Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1240274 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32808700_1.fastq.gz | Fastqsanger.gz | |||
| SRR32808700_2.fastq.gz | Fastqsanger.gz | |||
| SRR32808800_1.fastq.gz | Fastqsanger.gz | |||
| SRR32808800_2.fastq.gz | Fastqsanger.gz | |||
| SRR32808701_1.fastq.gz | Fastqsanger.gz |
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Project description:Cover cropping is an effective method to protect agricultural soils from erosion, promote nutrient and moisture retention, encourage beneficial microbial activity, and maintain soil structure. Reusing winter cover crop root channels with the maize roots during the summer allows the cash crop to extract resources from farther niches in the soil horizon. In this study, we investigate how reusing winter cover crop root channels to grow maize (Zea mays L.) affects the composition and function of the bacterial communities in the rhizosphere using 16S rRNA gene amplicon sequencing and metaproteomics. We discovered that the bacterial community significantly differed among cover crop variations, soil profile depths, and maize growth stages. Re-usage of the root channels increased bacterial abundance, and it further increases as we elevate the complexity from monocultures to mixtures. Upon mixing legumes with brassicas and grasses, the overall expression of several steps of the carbon cycle (C) and the nitrogen cycle (N) improved. The deeper root channels of legumes and brassicas compared to grasses correlated with higher bacterial 16S rRNA gene copy numbers and community roles in the respective variations in the subsoil regimes due to the increased availability of root exudates secreted by maize roots. In conclusion, root channel re-use (monocultures and mixtures) improved the expression of metabolic pathways of the important C and N cycles, and the bacterial communities, which is beneficial to the soil rhizosphere as well as to the growing crops.
2025-05-02 | PXD046832 | Pride
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:<p>Biological nitrogen fixation by free-living bacteria and rhizobial symbiosis with legumes plays a key role in sustainable crop production. Here, we study how different crop combinations influence the interaction between peanut plants and their rhizosphere microbiota via metabolite deposition and functional responses of free-living and symbiotic nitrogen-fixing bacteria. Based on a long-term (8 year) diversified cropping field experiment, we find that peanut co-cultured with maize and oilseed rape lead to specific changes in peanut rhizosphere metabolite profiles and bacterial functions and nodulation. Flavonoids and coumarins accumulate due to the activation of phenylpropanoid biosynthesis pathways in peanuts. These changes enhance the growth and nitrogen fixation activity of free-living bacterial isolates, and root nodulation by symbiotic Bradyrhizobium isolates. Peanut plant root metabolites interact with Bradyrhizobium isolates contributing to initiate nodulation. Our findings demonstrate that tailored intercropping could be used to improve soil nitrogen availability through changes in the rhizosphere microbiome and its functions.</p>
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Project description:These samples are a part of a study investigating microbial responses to cover crop root exudates. We utilized 4 cover crop species (each with unique root exudate profiles), collected the pure root exudates, and applied them to soil mirocosms. metaG, metaT, metaP, and targeted and untargeted metabolomics were applied to assess the microbial responses.
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Project description:These samples are a part of a study investigating microbial responses to cover crop root exudates. We utilized 4 cover crop species (each with unique root exudate profiles), collected the pure root exudates, and applied them to soil mirocosms. metaG, metaT, metaP, and targeted and untargeted metabolomics were applied to assess the microbial responses.
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Project description:cover crop (19) root exudate profiles analyzed by non-targeted LC-MS/MS DDA
2022-03-22 | MSV000089101 | MassIVE
Project description:Pearl millet [Pennisetum glaucum (L.) R.Br] is the fifth most important cereal crop next to rice, wheat, maize, and sorghum. It is cultivated especially by small holder farmers in arid and semi-arid regions because of its drought resistance. However, the molecular mechanisms during drought stress in Pennisetum remain elusive. In the present study we have used a shotgun proteomics approach (GEL-LC-Orbitrap-MS) for identification and quantification of proteins from different tissues (root, seed and leaf) under drought and control conditions. Plants were grown in a tube system to survey root growth under drought stress. The water content was measured in the upper and the lower part of the tube using soil moisture sensors. Under drought stress root elongation was observed. Measurement of stomatal conductance showed a clear response to drought stress. For proteomics measurements root, leaf and seed tissues were harvested. In total 2281 proteins were identified, 1095 in root, 1299 in seed, and 1208 in leaf in both stress and control conditions.
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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.
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