Soil metagenome
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ABSTRACT:
PROVIDER: PRJNA394812 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Soil bacterial community composition with artificial root exudates application Metagenome
| PRJNA394773 | ENA
Project description:Artificial Root Exudates Incubation experiment
| PRJNA562427 | ENA
Project description:Sorghum bicolor is one of the most important cereal crops in the world, predominantly grown in sub‑Saharan Africa by smallholder farmers. Despite its outstanding resilience to abiotic stresses, approximately 20% of sorghum yield is annually lost on the African continent due to infestation with the parasitic weed Striga hermonthica. Existing Striga management strategies to decrease Striga infestation often show low efficiency and are not easily integrated into current agricultural practices. Microbial-based solutions may prove an effective, low-cost mode for reducing Striga parasitism in sub-Saharan Africa. Here, we demonstrate that the microbiome component of a field soil suppresses Striga infection of sorghum. Potential mechanisms underlying the soil microbiome’s influence on the host plant include root endodermal suberization and aerenchyma formation. Moreover, we observed a depletion of haustorium inducing factors, compounds essential for Striga to establish the host-parasite association, in root exudates collected from sorghum grown in the presence of the soil microbiome as compared to sterile conditions. We further identified individual microbial taxa associated with reduced Striga infection via changes in root cellular anatomy and differentiation as well as in exudate composition. Our study identifies a suite of traits that can be harnessed by individual microbial isolates or their consortia to induce Striga resistance. Combining microbes that elicit Striga resistance directly (affecting the parasite) via repression of haustorium formation with those that act indirectly (affecting the host), by reducing of Striga penetration through root tissue, can broaden the effectiveness of microbe-induced protection from Striga.
2022-10-31 | GSE216351 | GEO
Project description:Arsenic (As) bioavailability in the rice rhizosphere is influenced by many microbial interactions, particularly by metal-transforming functional groups at the root-soil interface. This study was conducted to examine As-transforming microbes and As-speciation in the rice rhizosphere compartments, in response to two different water management practices (continuous and intermittently flooded), established on fields with high to low soil-As concentration. Microbial functional gene composition in the rhizosphere and root-plaque compartments were characterized using the GeoChip 4.0 microarray. Arsenic speciation and concentrations were analyzed in the rhizosphere soil, root-plaque, porewater and grain samples. Results indicated that intermittent flooding significantly altered As-speciation in the rhizosphere, and reduced methyl-As and AsIII concentrations in the pore water, root-plaque and rice grain. Ordination and taxonomic analysis of detected gene-probes indicated that root-plaque and rhizosphere assembled significantly different metal-transforming functional groups. Taxonomic non-redundancy was evident, suggesting that As-reduction, -oxidation and -methylation processes were performed by different microbial groups. As-transformation was coupled to different biogeochemical cycling processes establishing functional non-redundancy of rice-rhizosphere microbiome in response to both rhizosphere compartmentalization and experimental treatments. This study confirmed diverse As-biotransformation at root-soil interface and provided novel insights on their responses to water management, which can be applied for mitigating As-bioavailability and accumulation in rice grains.
2021-07-12 | GSE179671 | GEO
Project description:In general, the endosphere isolate EC18 showed more numbers of genes significantly altered in the presence of root exudates than the soil isolate SB8 . Some of the altered genes in the two strains showed overlap. Some of these genes were previously reported to be involved in microbe-plant interactions, such as organic substance metabolism, oxidation reduction, transmembrane transportation and a subset with putative or unknown function. It was also found some genes showed opposite trend among the two strains.
2017-04-26 | GSE98148 | GEO
Project description:Plants and rhizosphere microbes rely closely on each other, with plants supplying carbon to bacteria in root exudates, and bacteria mobilizing soil-bound phosphate for plant nutrition. When the phosphate supply becomes limiting for plant growth, the composition of root exudation changes, affecting rhizosphere microbial communities and microbially-mediated nutrient fluxes. To evaluate how plant phosphate deprivation affects rhizosphere bacteria, Lolium perenne seedlings were root-inoculated with Pseudomonas aeruginosa 7NR, and grown in axenic microcosms under different phosphate regimes (330 uM vs 3-6 uM phosphate). The effect of biological nutrient limitation was examined by DNA microarray studies of rhizobacterial gene expression.
2011-07-01 | E-MEXP-2812 | biostudies-arrayexpress
Project description:Anthropogenic nitrogen (N) deposition may affect soil organic carbon (SOC) decomposition, thus affecting the global terrestrial carbon (C) cycle. However, it remains unclear how the level of N deposition affects SOC decomposition by regulating microbial community composition and function, especially C-cycling functional genes structure. We investigated the effects of short-term N addition on soil microbial C-cycling functional gene composition, SOC-degrading enzyme activities, and CO2 emission in a 5-year field experiment established in an artificial Pinus tabulaeformis forest on the Loess Plateau, China.
2022-03-01 | GSE147041 | GEO
Project description:Reforestation is effective in restoring ecosystem functions and enhancing ecosystem services of degraded land. The three most commonly employed reforestation methods of natural reforestation, artificial reforestation with native Masson pine (Pinus massoniana Lamb.), and introduced slash pine (Pinus elliottii Engelm.) plantations were equally successful in biomass yield in southern China. However, it is not known if soil ecosystem functions, such as nitrogen (N) cycling, are also successfully restored. Here, we employed a functional microarray to illustrate soil N cycling. The composition and interactions of N-cycling genes in soils varied significantly with reforestation method. Natural reforestation had more superior organization of N-cycling genes, and higher functional potential (abundance of ammonification, denitrification, assimilatory, and dissimilatory nitrate reduction to ammonium genes) in soils, providing molecular insight into the effects of reforestation.
2019-11-04 | GSE100379 | GEO
Project description:The presence of genetic groups of the entomopathogenic fungus Metarhizium anisopliae in soil is shaped by its adaptability to specific soil and habitat types, and by soil insect populations. Although the entomopathogenic life style of this fungus is well studied, its saprophytic life style has received little consideration. While a set of functionally related genes can be commonly expressed for the adaptability of this fungus to different environments (insect cuticle, insect blood and root exudates), a different subset of genes is also expected for each environment. In order to increase the knowledge of the potential use of M. anisopliae as a rhizosphere competent organism, in this study we evaluated the genetic expression of this fungus while growing on plant root exudates in laboratory conditions during a time course.
2010-12-29 | GSE16848 | GEO
Project description:The rhizosphere is a small region surrounding plant roots that is enriched in biochemicals from root exudates and populated with fungi, nematode, and bacteria. Interaction of rhizosphere organisms with plants is mainly promoted by exudates from the roots. Root exudates contain biochemicals that come from primary and secondary metabolisms of plants. These biochemicals attract microbes, which influence plant nutrition. The rhizosphere bacteria (microbiome) are vital to plant nutrient uptake and influence biotic and abiotic stress and pathogenesis. Pseudomonas is a genus of gammaproteobacteria known for its ubiquitous presence in natural habitats and its striking ecological, metabolic, and biochemical diversity. Within the genus, members of the Pseudomonas fluorescens group are common inhabitants of soil and plant surfaces, and certain strains function in the biological control of plant disease, protecting plants from infection by soilborne and aerial plant pathogens. The soil bacterium Pseudomonas protegens Pf-5 (also known as Pseudomonas fluorescens Pf-5) is a well-characterized biological strain, which is distinguished by its prolific production of the secondary metabolite, pyoverdine. Knowledge of the distribution of P. fluorescens secretory activity around plant roots is very important for understanding the interaction between P. fluorescens and plants and can be achieved by real time tracking of pyoverdine. To achieve the capability of real-time tracking in soil, we have used a structure-switching SELEX strategy to select high affinity ssDNA aptamers with specificity for pyoverdine over other siderophores. Two DNA aptamers were isolated, and their features compared. The aptamers were applied to a nanoporous aluminum oxide biosensor and demonstrated to successfully detect PYO-Pf5. This sensor provides a future opportunity to track the locations around plant roots of P. protegens and to monitor PYO-Pf5 production and movement through the soil.
2024-07-18 | GSE225440 | GEO