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ABSTRACT: Root bacteria metagenome

PROVIDER: PRJNA613302 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11350517.fastq.gz	Fastqsanger.gz
	SRR11350518.fastq.gz	Fastqsanger.gz
	SRR11350519.fastq.gz	Fastqsanger.gz
	SRR11350520.fastq.gz	Fastqsanger.gz
	SRR11350521.fastq.gz	Fastqsanger.gz

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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.

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Project description:root associated bacteria metagenome

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Maize root bacteria degrade host-specialized metabolites through the lactonase BxdA

Project description:Root exudates contain specialised metabolites that affect the plant’s root microbiome. How host-specific microbes cope with these bioactive compounds, and how this ability shapes root microbiomes, remains largely unknown. We investigated how maize root bacteria metabolise benzoxazinoids, the main specialised metabolites of maize. Diverse and abundant bacteria metabolised the major compound in the maize rhizosphere MBOA and formed AMPO. AMPO forming bacteria are enriched in the rhizosphere of benzoxazinoid-producing maize and can use MBOA as carbon source. We identified a novel gene cluster associated with AMPO formation in microbacteria. The first gene in this cluster, bxdA encodes a lactonase that converts MBOA to AMPO in vitro. A deletion mutant of the homologous bxdA genes in the genus Sphingobium, does not form AMPO nor is it able to use MBOA as a carbon source. BxdA was identified in different genera of maize root bacteria. Here we show that plant-specialised metabolites select for metabolisation-competent root bacteria. BxdA represents a novel benzoxazinoid metabolisation gene whose carriers successfully colonize the maize rhizosphere and thereby shape the plant’s chemical environmental footprint

2024-04-05 | GSE263275 | GEO

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

Defining the Secrebiome: the expressed secretome of the gut microbiome and its role in obese Mexican children

Project description:high throughput sequencing of the metagenome of mexican children

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Project description:Root bacteria

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Sinorhizobium meliloti root nodule bacterial transcriptomes for wild type and four mutant strains.

Project description:We characterized transcriptomes of Sinorhizobium meliloti root nodule bacteria with mutations in sigma factor genes.

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Transcription profiling by array of Pseudomonas aeruginosa in a rhizopsphere during phosphate limitation conditions

Project description:Plants and rhizosphere microbes rely closely on each other, with plants supplying carbon to bacteria in root exudates, and bacteria mobilizing soil-bound phosphate for plant nutrition. When the phosphate supply becomes limiting for plant growth, the composition of root exudation changes, affecting rhizosphere microbial communities and microbially-mediated nutrient fluxes. To evaluate how plant phosphate deprivation affects rhizosphere bacteria, Lolium perenne seedlings were root-inoculated with Pseudomonas aeruginosa 7NR, and grown in axenic microcosms under different phosphate regimes (330 uM vs 3-6 uM phosphate). The effect of biological nutrient limitation was examined by DNA microarray studies of rhizobacterial gene expression.

2011-07-01 | E-MEXP-2812 | biostudies-arrayexpress

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