Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Garden soil

ABSTRACT: Arable soil Metagenome

PROVIDER: PRJNA757600 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR15676003_1.fastq.gz	Fastqsanger.gz
	SRR15676003_2.fastq.gz	Fastqsanger.gz
	SRR15676520_1.fastq.gz	Fastqsanger.gz
	SRR15676520_2.fastq.gz	Fastqsanger.gz
	SRR15676521_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 148

Similar Datasets

soil metagenome

Project description:Arable soil bacteria Metagenome

| PRJNA245766 | ENA

soil metagenome

Project description:Otumba arable soil Metagenome

| PRJNA241127 | ENA

Pinus garden soil

Project description:Pinus garden soil Metagenome

| PRJNA472835 | ENA

metagenome of tea garden soil

Project description:metagenome of tea garden soil Metagenome

| PRJNA1064111 | ENA

Metabolomics study of root, rhizosphere and leaf samples from a Populus Trichocarpa common garden

Project description:This data set contains 1376 mass spectrometry reads from root, rhizosphere and leaf sample of Populus Trichocarpa, as well as associated controls. This metabolomics data set was collected as part of a larger campaign which complements the metabolomics data with metagenome sequencing, transcriptomics, and soil measurement data.

2022-12-12 | MSV000090886 | MassIVE

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

RNA-Seq Analysis to confirm Different Transcriptomic Profiles of Soil-Derived Functional Module Consortia.

Project description:Purpose: Deconstructing the soil microbiome into reduced-complexity functional modules represents a novel method of microbiome analysis. The goals of this study are to confirm differences in transcriptomic patterns among five functional module consortia. Methods: mRNA profiles of 3 replicates each of functional module enrichments of soil inoculum in M9 media with either 1) xylose, 2) n-acetylglucosamine, 3) glucose and gentamycin, 4) xylan, or 5) pectin were generated by sequencing using an Illumina platform (GENEWIZ performed sequencing). Sequence reads that passed quality filters were aligned to a soil metagenome using Burrows Wheeler Aligner. Resulting SAM files were converted to raw reads using HTSeq, and annotated using Uniref90 or EGGNOG databases. Results: To reduce the size of the RNA-Seq counts table and increase its computational tractability, transcripts containing a minimum of 75 total counts, but no more than 3 zero counts, across the 15 samples were removed. The subsequent dataset was normalized using DESeq2, resulting in a dataset consisting of 6947 unique transcripts across the 15 samples, and 185,920,068 reads. We identified gene categories that were enriched in a sample type relative to the overall dataset using Fisher’s exact test. Conclusions: our dataset confirms that the functional module consortia generated from targeted enrichments of a starting soil inoculum had distinct functional trends by enrichment type.

2020-01-14 | GSE143587 | GEO

soil metagenome

Project description:Bacterial diversity in arable soil

| PRJNA223252 | ENA

soil metagenome

Project description:Arable soil Targeted Locus (Loci)

| PRJNA237277 | ENA

Burkholderia vietnamiensis strain:Garden Soil | isolate:Garden Soil

Project description:Burkholderia vietnamiensis strain:Garden Soil | isolate:Garden Soil Genome sequencing

| PRJNA660427 | ENA