Soil metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1057029 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:It includes analysis of different types of organic carbon
1 Model ligands and complexes
2 Lignin degradation materials
3 Quinones and adducts from biochars
4 Extraction and porewater of permafrost soils across the gradients of palsa-bog-fens
2023-02-06 | MSV000091211 | MassIVE
Project description:It includes analysis of different types of organic carbon
1 Model ligands and complexes
2 Lignin degradation materials
3 Quinones and adducts from biochars
4 Extraction and porewater of permafrost soils across the gradients of palsa-bog-fens
2023-02-06 | MSV000091211 | GNPS
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:miRNAs are small non-coding regulatory RNAs that play important functions in the regulation of gene expression at the post-transcriptional level by targeting mRNAs for degradation or by inhibiting protein translation. Bromeliaceae family is an example of a large and well described adaptive radiation of plant families in the Neotropics. This family is composed of terrestrial xerophytes and both facultative and obligatory epiphytes, occurring in a wide range of habitats. Bromeliads have different habits, varying from terrestrial to epiphytical, and are found from sea level to altitudes above 4,000 m, in both desert and humid regions, as well as in soils subject to regular floods and in places with very little or great luminosity. This huge habitat plasticity makes bromeliads an interesting model to study the expression of miRNAs in different natural conditions and the first step is to identify miRNAs and its targets. For this purpose, we used a high-throughput sequencing analysis (Solexa technology) of small RNAs (sRNAs) from the endemic South American species Vriesea carinata. RNA profiles in 1 leaf library of Vriesea carinata by deep sequencing (Illumina HiSeq2000)
2014-04-25 | E-GEOD-38248 | biostudies-arrayexpress
Project description:miRNAs are small non-coding regulatory RNAs that play important functions in the regulation of gene expression at the post-transcriptional level by targeting mRNAs for degradation or by inhibiting protein translation. Bromeliaceae family is an example of a large and well described adaptive radiation of plant families in the Neotropics. This family is composed of terrestrial xerophytes and both facultative and obligatory epiphytes, occurring in a wide range of habitats. Bromeliads have different habits, varying from terrestrial to epiphytical, and are found from sea level to altitudes above 4,000 m, in both desert and humid regions, as well as in soils subject to regular floods and in places with very little or great luminosity. This huge habitat plasticity makes bromeliads an interesting model to study the expression of miRNAs in different natural conditions and the first step is to identify miRNAs and its targets. For this purpose, we used a high-throughput sequencing analysis (Solexa technology) of small RNAs (sRNAs) from the endemic South American species Vriesea carinata. microRNA profiles in 1 leaf library of Vriesea carinata by deep sequencing (Illumina HiSeq2000)
2014-04-25 | E-GEOD-38249 | biostudies-arrayexpress