Soil metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB20635 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Many trees form ectomycorrhizal symbiosis with fungi. During symbiosis, the tree roots supply sugar to the fungi in exchange for nitrogen, and this process is critical for the nitrogen and carbon cycles in forest ecosystems. However, the extents to which ectomycorrhizal fungi can liberate nitrogen and modify the soil organic matter and the mechanisms by which they do so remain unclear since they have lost many enzymes for litter decomposition that were present in their free-living, saprotrophic ancestors. Using time-series spectroscopy and transcriptomics, we examined the ability of two ectomycorrhizal fungi from two independently evolved ectomycorrhizal lineages to mobilize soil organic nitrogen. Both species oxidized the organic matter and accessed the organic nitrogen. The expression of those events was controlled by the availability of glucose and inorganic nitrogen. Despite those similarities, the decomposition mechanisms, including the type of genes involved as well as the patterns of their expression, differed markedly between the two species. Our results suggest that in agreement with their diverse evolutionary origins, ectomycorrhizal fungi use different decomposition mechanisms to access organic nitrogen entrapped in soil organic matter. The timing and magnitude of the expression of the decomposition activity can be controlled by the below-ground nitrogen quality and the above-ground carbon supply.
2018-11-30 | GSE110485 | GEO
Project description:Proteomic data from moose fistulated rumen; metagenomic and viral sequencing performed; metabolic pathways reconstructed
2018-07-03 | PXD008667 | Pride
Project description:It has long been recognized that species occupy a specific ecological niche within their ecosystem. The ecological niche is defined as the number of conditions and resources that limit species distribution. Within their ecological niche, species do not exist in a single physiological state but in a number of states we call the Natural Operating Range. In this paper we link ecological niche theory to physiological ecology by measuring gene expression levels of collembolans exposed to various natural conditions. The soil-dwelling collembolan Folsomia candida was exposed to 26 natural soils with different soil characteristics (soil type, land use, practice, etc). The animals were exposed for two days and gene expression levels were measured. The main factor found to regulate gene expression was the soil type (sand or clay), in which 18.5% of the measured genes were differentially expressed. Gene Ontology analysis showed animals exposed to sandy soils experience general stress, affecting cell homeostasis and replication. Multivariate analysis linking soil chemical data to gene expression data revealed that soil fertility influences gene expression. Land-use and practice had less influence on gene expression; only forest soils showed a different expression pattern. A variation in gene expression variation analysis showed overall low variance in gene expression. The large difference in response to soil type was caused by the soil physicochemical properties where F. candida experiences clay soils and sandy soils as very different from each other. This collembolan prefers fertile soils with high organic matter content, as soil fertility was found to correlate with gene expression and animals exposed to sandy soils (which, in general, have lower organic matter content) experience more general stress. Finally, we conclude that there is no such thing as a fixed physiological state for animals in their ecological niche and the boundary between the ecological niche and a stressed state depends on the genes/pathways investigated.
2011-02-15 | GSE21213 | GEO
Project description:Recovery of organic matter decomposition inhibited by oxygen deficiency at the early thermophilic stage of composting
| PRJDB14327 | ENA
Project description:Permafrost soil microbial communities from the Arctic, to analyse light accelerated degradation of dissolved organic matter (DOM) - Organic soil DNA_2013-062 metagenome
| PRJNA365105 | ENA
Project description:Permafrost soil microbial communities from the Arctic, to analyse light accelerated degradation of dissolved organic matter (DOM) - Organic soil DNA_2013-063 metagenome
| PRJNA365106 | ENA
Project description:Permafrost soil microbial communities from the Arctic, to analyse light accelerated degradation of dissolved organic matter (DOM) - Organic soil DNA_2013-059 metagenome
| PRJNA365102 | ENA
Project description:Permafrost soil microbial communities from the Arctic, to analyse light accelerated degradation of dissolved organic matter (DOM) - Organic soil DNA_2013-058 metagenome
| PRJNA365101 | ENA
Project description:Permafrost soil microbial communities from the Arctic, to analyse light accelerated degradation of dissolved organic matter (DOM) - Organic soil DNA_2013-060 metagenome
| PRJNA365103 | ENA