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Crop plant rhizosphere metatranscriptomics

ABSTRACT: Transcriptomic analysis of microbial communities isolated from the rhizospheres of wheat, oat and pea, compared to unplanted soil.

PROVIDER: PRJEB6737 | ENA |

REPOSITORIES: ENA

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Crop plant rhizosphere metatranscriptomics

Project description:Transcriptomic analysis of microbial communities isolated from the rhizospheres of wheat, oat and pea, compared to unplanted soil

| PRJEB6752 | ENA

Wheat rhizosphere metatranscriptomics

Project description:Wheat rhizosphere metatranscriptomics

| PRJEB2451 | ENA

Genome sequencing of 22 Pseudomonas isolates from the rhizosphere of the barley variety Chevallier and 20 Psuedomonas isolates from the rhizosphere of the barley variety Tipple.

Project description:Chevallier is a heritage english landrace of barley first planted in 1820 while Tipple is modern cultivar of barley released in 2004. Pseudomonas strains were isolated from the rhizospheres of the two varieties and 22 and 20 of the most phylogenetically distinct ones were sequenced to find out the difference in genotypes preferentially selected in the rhizospheres of the two cultivars.

2023-06-15 | E-MTAB-12917 | biostudies-arrayexpress

Glyphosate effects on plant mineral nutrition, crop rhizosphere microbiota, and plant disease in glyphosate-resistant crops.

Project description:Claims have been made recently that glyphosate-resistant (GR) crops sometimes have mineral deficiencies and increased plant disease. This review evaluates the literature that is germane to these claims. Our conclusions are: (1) although there is conflicting literature on the effects of glyphosate on mineral nutrition on GR crops, most of the literature indicates that mineral nutrition in GR crops is not affected by either the GR trait or by application of glyphosate; (2) most of the available data support the view that neither the GR transgenes nor glyphosate use in GR crops increases crop disease; and (3) yield data on GR crops do not support the hypotheses that there are substantive mineral nutrition or disease problems that are specific to GR crops.

| S-EPMC3479986 | biostudies-other

RNA-seq on touch responses in cereals

Project description:RNA-seq time course covering the first 2 hours after gentle brushing of the second leaf in oat, wheat and barley.

2023-04-19 | E-MTAB-11762 | biostudies-arrayexpress

Rhizosphere microbes enhance plant salt tolerance: Toward crop production in saline soil.

Project description:The world's population continues to increase and thus requires more food production to take place in nonarable land, such as saline soil; therefore, it is urgent to find solutions to enhance the salinity tolerance of crops. As the second genome of plants, the rhizosphere microbiome plays critical roles in plant fitness under stress conditions. Many beneficial microbes that help plants cope with salinity stress have been identified, highlighting their roles in mitigating salt stress-induced negative effects on plants. However, a comprehensive review of the microbial species that are able to confer plant salt tolerance and the underlying mechanisms is still lacking. In this review, we compared the representative fungal and bacterial taxa that demonstrate the ability to enhance plant growth in saline soil. We also reviewed the mechanisms by which rhizosphere microbes enhance plant salt stress tolerance, i.e., by re-establishing ion and osmotic homeostasis, preventing damage to plant cells, and resuming plant growth under salt stress. Finally, future research efforts to explore the rhizosphere microbiome for agricultural sustainability are proposed.

| S-EPMC9712829 | biostudies-literature

Cross-species Detection in Barley1 GeneChip Array

Project description:This study was conducted to evaluate the efficiency of cross-species detection in Barley1 GeneChip array. We hybridized cRNA derived from first leaves of barley green seedlings (as a control), as well as the same stage of seedling leaf from representative genotypes of wheat, oat, rice, maize, and sorghum. Ten to twenty seedlings for each species were harvested and pooled for RNA preparation, labeling, and hybridization. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Rico Caldo. The equivalent experiment is BB1 at PLEXdb.] species: Barley(2-replications); species: Wheat(2-replications); species: Oat(2-replications); species: Sorghum(2-replications); species: Corn(2-replications); species: Rice(2-replications)

2011-11-22 | E-GEOD-33391 | biostudies-arrayexpress

Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants.

Project description:Plant-microbe interactions in the rhizosphere have important roles in biogeochemical cycling, and maintenance of plant health and productivity, yet remain poorly understood. Using RNA-based metatranscriptomics, the global active microbiomes were analysed in soil and rhizospheres of wheat, oat, pea and an oat mutant (sad1) deficient in production of anti-fungal avenacins. Rhizosphere microbiomes differed from bulk soil and between plant species. Pea (a legume) had a much stronger effect on the rhizosphere than wheat and oat (cereals), resulting in a dramatically different rhizosphere community. The relative abundance of eukaryotes in the oat and pea rhizospheres was more than fivefold higher than in the wheat rhizosphere or bulk soil. Nematodes and bacterivorous protozoa were enriched in all rhizospheres, whereas the pea rhizosphere was highly enriched for fungi. Metabolic capabilities for rhizosphere colonisation were selected, including cellulose degradation (cereals), H2 oxidation (pea) and methylotrophy (all plants). Avenacins had little effect on the prokaryotic community of oat, but the eukaryotic community was strongly altered in the sad1 mutant, suggesting that avenacins have a broader role than protecting from fungal pathogens. Profiling microbial communities with metatranscriptomics allows comparison of relative abundance, from multiple samples, across all domains of life, without polymerase chain reaction bias. This revealed profound differences in the rhizosphere microbiome, particularly at the kingdom level between plants.

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Crop plant

Project description:NGS-based genomic analysis of Eragrostis species

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rhizosphere metagenome

Project description:Flowering-time-selected Rhizospheres Raw sequence reads

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