Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1277538 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR34002200.fastq.gz | Fastqsanger.gz | |||
| SRR34002300.fastq.gz | Fastqsanger.gz | |||
| SRR34002201.fastq.gz | Fastqsanger.gz | |||
| SRR34002301.fastq.gz | Fastqsanger.gz | |||
| SRR34002202.fastq.gz | Fastqsanger.gz |
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Project description:Elevated atmospheric CO2 can influence the structure and function of rhizosphere microorganisms by altering root growth and the quality and quantity of compounds released into the rhizosphere via root exudation. In these studies we investigated the transcriptional responses of Bradyrhizobium japonicum cells growing in the rhizosphere of soybean plants exposed to elevated atmospheric CO2. The results of microarray analyses indicated that atmospheric elevated CO2 concentration indirectly influences on expression of large number of Bradyrhizobium genes through soybean roots. In addition, genes involved in C1 metabolism, denitrification and FixK2-associated genes, including those involved in nitrogen fixation, microanaerobic respiration, respiratory nitrite reductase, and heme biosynthesis, were significantly up-regulated under conditions of elevated CO2 in the rhizosphere, relative to plants and bacteria grown under ambient CO2 growth conditions. The expression profile of genes involved in lipochitinoligosaccharide Nod factor biosynthesis and negative transcriptional regulators of nodulation genes, nolA and nodD2, were also influenced by plant growth under conditions of elevated CO2. Taken together, results of these studies indicate that growth of soybeans under conditions of elevated atmospheric CO2 influences gene expressions in B. japonicum in the soybean rhizosphere, resulting in changes to carbon/nitrogen metabolism, respiration, and nodulation efficiency.
2010-07-29 | GSE23296 | GEO
Project description:Elevated atmospheric CO2 can influence the structure and function of rhizosphere microorganisms by altering root growth and the quality and quantity of compounds released into the rhizosphere via root exudation. In these studies we investigated the transcriptional responses of Bradyrhizobium japonicum cells growing in the rhizosphere of soybean plants exposed to elevated atmospheric CO2. Transciptomic expression profiles indicated that genes involved in carbon/nitrogen metabolism, and FixK2-associated genes, including those involved in nitrogen fixation, microanaerobic respiration, respiratory nitrite reductase, and heme biosynthesis, were significantly up-regulated under conditions of elevated CO2, relative to plants and bacteria grown under ambient CO2 growth conditions. The expression profile of genes involved in lipochitinoligosaccharide Nod factor biosynthesis and negative transcriptional regulators of nodulation genes, nolA and nodD2, were also influenced by plant growth under conditions of elevated CO2. Taken together, results of these studies indicate that growth of soybeans under conditions of elevated atmospheric CO2 influences gene expressions in B. japonicum in the soybean rhizosphere, resulting in changes to carbon/nitrogen metabolism, respiration, and nodulation efficiency. Bradyrhizobium japonicum strains were grown in the soybean rhizosphere under two different CO2 concentrations. Transcriptional profiling of B. japonicum was compared between cells grown under elevated CO2 and ambient conditions. Four biological replicates of each treatment were prepared, and four microarray slides were used for each strain.
2010-07-28 | E-GEOD-23296 | biostudies-arrayexpress
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:Increased root H+ secretion is known as a strategy of plant adaption to low phosphorus (P) stress by enhancing mobilization of sparingly soluble P-sources. However, it remains fragmentarywhether enhanced H+ exudation could reconstruct the plant rhizosphere microbial community under low P stress. The present study found that P deficiency led to enhanced H+ exudation from soybean (Glycine max) roots. Three out of all eleven soybean H+-pyrophosphatases (GmVP) geneswere up-regulated by Pi starvation in soybean roots. Among them, GmVP2 showed the highest expression level under low P conditions. Transient expression of a GmVP2-green fluorescent protein chimera in tobacco (Nicotiana tabacum) leaves, and functional characterization of GmVP2 in transgenic soybean hairy roots demonstrated that GmVP2 encoded a plasma membrane transporter that mediated H+ exudation. Meanwhile, GmVP2-overexpression in Arabidopsis thaliana resulted in enhanced root H+ exudation, promoted plant growth, and improved sparingly soluble Ca-P utilization. Overexpression of GmVP2 also changed the rhizospheric microbial community structures, as reflected by a preferential accumulation of acidobacteria in the rhizosphere soils. These results suggested that GmVP2 mediated Pi-starvation responsive H+ exudation,which is not only involved in plant growth and mobilization of sparingly soluble P-sources, but also affects microbial community structures in soils.
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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:Soybean (Glycine max) is susceptible to root rot when subjected to continuous cropping, and this disease can seriously diminish the crop yield. Herein, isobaric tag for relative and absolute quantitation (iTRAQ) labeling and liquid chromatography-tandem mass spectrometry (LC-MS/MS) were employed for proteomic analysis of continuously cropped soybean inoculated with the arbuscular mycorrhizal (AM) fungus Funneliformis mosseae. Differential expression of proteins in soybean roots was determined following 1 year of continuous cropping. A total of 131 differentially expressed proteins (DEPs) were identified in F. mosseae-treated samples, of which 49 and 82 were up- and down-regulated, respectively. The DEPs were annotated with 117 Gene Ontology (GO) terms, with 48 involved in biological processes, 31 linked to molecular functions, and 39 associated with cell components. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis mapped the DEPs to 113 mainly metabolic pathways including oxidative phosphorylation, glycolysis and amino acid metabolism. Expression of glucan 1,3-beta-glucosidase, chalcone isomerase, calcium-dependent phospholipid binding and other defense-related proteins was up-regulated by F. mosseae, suggesting inoculation promotes the growth and development of soybean and increases disease resistance. The findings provide an experimental basis for further research on the molecular mechanisms of AM fungi in resolving problems associated with continuous soybean cropping.
2019-11-12 | PXD009911 | Pride