Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1177223 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31152563_1.fastq.gz | Fastqsanger.gz | |||
| SRR31152563_2.fastq.gz | Fastqsanger.gz | |||
| SRR31152564_1.fastq.gz | Fastqsanger.gz | |||
| SRR31152564_2.fastq.gz | Fastqsanger.gz | |||
| SRR31152565_1.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:<p>Background</p><p>Soil salinization and alkalization severely threaten soybean growth and yield. Arbuscular mycorrhizal fungi (AMF), specifically Rhizophagus intraradices (Ri), enhance stress tolerance and soil quality, yet their mechanisms in regulating microbial-metabolite interactions during critical soybean growth stages remain unclear.</p><p>Results</p><p>This research employed partitioned (rhizosphere and hyphosphere) pot experiments in natural saline-alkaline soil, integrating high-throughput sequencing and untargeted metabolomics to analyze Ri effects on microbial communities and metabolic functions at branching (V5), pod development (R4), and mature pod (R8) stages. Results revealed V5 stage for Ri to activate host resistance, R4 for hyphal expansion (density 21.13 m/g), enhancing nutrient uptake, and R8 stage for increased spore and glomalin-related soil protein (GRSP) secretion to alleviate stress. Ri differentially regulates bacterial-fungal networks, enriching biomarker and driving stochastic microbial assembly. Ri shifted bacterial assembly toward stochasticity and enriched biomarkers. Bacterial richness peaked under RiRR4 (+Ri, R4 rhizosphere; +27.06% vs CRR4). Fungal assembly showed a different trend, peaking under RiRV5 (+Ri, V5 rhizosphere; +39.75% vs CRV5). Ri enhanced plant resistance and soybean growth via bacterial diversity in rhizosphere soil. Metabolomics identified phenylalanine metabolism as a core Ri-regulated pathway under saline-alkaline stress, facilitating carbon-nitrogen cycling and secondary metabolite accumulation.</p><p>Conclusions</p><p>This research reveals how Ri coordinates microbial and metabolic processes to enhance saline-alkaline resistance in soybean.</p>
2026-01-12 | MTBLS13661 | MetaboLights
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: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.
2023-06-01 | GSE205273 | GEO
Project description:<p> Soil contamination with heavy metals, particularly lead (Pb) and cadmium (Cd), has become a growing environmental concern due to rapid industrialization. Salix matsudana, a woody energy plant with notable tolerance to heavy metals, exhibits considerable potential for use in phytoremediation. Although nitrogen (N) fertilization is known to promote the growth of S. matsudana, its dual role in enhancing plant development and improving soil conditions remains insufficiently understood. In this study, we systematically examined the effects of varying nitrogen fertilizer concentrations on the growth of S. matsudana, heavy metal uptake, and rhizosphere soil characteristics through integrated physiological and multi-omics approaches. Our findings revealed that high nitrogen levels significantly increased plant biomass and the accumulation of Pb and Cd compared to control conditions. Detailed physiological analyses demonstrated enhanced heavy metal absorption in roots under nitrogen fertilization. Microbial community analysis further indicated that nitrogen application altered rhizosphere microbial activity, particularly enriching bacterial taxa associated with metal mobilization. Metabolomic profiling corroborated improvements in soil quality, showing significant changes in organic acid metabolites involved in metal chelation. These results provide new insights into the mechanisms by which nitrogen fertilization synergistically enhances both the growth of S. matsudana and the efficiency of soil remediation, offering valuable guidance for optimizing phytoremediation strategies in heavy metal-contaminated environments.</p>
2025-07-19 | MTBLS12749 | MetaboLights
Project description:Phosphate (P) fertilization impacts many rhizosphere processes, driving plant P use efficiency. However, less is known about the induced molecular and physiological root-rhizosphere traits in responses to polyphosphates (PolyP), particularly root transcriptome and belowground functional traits responsible for P acquisition. The present study aims to investigate physiological and transcriptomic belowground mechanisms explaining the enhanced durum wheat P acquisition under PolyP (PolyB and PolyC) supply. Root molecular traits were differentially expressed in response to PolyP, where PolyB induced upregulation of OGDH, MDH, and ENO, PAP21 and downregulation of PFK, and LDH genes. The modulation of gene expression can presumably explain the PolyP-induced changes in rhizosphere (root, rhizosphere soil, soil solution) acidification (pH decreased from 8 to 6.3) and acid phosphatase activities, which were concomitant with enhanced rhizosphere soil P availability and shoot Pi content (145% and 36% compared to OrthoP, respectively) along with changes in morphological and transcriptomic root (particularly, the upregulation of AUX1 and ABA transporter genes) traits. These findings provide novel insights that P acquisition from polyphosphates involves the coordinated regulation of genes governing root-rhizosphere processes and root development, ultimately enhancing wheat P acquisition.
2025-05-31 | GSE277488 | GEO
Project description:In the study, two soybean genotypes were selected to conduct high and low P, high and low Mg, and AM fungal inoculation treatments, combined with RNA-seq sequencing technique in order to investigate the physiological and molecular mechanisms of the symbiosis between soybean and AM fungi affected by P and Mg treatments. The results showed that both Mg application and AM fungal inoculation were beneficial to promote soybean growth under low P condition. And there was a synergistic effect between the Mg concentration and the P concentration in the root of HN112 under the inoculation condition. RNA-seq sequencing was carried out using the roots of P-efficient soybean HN89 under different Mg and inoculation treatments with low P condition, and the difference of gene expression profiles was analyzed between high and low Mg treatments, and different inoculation treatments. According to the analysis of GO function classification and KEGG enrichment, under high Mg condition, the metabolic pathway was mainly enriched in lipid metabolism and glucose metabolism pathway under the inoculation treatment compared with the non-inoculation treatment, which regulated carbon metabolism pathway. Under the low Mg condition, the metabolic pathway was mainly enriched in the photosynthesis- antenna protein pathway to regulate the photosynthesis pathway under the inoculation treatment compared with the non-inoculation treatment. At the same time, the inoculation treatment significantly increased soybean root starch concentration under low Mg condition, compared with the non-inoculation treatment, suggesting that the significant up-regulation of a large number of photosynthesis related genes might be related to the significant increase of starch concentration at this treatment.
2022-06-13 | GSE132679 | GEO