Bacteria
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1008182 | 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:Root exudates contain specialised metabolites that affect the plant’s root microbiome. How host-specific microbes cope with these bioactive compounds, and how this ability shapes root microbiomes, remains largely unknown. We investigated how maize root bacteria metabolise benzoxazinoids, the main specialised metabolites of maize. Diverse and abundant bacteria metabolised the major compound in the maize rhizosphere MBOA and formed AMPO. AMPO forming bacteria are enriched in the rhizosphere of benzoxazinoid-producing maize and can use MBOA as carbon source. We identified a novel gene cluster associated with AMPO formation in microbacteria. The first gene in this cluster, bxdA encodes a lactonase that converts MBOA to AMPO in vitro. A deletion mutant of the homologous bxdA genes in the genus Sphingobium, does not form AMPO nor is it able to use MBOA as a carbon source. BxdA was identified in different genera of maize root bacteria. Here we show that plant-specialised metabolites select for metabolisation-competent root bacteria. BxdA represents a novel benzoxazinoid metabolisation gene whose carriers successfully colonize the maize rhizosphere and thereby shape the plant’s chemical environmental footprint
2024-04-05 | GSE263275 | GEO
Project description:This project is designed for whole transcriptome sequencing of bacteria isolated from Rhizosphere of Wheat Plant, which has its impact on overall plant growth.
2024-02-28 | E-MTAB-11516 | biostudies-arrayexpress
Project description:We developed Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) for de novo detection of global chromatin interactions, and comprehensively mapped the chromatin interaction network bound by estrogen receptor α (ERα) in the human genome. We performed 454 and Illumina sequencing analyses. Keywords: Epigenetics Using 454, we examined 3 libraries: IHM001 (Estrogen Receptor ChIA-PET), IHM043 (Estrogen Receptor ChIP-PET) and IHM062 (IgG ChIA-PET) Using Illumina, we examined 4 libraries: IHM001 (Estrogen Receptor ChIA-PET replicate 1, Paired End Sequencing), IHH015 (Estrogen Receptor ChIA-PET replicate 2, Paired End Sequencing), H3K4me3 ChIP-Seq and RNA polymerase II ChIP-Seq
2009-09-11 | E-GEOD-18046 | biostudies-arrayexpress
Project description:This data set contains 1376 mass spectrometry reads from root, rhizosphere and leaf sample of Populus Trichocarpa, as well as associated controls. This metabolomics data set was collected as part of a larger campaign which complements the metabolomics data with metagenome sequencing, transcriptomics, and soil measurement data.
2022-12-12 | MSV000090886 | MassIVE
Project description:We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to https://www.encodeproject.org/about/data-use-policy Chromatin interactions identified by ChIA-PET for 4 different histone modifications (H3K4me1, H3K4me2, H3K4me3, H3K27ac), RAD21 and RNAPII in the K562 cell line, two biological replicates each. Additionally, chromatin interactions were identified by ChIA-PET in the GM12878 cell line for RAD21.
2014-08-21 | E-GEOD-59395 | biostudies-arrayexpress
Project description:Microbial communities in the rhizosphere make significant contributions to crop health and nutrient cycling. However, their ability to perform important biogeochemical processes remains uncharacterized. Important functional genes, which characterize the rhizosphere microbial community, were identified to understand metabolic capabilities in the maize rhizosphere using GeoChip 3.0-based functional gene array method.
2014-09-12 | GSE61338 | GEO
Project description:This Project investigates the impact of elevated temperatures and relative humidity on the aging process of chia seeds (Salvia hispanica L.). The study employs proteomics to examine molecular responses to accelerated aging in two chia genotypes. The results underscore the importance of evaluating changes in proteins of aged seeds to gain insights into the biological mechanisms responsible for maintaining chia seed integrity during the aging process.
2024-08-06 | PXD049229 | Pride
Project description:Priestia endophytica FH5, which was isolated from healthy tomato rhizosphere soil, had biological activity against a variety of plant diseases, including R. solani. We isolated the chemicals generated by strain FH5 to better understand the interaction between strain FH5 and R. solani. A transcriptome study of strain FH5 with and without R. solani exposure was also performed. In response to the fungal pathogen R. solani, strain FH5 changed genes linked to amino acid transport, carbohydrate transport, energy generation and conversion, and inorganic ion transport and metabolism, according to our findings.
2021-07-09 | GSE179605 | GEO
Project description:The Atlantic salmon (Salmo salar) genome contains 10 chitinase encoding genes, but little is known about the function of these chitinases. Three of the chitinase genes have previously been shown to be expressed in the stomach tissue of Atlantic salmon. In the current study we show that the protein products of these genes, the family 18 glycoside hydrolase (GH18) chitinases, Chia.3, Chia.4 and Chia.7 are secreted into the stomach mucosa and are amongst the most abundant proteins in this matrix.
2022-05-08 | PXD030291 | Pride