Rhizosphere metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB12038 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR319815.fastq.gz | Fastqsanger.gz | |||
| DRR319816.fastq.gz | Fastqsanger.gz |
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Project description:Rhizobia are soil bacteria that induce nodule formation on leguminous plants. In the nodules, they reduce dinitrogen to ammonium that can be utilized by plants. Besides nitrogen fixation, rhizobia have other symbiotic functions in plants including phosphorus and iron mobilization and protection of the plants against various abiotic stresses including salinity. Worldwide, about 20% of cultivable and 33% of irrigation land is saline, and it is estimated that around 50% of the arable land will be saline by 2050. Salinity inhibits plant growth and development, results in senescence, and ultimately plant death. The purpose of this study was to investigate how rhizobia, isolated from Kenyan soils, relieve common beans from salinity stress. The yield loss of common bean plants, which were either not inoculated or inoculated with the commercial R. tropici rhizobia CIAT899 was reduced by 73% when the plants were exposed to 300 mM NaCl, while only 60% yield loss was observed after inoculation with a novel indigenous isolate from Kenyan soil, named S3. Expression profiles showed that genes involved in the transport of mineral ions (such as K+, Ca2+, Fe3+, PO43-, and NO3-) to the host plant, and for the synthesis and transport of osmotolerance molecules (soluble carbohydrates, amino acids, and nucleotides) are highly expressed in S3 bacteroids during salt stress than in the controls. Furthermore, genes for the synthesis and transport of glutathione and γ-aminobutyric acid were upregulated in salt-stressed and S3-inocculated common bean plants. We conclude that microbial osmolytes, mineral ions, and antioxidant molecules from rhizobia enhance salt tolerance in common beans.
2022-10-31 | GSE216374 | GEO
Project description:Plant-released flavonoids induce the transcription of symbiotic genes in rhizobia and one of the first bacterial responses is the synthesis of so called Nod factors. They are responsible for the initial root hair curling during onset of root nodule development. This signal exchange is believed to be essential for initiating the plant symbiosis with rhizobia affiliated with the alphaproteobacteria. Here, we provide evidence that in broad host range rhizobia the complete lack of quorum sensing molecules results in an elevated copy number of its symbiotic plasmid (pNGR234a). This in turn triggers the expression of symbiotic genes and the production of Nod factors in the absence of plant signals. Therefore, increasing the copy number of specific plasmids could be a widespread mechanism of specialized bacterial populations bridging gaps in signalling cascades and providing a competitive advantage.
2017-02-10 | GSE78039 | GEO
Project description:Whole Genome Analysis of symbiotic rhizobacteria isolated from Vigna marina
| PRJDB13357 | ENA
Project description:NGS2013-04: Transcriptomic response to Nod Factor treatments on Medicago Role of the root hair in water and nutrient uptake and the establishment of the nitrogen-fixing symbiotic interaction with rhizobia.
2016-06-01 | GSE67921 | GEO
Project description:Aging and age-related neurodegeneration are among the major challenges because of the progressive increase in the number of elder people in the wold population. Nutrition, which has important long-term consequences for health, is actually considered a means to prevent diseases and to reach a healthy aging. Here we investigate the role of Vigna unguiculata beans on senescence by using Saccharomyces cerevisiae and Drosophila melanogaster as model systems. Aqueous extract, mainly containing starch, proteins and amino acids, extends chronological lifespan in yeast cells, showing a remarkable synergistic effect in combination with caloric restriction. The extension of yeast longevity requires both the anti-aging Snf1/AMPK and the pro-aging Ras2/PKA pathways. A significant marked increase of lifespan was observed also in fruit flies supplemented with the V. unguiculata extract, which is accompanied by the increased expression of FOXO, NOTCH, SIRT1 and heme oxygenase (HO) genes, already known to be required for the extension of fruit fly longevity. α-synuclein forms toxic intracellular protein inclusions in Parkinson’s disease (PD) and actually preventing α-synuclein self-assembly has become one of the most promising approaches for the treatment of this neurodegenerative disorder. Here, we report that in vitro aggregation of -synuclein, as well as its toxicity in yeast and in neuroblastoma cells, are strongly decreased in the presence of bean extract. In addition, in a Caenorhabditis elegans model of PD that expresses α-synuclein, Vigna unguiculate extract substantially reduces the number of the age-dependent degeneration of the cephalic dopaminergic neurons. Overall, our data support the role of Vigna unguiculata beans as a functional food, worth to be further explored in order to develop lead molecules for therapeutic intervention in age-related disorders.
2021-09-08 | PXD017716 | Pride
Project description:12plex_medicago_2013-08 - r108 in symbiosis with rhizobia wt or rhizobia mutant for baca. - Two experiments to compare the transcriptomic response of medicago plants: Agar medium versus Phytagel medium (exp1) and rhizobium WT versus BacA (exp2). - Medicago truncatula ecotype R108 was inoculated with the symbiotic rhizobium Sinorhizobium meliloti strain Sm1021 and with its derivative mutant delta bacA. Nodules were collected 13 days after inoculation, and RNA were prepared for transcriptome analysis, there were three biological independant experiements.
2018-11-01 | GSE121775 | GEO
Project description:NGS2013-04: Transcriptomic response to Nod Factor treatments on Medicago Role of the root hair in water and nutrient uptake and the establishment of the nitrogen-fixing symbiotic interaction with rhizobia. The RNA was extracted from root hairs of Medicago: control vs treated by nod factors (2 biological replicates)
2016-06-01 | E-GEOD-67921 | biostudies-arrayexpress
Project description:Rhizobia are soil bacteria that can enter into complex symbiotic relationships with legumes, where rhizobia induce the formation of nodules on the plant root. Inside nodules, rhizobia differentiate into nitrogen-fixing bacteroids that reduce atmospheric nitrogen into ammonia, secreting it to the plant host in exchange for carbon. During the transition from free-living bacteria to bacteroids, rhizobial metabolism undergoes major changes. To investigate the metabolism of bacteroids and contrast it with the free-living state, we quantified the proteome of unlabelled bacteroids relative to 15N-labelled free-living rhizobia. The data were used to build a core metabolic model of pea bacteroids for the strain Rhizobium leguminosarum bv. viciae 3841.
2021-09-09 | PXD019467 | Pride
Project description:Legume plants form symbiotic relationships with diazotrophic bacteria called rhizobia. During such symbiosis, plants provide bacteria with preferred carbon sources such as malate and succinate in return for essential reduced nitrogen. Compatible interactions result in a series of plant root modifications that eventually result in nodule formation. Bacteria living in the nodule cells fix nitrogen via the nitrogenase enzyme complex. Interestingly, as in plant-pathogen interactions, incompatibility in legume-rhizobia associations is also regulated in a genotype-specific manner. For example, the dominant Rj2 gene is presumed to help exclude poor nitrogen-fixing or less-beneficial rhizobia such as B. japonicum USDA122 (U122). The process likely involves recognition of bacterial effectors by host receptor proteins similar to the perception of pathogenic microbes. Our results show that genetic exclusion of incompatible rhizobia in the root requires conserved molecular components of the plant immune response pathway and results in the induction of systemic signaling in the distal tissue. To better understand the mechanism underlying incompatible rhizobia-induced systemic signaling, we compared the transcriptional changes in the foliar tissue of Rj2 plants inoculated with compatible or incompatible rhizobia strains, using RNA-Seq analysis.
2019-10-24 | GSE139303 | GEO
Project description:Whole Genome Sequencing of Vigna marina subsp. marina
| PRJNA445647 | ENA