Soil metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA377423 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6332678.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 1 of 1 |
Similar Datasets
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:Root and leave samples of 4 different apple genotypes were investigated in order to analyse the gene expression after infection with Apple Replant Disease (ARD). All genotypes were cultivated in ARD-infected soil and gamma-irradiated (disinfected) soil in the greenhouse for 7 days. The ARD soil originated from two different orchards representing two different soil compositions. After 7 days root tissue was collected from each plant and used for the subsequent gene expression analysis. This work was part of the project BonaRes-ORDIAmur funded by the German Federal Ministry of Research and Education within the frame of the program BonaRes (grant no. 031B0025B). It was also funded by the German Research Foundation (DFG) via the research training group GRK1798 "Signaling at the Plant-Soil Interface" and a grant to BL and LB (BE 1174/19-1).
2019-12-09 | GSE135081 | GEO
Project description:In order to get insights into the ability of ectomycorrhizal fungi to perceive their biotic environment as well as into the mechanisms of the interactions between ectomycorrhizal fungi and soil bacteria, we analysed the transcriptomic response of the ectomycorrhizal fungus L. bicolor and of two beneficial, and neutral soil bacteria during their interactions in vitro.
2014-06-12 | GSE53608 | GEO
Project description:Diclofenac is widely used as nonsteroidal anti-inflammatory drug leaving residues in the environment. To investigate effects on terrestrial ecosystems, we measured dissipation rate in soil and investigated ecotoxicological and transcriptome-wide responses in Folsomia candida. Exposure for 4 weeks to diclofenac reduced both survival and reproduction of F. candida in a dose-dependent manner. At concentrations ≥200 mg/kg soil diclofenac remained stable in the soil during a 21-day incubation period. Microarrays examined transcriptional changes at low and high diclofenac exposure concentrations. The results indicated that development and growth were severely hampered and immunity-related genes, mainly directed against bacteria and fungi, were significantly up-regulated. Furthermore, neural metabolic processes were significantly affected only at the high concentration. We conclude that diclofenac is toxic to non-target soil invertebrates, although its mode of action is different from the mammalian toxicity. The genetic markers proposed in this study may be promising early markers for diclofenac ecotoxicity.
2014-10-01 | GSE59589 | GEO
Project description:Because of severe abiotic limitations, Antarctic soils represent simplified ecosystems, where microorganisms are the principle drivers of nutrient cycling. This relative simplicity makes these ecosystems particularly vulnerable to perturbations, like global warming, and the Antarctic Peninsula is among the most rapidly warming regions on the planet. However, the consequences of the ongoing warming of Antarctica on microorganisms and the processes they mediate are unknown. Here, using 16S rRNA gene pyrosequencing and qPCR, we report a number of highly consistent changes in microbial community structure and abundance across very disparate sub-Antarctic and Antarctic environments following three years of experimental field warming (+ 0.5-2°C). Specifically, we found significant increases in the abundance of fungi and bacteria and in the Alphaproteobacteria-to-Acidobacteria ratio. These alterations were linked to a significant increase in soil respiration. Furthermore, the shifts toward generalist or opportunistic bacterial communities following warming weakened the linkage between bacterial diversity and functional diversity. Warming also increased the abundance of some organisms related to the N-cycle, detected as an increase in the relative abundance of nitrogenase genes via GeoChip microarray analyses. Our results demonstrate that soil microorganisms across a range of sub-Antarctic and Antarctic environments can respond consistently and rapidly to increasing temperatures, thereby potentially disrupting soil functioning.
2010-12-30 | GSE22825 | GEO
Project description:Phosphorus (P) limitation will play a key role in the productivity of agriculture in the coming decades. Struvite is an ammonium magnesium phosphate mineral that can be recovered from wastewater-treatment plants and can be considered as an alternative source of P. However, the impact of struvite on the plant yield and, particularly, on the soil microbial community is barely known. Here, we tested the impacts of struvite, sewage sludge, and their combination on the barley yield, soil macro and micronutrients, and biochemical and microbiological soil properties. Amendment with struvite alone and its combination with sludge increased the availability of P in soil, the plant uptake of P and Mg, and the barley yield. The analysis of phospholipid fatty acids (PLFAs) and metaproteomics approaches revealed significant effects of struvite on the biomass of Gram-positive bacteria and, particularly, on actinobacterial populations in soil.
2019-03-13 | PXD009595 | Pride
Project description:Understanding the mechanisms underlying the establishment of invasive plants is critical in community ecology. According to a widely accepted theory, plant-soil-microbe interactions mediate the effects of invasive plants on native species, thereby affecting invasion success. However, the roles and molecular mechanisms associated with such microbes remain elusive. Using high throughput sequencing and a functional gene microarray, we found that soil taxonomic and functional microbial communities in plots dominated by Ageratina adenophora developed to benefit the invasive plant. There were increases in nitrogen-fixing bacteria and labile carbon degraders, as well as soil-borne pathogens in bulk soil, which potentially suppressed native plant growth. Meanwhile, there was an increase of microbial antagonism in the A. adenophora rhizosphere, which could inhibit pathogenicity against plant invader. These results suggest that the invasive plant A. adenophora establishes a self-reinforcing soil environment by changing the soil microbial community. It could be defined as a ‘bodyguard/mercenary army’ strategy for invasive plants, which has important insights for the mitigation of plant invasion.
2019-05-01 | GSE114498 | GEO
Project description:Here we have compared adult wildtype (N2) C. elegans gene expression when grown on different bacterial environments/fod sources in an effort to model naturally occuring nematode-bacteria interactions at the Konza Prairie. We hypothesize that human-induced changes to natural environments, such as the addition of nitrogen fertalizer, have effects on the bacterial community in soils and this drives downstream changes in the structure on soil bacterial-feeding nematode community structure. Here we have used transcriptional profiling to identify candidate genes involved in the interaction of nematodes and bacteria in nature.
2009-05-02 | GSE15923 | 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:To study the soil mcirobial functional communities and the nutrient cycles couplings changes after exposure to different contaminant
2020-12-31 | GSE135153 | GEO