High altitude soils
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB34034 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:High-resolution metagenomic study on near-subsurface soils samples from the Salar de Atacama in Chile
| PRJEB24329 | ENA
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: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:Three-day metatranscriptome of surface gravel plain soils from the Central Namib Desert. Samples were collected at four times (6:00, 12:00, 18:00 and 24:00h) on each day (n=12). rRNA-depleted RNA was used to construct stranded libraries with the ScriptSeq v2 complete kit (Epicentre) adding unique barcodes in TruSeq adapters (ScriptSeq Index PCR primers, set 1, Epicentre). Libraries were single-end sequenced in a NextSeq 500 v2 sequencer, with read length of 75bp.
2018-08-01 | E-MTAB-6601 | biostudies-arrayexpress
Project description:Petroleum contaminated soils Metagenomic assembly
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Project description:Soils from Wayan Mountain. Metagenomic
| PRJNA834398 | ENA
Project description:This study evaluates genetic and phenotypic variation in the high altitude Colla population living in the Argentinean Andes above 3500 m. They were compared to the Wichà population living in the nearby lowlands of the Gran Chaco region. This study attempts to pinpoint evolutionary mechanisms underlying adaptation to hypobaric hypoxia. We have genotyped 25 individuals from both populations for 730,525 SNPs. DNA from 25 saliva samples from Collas living >3500 m and 25 saliva samples from Wichà living <500 m from the Province of Salta in Argentina was genotyped
2014-02-20 | E-GEOD-55175 | biostudies-arrayexpress
Project description:Desert microbial communities live in a pulsed ecosystem shaped by isolated and rare precipitation events. The Namib desert is one of the oldest continuously hyperarid ecosystems on Earth. In this study, surface microbial communities of open soils (without sheltering features like rocks, vegetation or biological soil crusts) are analysed. We designed an artificial rainfall experiment where a 7x7 (3.5 x 3.5 m) plot remained dry while an adjacent one received a 30 mm simulated rain. Samples were taken randomly in parallel from both plots at 10 min, 1 h, 3 h, 7 h, 24 h and 7 days after the watering moment. Duplicate libraries were generated from total (rRNA depleted) RNA and sequenced 2x150 bp in an Illumina Hiseq 4000 instrument.
2021-06-01 | E-MTAB-9439 | biostudies-arrayexpress
Project description:metagenomic amplicon sequensing from soils for novel natural products (16S_NRPS_PKS)
| PRJEB11689 | ENA