Ontology highlight
ABSTRACT:
PROVIDER: PRJNA786545 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17139700_1.fastq.gz | Fastqsanger.gz | |||
| SRR17139700_2.fastq.gz | Fastqsanger.gz | |||
| SRR17139800_1.fastq.gz | Fastqsanger.gz | |||
| SRR17139800_2.fastq.gz | Fastqsanger.gz | |||
| SRR17139900_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 1800 |
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:Cropping soils vary in extent of natural suppression of soil-borne plant diseases. However, it is unknown whether similar variation occurs across pastoral agricultural systems. We examined soil microbial community properties known to be associated with disease suppression across 50 pastoral fields varying in management intensity. The composition and abundance of the disease-suppressive community were assessed from both taxonomic and functional perspectives.
2018-03-30 | GSE112489 | GEO
Project description:The spread of antibiotic resistance genes (ARG) into agricultural soils, products, and foods severely limits the use of organic fertilizers in agriculture. In this study, experimental land plots were fertilized, sown, and harvested for two consecutive agricultural cycles using either mineral or three types of organic fertilizers: sewage sludge, pig slurry, or composted organic fraction of municipal solid waste. The analysis of the relative abundances of more than 200,000 ASV (Amplicon Sequence Variants) allowed the identification of a small, but significant (<10%) overlap between soil and fertilizer microbiomes, particularly in soils sampled the same day of the harvest (post-harvest soils). Loads of clinically relevant ARG were significantly higher (up to 100 fold) in fertilized soils relative to the initial soil. The highest increases corresponded to post-harvest soils treated with organic fertilizers, and they correlated with the extend of the contribution of fertilizers to the soil microbiome. Edible products (lettuce and radish) showed low, but measurable loads of ARG (sul1 for lettuces and radish, tetM for lettuces). These loads were minimal in mineral fertilized soils, and strongly dependent on the type of fertilizer. We concluded that at least part of the observed increase on ARG loads in soils and foodstuffs were actual contributions from the fertilizer microbiomes. Thus, we propose that adequate waste management and good pharmacological and veterinarian practices may significantly reduce the potential health risk posed by the presence of ARG in agricultural soils and plant products.
2021-07-09 | GSE179685 | GEO
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:The experiment at three long-term agricultural experimental stations (namely the N, M and S sites) across northeast to southeast China was setup and operated by the Institute of Soil Science, Chinese Academy of Sciences. This experiment belongs to an integrated project (The Soil Reciprocal Transplant Experiment, SRTE) which serves as a platform for a number of studies evaluating climate and cropping effects on soil microbial diversity and its agro-ecosystem functioning. Soil transplant serves as a proxy to simulate climate change in realistic climate regimes. Here, we assessed the effects of soil type, soil transplant and landuse changes on soil microbial communities, which are key drivers in Earth’s biogeochemical cycles.
2016-02-04 | GSE77546 | GEO
Project description:Earthworms enhance plant growth but the precise mechanism by which this occurs is not known. An understanding of the mechanism could potentially support changes in agricultural management reducing fertiliser usage and therefore costs and the carbon footprint of agriculture. We conducted a factorial experiment in which 5 strains of wheat were grown in the presence and absence of earthworms under regular watering and droughted conditions. The different wheat strains all responded in a similar fashion. Plant biomass was greater in the presence of earthworms and under regular watering. The presence of earthworms reduced the impact of drought on plant biomass and also slowed down the rate of drying of the droughted soils. Plant nutrient content (N, P, Si) showed no consistent pattern with treatments but total N, P and Si mirrored plant biomass and decreased in the order earthworm-present watered > earthworm-present droughted > earthworm-absent watered > earthworm-absent droughted. Nutrient availability in the soil, as assessed by chemical extractions showed no consistent pattern with treatments. Differential gene expression of plants was greater between watering treatments than between earthworm treatments. Genes that were differentially expressed between the earthworm treatments predominantly related to plant defences, abiotic stress and control of plant growth though a couple were linked to both nitrogen cycling and stress responses. The soil microbiome of the earthworm-present treatments was more associated with nutrient-rich environments, the promotion of plant growth and the suppression of plant pathogens. Our data suggest that enhanced plant growth was due to changes in the microbiome due to earthworm processing of the soil rather than changes in nutrient availability due to the presence of earthworms.
2025-03-03 | GSE214932 | GEO
Project description:The effects of agricultural management on soil microbial carbon use efficiency
| PRJEB47841 | ENA
Project description:Bile acids are steroid compounds from the digestive tracts of vertebrates that enter agricultural environments in unusual high amounts with manure. Bacteria degrading bile acids can readily be isolated from soils and waters including agricultural areas. Under laboratory conditions, these bacteria transiently release steroid compounds as degradation intermediates into the environment. These compounds include androstadienediones (ADDs), which are C19-steroids with potential hormonal effects. Experiments with Caenorhabditis elegans showed that ADDs derived from bacterial bile acid degradation had effects on its tactile response, reproduction rate, and developmental speed. Additional experiments with a deletion mutant as well as transcriptomic analyses revealed that these effects might be conveyed by the putative testosterone receptor NHR-69. Soil microcosms showed that the natural microflora of agricultural soil is readily induced for bile acid degradation accompanied by the transient release of steroid intermediates. Establishment of a model system with a Pseudomonas strain and C. elegans in sand microcosms indicated transient release of ADDs during the course of bile acid degradation and negative effects on the reproduction rate of the nematode. This proof-of-principle study points at bacterial degradation of manure-derived bile acids as a potential and so-far overlooked risk for invertebrates in agricultural soils.
2019-02-08 | GSE126214 | GEO