SKNNNGH
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA966895 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:ngs2021_12_endomix-phe-gradient-Identify the physiological response of poplar to the presence of 8 Phenanthrene gradient concentration.-As part of the ANR EndOMiX project, we carried out an experiment with poplars (Populus canadensis: hybrid Populus deltoides x nigra) grown in soil with a gradient of contamination in Phenanthrene (PHE), we have 8 different concentrations of PHE, and 4 biological replicates (pots with independent plants). We harvested after 4 weeks of growth, the roots and leaves of the poplars from which the RNAs were extracted for sequencing.
2025-06-04 | GSE263776 | GEO
Project description:Heavy metal contamination poses an escalating global challenge to soil ecosystems. Hyperaccumulators play a crucial role in environmental remediation and resource recovery. The enrichment of diazotrophs and resulting nitrogen accumulation promoted hyperaccumulator growth and facilitated phytoremediation. Nonetheless, the regulatory mechanism of hyperaccumulator biological nitrogen fixation has remained elusive. Here, we report the mechanism by which arsenic regulates biological nitrogen fixation in the arsenic-hyperaccumulator Pteris vittata. Field investigations and greenhouse experiments, based on multi-omics approaches, reveal that elevated arsenic stress induces an enrichment of key diazotrophs, enhances plant nitrogen acquisition, and thus improves plant growth. Metabolomic analysis and microfluidic experiments further demonstrate that the upregulation of specific root metabolites plays a crucial role in recruiting key diazotrophic bacteria. These findings highlight the pivotal role of nitrogen-acquisition mechanisms in the arsenic hyperaccumulation of Pteris vittata, and provide valuable insights into the plant stress resistance.
2024-11-01 | MTBLS11419 | MetaboLights
Project description:Metagenome data from soil samples were collected at 0 to 10cm deep from 2 avocado orchards in Channybearup, Western Australia, in 2024. Amplicon sequence variant (ASV) tables were constructed based on the DADA2 pipeline with default parameters.
2025-06-15 | GSE298403 | GEO
Project description:Plant-associated outbreaks with enterohemorrhagic E. coli (EHEC) increased worldwide during the last decades. Agricultural soil is an important contamination source for edible plants. Thus, the survival of pathogenic E. coli in agricultural soil samples was analyzed in previous studies. Thereby, the influence of environmental factors and biotic factors was investigated. In the current study, genetic factors that influence the survival of enterohemorrhagic/enteroaggregative E. coli (EHEC/EAEC) O104:H4 strain C227/11Φcu in agricultural soil microenvironments was investigated. The strain was incubated in alluvial loam (AL) for up to 4 weeks and total RNA was prepared from samples taken immediately after inoculation (time point 0), after 1 week and after 4 weeks. Differential transcriptomic analysis was performed by RNA sequencing analysis and values obtained at weeks 1 and 4 were compared to those of time point 0. We found differential expression of more than 1500 genes. The two lists of differentially expressed genes were then subject to gene set enrichment of Gene ontology terms. After 1 week of incubation 36 gene sets were significantly enriched while only 38 gene sets were found to be enriched for the genes that were differentially expressed after 4 weeks. Especially stress response genes and genes of the primary metabolism such as carbohydrate and amino acid metabolism were concerned for both time points. Genes and gene sets for uptake of carbohydrates, amino acids were strongly upregulated, indicating adjustment to a low nutrient environment
2023-11-29 | GSE222589 | GEO
Project description:Sequencing the metatranscriptome can provide information about the response of organisms to varying environmental conditions. We present a methodology for obtaining random whole-community mRNA from a complex microbial assemblage using Pyrosequencing. The metatranscriptome had, with minimum contamination by ribosomal RNA, significant coverage of abundant transcripts, and included significantly more potentially novel proteins than in the metagenome. Keywords: metatranscriptome, mesocosm, ocean acidification
2008-02-08 | GSE10119 | GEO