Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7066970_1.fastq.gz | Fastqsanger.gz | |||
| SRR7066970_2.fastq.gz | Fastqsanger.gz | |||
| SRR7066980_1.fastq.gz | Fastqsanger.gz | |||
| SRR7066980_2.fastq.gz | Fastqsanger.gz | |||
| SRR7066990_1.fastq.gz | Fastqsanger.gz |
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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. 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:This data set contains 1376 mass spectrometry reads from root, rhizosphere and leaf sample of Populus Trichocarpa, as well as associated controls. This metabolomics data set was collected as part of a larger campaign which complements the metabolomics data with metagenome sequencing, transcriptomics, and soil measurement data.
2022-12-12 | MSV000090886 | MassIVE
Project description:Purpose: Deconstructing the soil microbiome into reduced-complexity functional modules represents a novel method of microbiome analysis. The goals of this study are to confirm differences in transcriptomic patterns among five functional module consortia. Methods: mRNA profiles of 3 replicates each of functional module enrichments of soil inoculum in M9 media with either 1) xylose, 2) n-acetylglucosamine, 3) glucose and gentamycin, 4) xylan, or 5) pectin were generated by sequencing using an Illumina platform (GENEWIZ performed sequencing). Sequence reads that passed quality filters were aligned to a soil metagenome using Burrows Wheeler Aligner. Resulting SAM files were converted to raw reads using HTSeq, and annotated using Uniref90 or EGGNOG databases. Results: To reduce the size of the RNA-Seq counts table and increase its computational tractability, transcripts containing a minimum of 75 total counts, but no more than 3 zero counts, across the 15 samples were removed. The subsequent dataset was normalized using DESeq2, resulting in a dataset consisting of 6947 unique transcripts across the 15 samples, and 185,920,068 reads. We identified gene categories that were enriched in a sample type relative to the overall dataset using Fisher’s exact test. Conclusions: our dataset confirms that the functional module consortia generated from targeted enrichments of a starting soil inoculum had distinct functional trends by enrichment type.
2020-01-14 | GSE143587 | GEO
Project description:high throughput sequencing of the metagenome of mexican children
2020-03-16 | GSE143207 | 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:Thiabendazole (TBZ), a benzimidazole used against postharvest fungal growth and as anthelmintic in livestock farming, is highly persistent in soil (DT50> 1-2 years) and therefore challenging concerning its environmental management. In our recent copious attempts to isolate organisms that degrade TBZ, at best, we ended up with a soil microbial enrichment capable of accelerated TBZ degradation. Here, we employed a multi-omic approach combined with DNA stable isotope probing (SIP) for elucidating the underlying system complexity. We obtained 18 high-quality metagenome-assembled genomes, with six being dominant and versatile concerning their putative xenobiotics degradation ability. SIP combined with microbiome analysis verified our previous results about the key role of a Sphingomonas strain in TBZ degradation. Next to this, metabolomics suggested minimal/no cross-feeding events, and Sphingomonas being the sole TBZ degrader. RNA sequencing and proteomics analysis of the consortium using TBZ or succinate as sole carbon sources showed the enhanced expression in Sphingomonas of a carbazole dioxygenase locus with putative role in the TBZ degradation. Gene expression networking analysis suggested the interaction of Sphingomonas with a Hydrogenophaga strain that possibly contributes to the overall cobalamin balance. Our study depicts the need for integrated omic approaches for understanding complex interactions frequently occurring in bioremediation.
2019-07-20 | GSE134575 | GEO
Project description:This data set contains 1376 mass spectrometry reads from root, rhizosphere and leaf sample of Populus Trichocarpa, as well as associated controls. This metabolomics data set was collected as part of a larger campaign which complements the metabolomics data with metagenome sequencing, transcriptomics, and soil measurement data.
2022-12-12 | MSV000090886 | GNPS
Project description:DNA, RNA and protein were extracted from the culture and subjected to massive parallel sequencing and nano-LC-MS-MS respectively Combination of these methods enabled the reconstruction of the complete genome sequence of M oxyfera from the metagenome and identification of the functionally relevant enzymes and genes
2010-03-25 | E-GEOD-18535 | biostudies-arrayexpress