Soil metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA353748 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Bacteria belonging to phylum Gemmatimonadetes are found in a wide variety of environments and are particularly abundant in soils. To date, only two Gemmatimonadetes strains have been characterized. Here we report the complete genome sequence and methylation pattern of Gemmatirosa kalamazoonensis KBS708 (ATCC BAA-2150; NCCB 100411), the first characterized Gemmatimondetes strain isolated from soil. Examination of the methylome of Gemmatirosa kalamazoonenis KBS708 using kinetic data from single-molecule, real-time (SMRT) sequencing on the PacBio RS
2014-03-12 | E-GEOD-55390 | biostudies-arrayexpress
Project description:soil-borne bacteria Genome sequencing and assembly
| PRJNA420159 | ENA
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:Bacteria belonging to phylum Gemmatimonadetes are found in a wide variety of environments and are particularly abundant in soils. To date, only two Gemmatimonadetes strains have been characterized. Here we report the complete genome sequence and methylation pattern of Gemmatirosa kalamazoonensis KBS708 (ATCC BAA-2150; NCCB 100411), the first characterized Gemmatimondetes strain isolated from soil.
2014-03-12 | GSE55390 | 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:Soil water repellency (SWR) (i.e. soil hydrophobicity or decreased soil wettability) is a major cause of global soil degradation and a key agricultural concern. This metabolomics data will support the larger effort measuring soil water repellency and soil aggregate formation caused by microbial community composition through a combination of the standard drop penetration test, transmission electron microscopy characterization and physico-chemical analyses of soil aggregates at 6 timepoints. Model soils created from clay/sand mixtures as described in Kallenbach et al. (2016, Nature Communications) with sterile, ground pine litter as a carbon/nitrogen source were inoculated with 15 different microbial communities known to have significantly different compositions based on 16S rRNA sequencing. This data will allow assessment of the direct influence of microbial community composition on soil water repellency and soil aggregate stability, which are main causes of soil degradation.
The work (proposal:https://doi.org/10.46936/10.25585/60001346) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.
2024-02-14 | MSV000094090 | MassIVE
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