Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1084772 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28242586.fastq.gz | Fastqsanger.gz | |||
| SRR28242587.fastq.gz | Fastqsanger.gz | |||
| SRR28242588.fastq.gz | Fastqsanger.gz |
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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: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: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:The fate of the carbon stocked in permafrost soils following global warming and permafrost thaw is of major concern in view of the potential for increased CH4 and CO2 emissions from these soils. Complex carbon compound degradation and greenhouse gas emissions are due to soil microbial communities, but their composition and functional potential in permafrost soils are largely unknown. Here, a 2 m deep permafrost and its overlying active layer soil were subjected to metagenome sequencing, quantitative PCR, and microarray analyses. The active layer soil and 2 m permafrost soil microbial community structures were very similar, with Actinobacteria being the dominant phylum. The two soils also possessed a highly similar spectrum of functional genes, especially when compared to other already published metagenomes. Key genes related to methane generation, methane oxidation and organic matter degradation were highly diverse for both soils in the metagenomic libraries and some (e.g. pmoA) showed relatively high abundance in qPCR assays. Genes related to nitrogen fixation and ammonia oxidation, which could have important roles following climatic change in these nitrogen-limited environments, showed low diversity but high abundance. The 2 m permafrost soil showed lower abundance and diversity for all the assessed genes and taxa. Experimental biases were also evaluated and showed that the whole community genome amplification technique used caused large representational biases in the metagenomic libraries. This study described for the first time the detailed functional potential of permafrost-affected soils and detected several genes and microorganisms that could have crucial importance following permafrost thaw. A 2m deep permafrost sample and it overlying active layer were sampled and their metagenome analysed. For microarray analyses, 8 other soil samples from the same region were used for comparison purposes.
2010-05-06 | E-GEOD-20073 | biostudies-arrayexpress
Project description:Microbial community analysis with DNA oligonucleotide microarrays targeting ribosomal RNA (rRNA) provides a highly parallel interrogation of nucleic acids isolated from environmental samples. High fidelity readout is essential for accurate interpretation of hybridisations. We describe the hybridisation of in vitro transcribed 16S rRNA from an uncontaminated and 2,4,6-trinitrotoluene contaminated soil to an oligonucleotide microarray containing group- and species-specific perfect match (PM) probes and their 2 corresponding mismatch (MM) probes. Thermal dissociation analysis was used to determine the specificity of each PM-MM probe set. Functional ANOVA often discriminated PM-MM probe sets when Td values (temperature at 50% probe-target dissociation) could not. Maximum discrimination for many PM and MM probes often occurred at temperatures greater than the Td. Comparison of signal intensities measured prior to dissociation analysis from hybridisations of the two soil samples revealed significant differences in domain-, group- and species-specific probes. Functional ANOVA showed significantly different dissociation curves for 11 PM probes when hybridisations from the two soil samples were compared, even though initial signal intensities for 3 of the 11 did not vary. This approach provides a highly parallel, multi-level analysis that incorporates MM probes and dissociation curves into high fidelity microarray analysis of complex environmental nucleic acid profiles. Keywords: Microbial diversity, thermal dissociation analysis
2005-10-26 | GSE3499 | GEO
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:The fate of the carbon stocked in permafrost soils following global warming and permafrost thaw is of major concern in view of the potential for increased CH4 and CO2 emissions from these soils. Complex carbon compound degradation and greenhouse gas emissions are due to soil microbial communities, but their composition and functional potential in permafrost soils are largely unknown. Here, a 2 m deep permafrost and its overlying active layer soil were subjected to metagenome sequencing, quantitative PCR, and microarray analyses. The active layer soil and 2 m permafrost soil microbial community structures were very similar, with Actinobacteria being the dominant phylum. The two soils also possessed a highly similar spectrum of functional genes, especially when compared to other already published metagenomes. Key genes related to methane generation, methane oxidation and organic matter degradation were highly diverse for both soils in the metagenomic libraries and some (e.g. pmoA) showed relatively high abundance in qPCR assays. Genes related to nitrogen fixation and ammonia oxidation, which could have important roles following climatic change in these nitrogen-limited environments, showed low diversity but high abundance. The 2 m permafrost soil showed lower abundance and diversity for all the assessed genes and taxa. Experimental biases were also evaluated and showed that the whole community genome amplification technique used caused large representational biases in the metagenomic libraries. This study described for the first time the detailed functional potential of permafrost-affected soils and detected several genes and microorganisms that could have crucial importance following permafrost thaw.
2010-03-08 | GSE20073 | GEO
Project description:Xiangjiang River (Hunan, China) has been contaminated with heavy metal for several decades by surrounding factories. However, little is known about the influence of a gradient of heavy metal contamination on the diversity, structure of microbial functional gene in sediment. To deeply understand the impact of heavy metal contamination on microbial community, a comprehensive functional gene array (GeoChip 5.0) has been used to study the functional genes structure, composition, diversity and metabolic potential of microbial community from three heavy metal polluted sites of Xiangjiang River. Three groups of samples, A, B and C. Every group has 3 replicates.
2016-08-02 | E-GEOD-85064 | biostudies-arrayexpress
Project description:We have developed a 60-mer oligonucleotide multibacterial microarray for detection and expression profiling of biodegradative genes and bacterial diversity (16S rRNA gene) in different habitats contaminated with varieties of hazardous chemicals. The genes selected were involved in biodegradation and biotransformation of various groups of compounds viz. nitroaromatic compounds (148 genes), chloroaromatic compounds (75 genes), monoaromatic compounds (373 genes), polyaromatic hydrocarbons (174 genes), pesticides/ herbicides (34 genes), alkanes/aliphatics (185 genes) and heavy metals (68 genes), which covered a total number of 133 chemicals. The efficiency (specificity, detection sensitivity) of the developed array was evaluated using the labeled genomic DNA of pure bacterial strains, Escherichia coli DH5α and Sphingomonas sp. strain NM-05 (involved in the biodegradation of γ-hexachlorohexane isolated from IPL, Lucknow) at different concentrations of 300ng, 500ng, 800ng, 1000ng and 1250ng. The specificity of the developed array was further validated using mixed cultures containing three strains (Sphingomonas sp. strain NM-05, Rhodococcus sp. strain RHA1 and Bordetella sp. strain IITR-02) involved in biodegradation of γ-hexachlorohexane, biphenyl and chlorobenzenes respectively. The mixed culture also contained non-target/non-degrader strains (E. coli DHα, E.coli BL21 and E.coli K12 NCTC50192). The developed array was applied for profiling using the total soil DNA in five contaminated habitats of north India, viz. chloroaromatic chemicals contaminated site (India Pesticide Limited, Chinhat, Lucknow), a river sediments (Gomti river sediment, Lucknow), heavy metal industry dump site (Jajmau industrial area Kanpur), a effluent treatment plant (CETP along Ganges river near Kanpur), and an oil refinery (Mathura oil refinery). Hybridization of 16S rRNA probes revealed the presence of bacteria similar to well characterized genera involved in biodegradation of pollutants. Genes involved in complete degradation pathways for hexachlorocyclohexane (lin), 1,2,4-trichlorobenzene (tcb), naphthalene (nah), phenol (mph), biphenyl (bph), benzene (ben), toluene (tbm), xylene (xyl), phthalate (pht), Salicylate (sal) and resistance to mercury (mer) were detected with highest intensity. The most abundant genes belonged to hydroxylases, monooxygenases and dehydrogenases which were present in all the five samples. Many compound specific genes which initiate the degradation pathway were also detected. Thus, the array developed and validated here may be useful in assessing the biodegradative potential and composition of environmentally useful bacteria in hazardous ecosystems.
2011-04-15 | GSE24353 | GEO