-As concentrations

Project description:Arsenic (As) bioavailability in the rice rhizosphere is influenced by many microbial interactions, particularly by metal-transforming functional groups at the root-soil interface. This study was conducted to examine As-transforming microbes and As-speciation in the rice rhizosphere compartments, in response to two different water management practices (continuous and intermittently flooded), established on fields with high to low soil-As concentration. Microbial functional gene composition in the rhizosphere and root-plaque compartments were characterized using the GeoChip 4.0 microarray. Arsenic speciation and concentrations were analyzed in the rhizosphere soil, root-plaque, porewater and grain samples. Results indicated that intermittent flooding significantly altered As-speciation in the rhizosphere, and reduced methyl-As and AsIII concentrations in the pore water, root-plaque and rice grain. Ordination and taxonomic analysis of detected gene-probes indicated that root-plaque and rhizosphere assembled significantly different metal-transforming functional groups. Taxonomic non-redundancy was evident, suggesting that As-reduction, -oxidation and -methylation processes were performed by different microbial groups. As-transformation was coupled to different biogeochemical cycling processes establishing functional non-redundancy of rice-rhizosphere microbiome in response to both rhizosphere compartmentalization and experimental treatments. This study confirmed diverse As-biotransformation at root-soil interface and provided novel insights on their responses to water management, which can be applied for mitigating As-bioavailability and accumulation in rice grains.

2021-07-12 | GSE179671 | GEO

rhizosphere metagenome

Project description:Rice rhizosphere Metagenome

| PRJNA398443 | ENA

rhizosphere metagenome

Project description:Rice rhizosphere metagenome Raw sequence reads

| PRJNA663614 | ENA

rhizosphere metagenome

Project description:Rhizosphere bacterial metagenome of wheat and rice

| PRJDB6513 | ENA

GeoChip data of soil microbial communities in the maize rhizosphere and bulk soils

Project description:Microbial communities in the rhizosphere make significant contributions to crop health and nutrient cycling. However, their ability to perform important biogeochemical processes remains uncharacterized. Important functional genes, which characterize the rhizosphere microbial community, were identified to understand metabolic capabilities in the maize rhizosphere using GeoChip 3.0-based functional gene array method.

2014-09-12 | GSE61338 | GEO

Soil metagenome from avocado orchards in Channybearup, Western Australia in 2024

Project description:Metagenome data from soil samples were collected at 0 to 10cm deep from 2 avocado orchards in Channybearup, Western Australia, in 2024. Amplicon sequence variant (ASV) tables were constructed based on the DADA2 pipeline with default parameters.

2025-06-15 | GSE298403 | GEO

Rice Rhizosphere Soil

Project description:Rice Rhizosphere Soil Metagenome

| PRJNA1097453 | ENA

Rice rhizosphere Soil

Project description:Rice rhizosphere Soil Metagenome

| PRJNA790010 | ENA

Rice rhizosphere soil

Project description:Rice rhizosphere soil Metagenome

| PRJNA505747 | ENA