Ontology highlight
ABSTRACT:
PROVIDER: PRJNA634803 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11838800_1.fastq.gz | Fastqsanger.gz | |||
| SRR11838800_2.fastq.gz | Fastqsanger.gz | |||
| SRR11838900_1.fastq.gz | Fastqsanger.gz | |||
| SRR11838900_2.fastq.gz | Fastqsanger.gz | |||
| SRR11838801_1.fastq.gz | Fastqsanger.gz |
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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.
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Project description:The goal of this study was to compare differentially expressed transcripts in onion bulbs induced in response to managed stress under field conditions using transcriptome profiling (RNA-seq). The clean reads were aligned to the reference genome (a doubled haploid onion line DHCU066619 (https://www.oniongenome.wur.nl/) and the transcriptions assembly. The read count for every transcript was determined from the findings of the mapping process. Genes identified as differentially expressed genes (DEGs) had an adjusted P-value <0.05 and an absolute log2FC ≥0, as determined by DESeq2. Transcriptomic analysis of onion bulb tissue (variety Matahari) in response to nitrogen stress under optimal water identified 3092 and 2204 Differentially Expressed Genes (DEGs) unique genes under optimal nitrogen vs low nitrogen. while under sub-optimal nitrogen, 2770 and 2198 unique genes were identified under optimal nitrogen vs low nitrogen respectively.
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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.
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Project description:RNA-Sequencing of onion bulbs exposed to managed stress
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Project description:Forming symbiotic associations with beneficial microbes are important strategies for sessile plants to acquire nitrogen and phosphorus nutrients from the soil. Root exudates play key roles on set-up of the rhizosphere microbiome. According to the needs for nitrogen or phosphorus, plants can adjust the root exudates composition to attract proper microbes. Flavonoids are a group of secondary metabolites that are well studied in shaping the root microbiome, especially the root nodule symbiosis in legumes. Here, we show the medicago truncatula phosphate sensors SPX1 and SPX3 regulate flavonoids biosynthesis to recruit nitrogen-fixing microbes for nitrogen acquisition. Nitrogen-fixing microbes were less recruited in spx1spx3 double mutant root rhizosphere. This was caused by lower flavonoids biosynthesis related genes expression, which resulted in lower flavonoids levels in the root exudates compared to wild type plant R108. Further analysis indicates the regulation of flavonoids biosynthesis is through the SPX1 and SPX3 interaction transcription factor PHR2. We propose the SPX-PHR phosphate homeostasis regulation network also control microbe-dependent nitrogen acquisition according to phosphate levels. Thus, SPX1 and SPX3 play important roles to keep a microbe-dependent nitrogen and phosphorus absorption balance for optimal growth.
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