Ontology highlight
ABSTRACT:
PROVIDER: PRJNA885096 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21802461_1.fastq.gz | Fastqsanger.gz | |||
| SRR21802461_2.fastq.gz | Fastqsanger.gz | |||
| SRR21802462_1.fastq.gz | Fastqsanger.gz | |||
| SRR21802462_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 4 of 4 |
Similar Datasets
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
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
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.
2025-02-28 | GSE289310 | GEO
Project description:Phosphate (P) fertilization induces a myriad of plant rhizosphere processes, required for a better P plant use. However, extended knowledge about plant responses to polyphosphates (PolyP) is still scarce, particularly transcriptomic and functional traits of root-induced rhizosphere processes. The present study aims to investigate belowground traits related to root transcriptomic changes, rhizosphere acidification, root growth, and P acquisition of durum wheat under PolyPs (PolyB and PolyC) supply. Root molecular traits were differentially expressed in response to PolyPs types, with 2481 and 184 genes were differentially expressed (compared to OrthoP) under PolyB (445 up- and 2036 down-regulated) and PolyC (71 up- and 113 down-regulated), respectively. Specifically, PolyB significantly influenced the expression of genes encoding the key enzymes in glycolysis, citrate cycle and acid phosphatases, OGDH, MDH, and ENO, PAP21 genes were upregulated, while TPI, PFK and LDH genes were downregulated. The modulated expression of TCA cycle and PAP genes can presumably explain the induced rhizosphere acidification (pH decreased from 8 to 6.3) and acid phosphatases activity (in root, rhizosphere soil and rhizosphere soil solution) under PolyPs, which consequently increased rhizosphere soil P availability (145% compared to OrthoP). This increase in P availability was concomitant with the modulation of root morphological traits and the upregulation of the AUX1 and ABA transporters genes, indicating PolyPs regulatory role in root growth for efficient P uptake. Moreover, PolyB significantly upregulated the expression of SPX3, which is indispensable for the absorption and transport of inorganic P to both roots and shoots. This was physiologically reflected by the increased shoot (36%) and root (61%) Pi contents in response to PolyB compared to OrthoP. Taken together, our findings provide novel and consistent evidence that enhanced P acquisition from PolyPs entails coordinated regulation of the expression of genes related to root-rhizosphere processes (rhizosphere acidification and phosphatases exudation) and root morphology, which consequently induces physiological adaptive traits enabling enhanced availability, acquisition of P, and wheat growth performance.
2025-05-31 | GSE277488 | GEO
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
Project description:Biofumigation affects the root and rhizosphere soil fungal microbiome of strawberry
| PRJEB21579 | ENA
Project description:We used wheat as rotational crop to assess the influence of continuous cropping on microbiome in Pinellia ternata rhizosphere and the remediation of rotational cropping to the impacted microbiota. Illumina high-throughput sequencing technology was utilized for this method to explore the rhizosphere microbial structure and diversity based on continuous and rotational cropping.
2016-12-10 | GSE91083 | GEO
Project description:It has been performed a genome-wide analysis of gene expression of the root-colonizing bacterium Pseudomonas putida KT2440 in the rhizosphere of corn (Zea mays var. Girona. To identify reliable rhizosphere differentially expressed genes, rhizosphere populations of P. putida bacteria cells were compared with three alternative controls: i) planktonic cells growing exponentially in rich medium (LB), ii) planktonic cells in stationary phase in LB, and iii) sessile populations established in sand microcosms, under the same conditions used to grow inoculated corn plants.
2007-09-02 | E-MEXP-949 | biostudies-arrayexpress
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