Soil metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA419646 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6320610.fastq.gz | Fastqsanger.gz | |||
| SRR6320610_1.fastq.gz | Fastqsanger.gz | |||
| SRR6320610_2.fastq.gz | Fastqsanger.gz | |||
| SRR6320620_1.fastq.gz | Fastqsanger.gz | |||
| SRR6320620_2.fastq.gz | Fastqsanger.gz |
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Project description:Despite the global importance of forests, it is virtually unknown how their soil microbial communities adapt at the phylogenetic and functional level to long term metal pollution. Studying twelve sites located along two distinct gradients of metal pollution in Southern Poland revealed that both community composition (via MiSeq Illumina sequencing of 16S rRNA genes) and functional gene potential (using GeoChip 4.2) were highly similar across the gradients despite drastically diverging metal contamination levels. Metal pollution level significantly impacted microbial community structure (p = 0.037), but not bacterial taxon richness. Metal pollution altered the relative abundance of specific bacterial taxa, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes and Proteobacteria. Also, a group of metal resistance genes showed significant correlations with metal concentrations in soil, although no clear impact of metal pollution levels on overall functional diversity and structure of microbial communities was observed. While screens of phylogenetic marker genes, such as 16S rRNA, provided only limited insight into resilience mechanisms, analysis of specific functional genes, e.g. involved in metal resistance, appeared to be a more promising strategy. This study showed that the effect of metal pollution on soil microbial communities was not straightforward, but could be filtered out from natural variation and habitat factors by multivariate statistical analysis and spatial sampling involving separate pollution gradients.
2014-07-22 | GSE59620 | 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.
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Project description:To study long-term elevated CO2 and enriched N deposition interactive effects on microbial community and soil ecoprocess, here we investigated soil microbial community in a grassland ecosystem subjected to ambient CO2 (aCO2, 368 ppm), elevated CO2 (eCO2, 560 ppm), ambient nitrogen deposition (aN) or elevated nitrogen deposition (eN) treatments for a decade. There exist antagonistic CO2×N interactions on microbial functional genes associated with C, N, P S cycling processes. More strong antagonistic CO2×N interactions are observed on C degradation genes than other genes. Remarkably antagonistic CO2×N interactions on soil microbial communities could enhance soil C accumulation.
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Project description:Despite the global importance of forests, it is virtually unknown how their soil microbial communities adapt at the phylogenetic and functional level to long term metal pollution. Studying twelve sites located along two distinct gradients of metal pollution in Southern Poland revealed that both community composition (via MiSeq Illumina sequencing of 16S rRNA genes) and functional gene potential (using GeoChip 4.2) were highly similar across the gradients despite drastically diverging metal contamination levels. Metal pollution level significantly impacted microbial community structure (p = 0.037), but not bacterial taxon richness. Metal pollution altered the relative abundance of specific bacterial taxa, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes and Proteobacteria. Also, a group of metal resistance genes showed significant correlations with metal concentrations in soil, although no clear impact of metal pollution levels on overall functional diversity and structure of microbial communities was observed. While screens of phylogenetic marker genes, such as 16S rRNA, provided only limited insight into resilience mechanisms, analysis of specific functional genes, e.g. involved in metal resistance, appeared to be a more promising strategy. This study showed that the effect of metal pollution on soil microbial communities was not straightforward, but could be filtered out from natural variation and habitat factors by multivariate statistical analysis and spatial sampling involving separate pollution gradients. 12 samples were collected from two long-term polluted areas (Olkusz and Miasteczko M-EM-^ZlM-DM-^Eskie) in Southern Poland. In the study presented here, a consecutively operated, well-defined cohort of 50 NSCLC cases, followed up more than five years, was used to acquire expression profiles of a total of 8,644 unique genes, leading to the successful construction of supervised
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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.
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