Soil metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA387168 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Soil microbial diversity in the Maintenance of Exotic vs. Native Diversity experiment (depth study)
| PRJNA413392 | ENA
Project description:Soil fungal diversity in the Maintenance of Exotic vs. Native Diversity experiment (fraction study)
| PRJNA413393 | ENA
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:Comparison of probe-target dissociations of probe Eub338 and Gam42a with native RNA of P. putida, in vitro transcribed 16s rRNA of P. putida, in vitro transcribed 16S rRNA of a 2,4,6-trinitrotoluene contaminated soil and an uncontaminated soil sample. Functional ANOVA revealed no significant differences in the dissociation curves of probe Eub338 when hybridised to the different samples. On the opposite, the dissociation curve of probe Gam42a with native RNA of P. putida was significantly different than the dissociation curves obtained with in vitro transcribed 16S rRNA samples. Keywords: Microbial diversity, thermal dissociation analysis, CodeLink microarray
2005-11-05 | GSE3525 | GEO
Project description:Soil transplant serves as a proxy to simulate climate change in realistic climate regimes. Here, we assessed the effects of climate warming and cooling on soil microbial communities, which are key drivers in Earth’s biogeochemical cycles, four years after soil transplant over large transects from northern (N site) to central (NC site) and southern China (NS site) and vice versa. Four years after soil transplant, soil nitrogen components, microbial biomass, community phylogenetic and functional structures were altered. Microbial functional diversity, measured by a metagenomic tool named GeoChip, and phylogenetic diversity are increased with temperature, while microbial biomass were similar or decreased. Nevertheless, the effects of climate change was overridden by maize cropping, underscoring the need to disentangle them in research. Mantel tests and canonical correspondence analysis (CCA) demonstrated that vegetation, climatic factors (e.g., temperature and precipitation), soil nitrogen components and CO2 efflux were significantly correlated to the microbial community composition. Further investigation unveiled strong correlations between carbon cycling genes and CO2 efflux in bare soil but not cropped soil, and between nitrogen cycling genes and nitrification, which provides mechanistic understanding of these microbe-mediated processes and empowers an interesting possibility of incorporating bacterial gene abundance in greenhouse gas emission modeling.
2013-10-30 | GSE51592 | GEO
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:Soil transplant serves as a proxy to simulate climate change in realistic climate regimes. Here, we assessed the effects of climate warming and cooling on soil microbial communities, which are key drivers in EarthM-bM-^@M-^Ys biogeochemical cycles, four years after soil transplant over large transects from northern (N site) to central (NC site) and southern China (NS site) and vice versa. Four years after soil transplant, soil nitrogen components, microbial biomass, community phylogenetic and functional structures were altered. Microbial functional diversity, measured by a metagenomic tool named GeoChip, and phylogenetic diversity are increased with temperature, while microbial biomass were similar or decreased. Nevertheless, the effects of climate change was overridden by maize cropping, underscoring the need to disentangle them in research. Mantel tests and canonical correspondence analysis (CCA) demonstrated that vegetation, climatic factors (e.g., temperature and precipitation), soil nitrogen components and CO2 efflux were significantly correlated to the microbial community composition. Further investigation unveiled strong correlations between carbon cycling genes and CO2 efflux in bare soil but not cropped soil, and between nitrogen cycling genes and nitrification, which provides mechanistic understanding of these microbe-mediated processes and empowers an interesting possibility of incorporating bacterial gene abundance in greenhouse gas emission modeling. Fifty four samples were collected from three soil types (Phaeozem,Cambisol,Acrisol) in three sites (Hailun, Fengqiu and Yingtan) along a latitude with reciprocal transplant; Both with and without maize cropping in each site; Three replicates in every treatments.
2013-10-30 | E-GEOD-51592 | biostudies-arrayexpress
Project description:Soil microbial community is a complex blackbox that requires a multi-conceptual approach (Hultman et al., 2015; Bastida et al., 2016). Most methods focus on evaluating total microbial community and fail to determine its active fraction (Blagodatskaya & Kuzyakov 2013). This issue has ecological consequences since the behavior of the active community is more important (or even essential) and can be different to that of the total community. The sensitivity of the active microbial community can be considered as a biological mechanism that regulates the functional responses of soil against direct (i.e. forest management) and indirect (i.e. climate change) human-induced alterations. Indeed, it has been highglihted that the diversity of the active community (analyzed by metaproteomics) is more connected to soil functionality than the that of the total community (analyzed by 16S rRNA gene and ITS sequencing) (Bastida et al., 2016). Recently, the increasing application of soil metaproteomics is providing unprecedented, in-depth characterisation of the composition and functionality of active microbial communities and overall, allowing deeper insights into terrestrial microbial ecology (Chourey et al., 2012; Bastida et al., 2015, 2016; Keiblinger et al., 2016). Here, we predict the responsiveness of the soil microbial community to forest management in a climate change scenario. Particularly, we aim: i) to evaluate the impacts of 6-years of induced drought on the diversity, biomass and activity of the microbial community in a semiarid forest ecocosystem; and ii) to discriminate if forest management (thinning) influences the resistance of the microbial community against induced drought. Furthermore, we aim to ascertain if the functional diversity of each phylum is a trait that can be used to predict changes in microbial abundance and ecosystem functioning.
2021-02-02 | PXD005447 | Pride
Project description:A comparision of soil microbial functional genes of three types of subtropical broad-leaved forests Microbial functional structure was significantly different among SBFs (P < 0.05). Compared to the DBF and the EBF, the MBF had higher alpha-diversity of functional genes but lower beta-diversity, and showed more complex functional gene networks.
2021-01-29 | GSE165723 | GEO
Project description:The functional diversity of soil microbial communities was explored for a poplar plantation, which was treated solely with biogas slurry, or combined with biochar at different fertilization intensities over several years.
2020-03-30 | GSE133800 | GEO