Soil metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA292998 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2170774_1.fastq.gz | Fastqsanger.gz | |||
| SRR2170774_2.fastq.gz | Fastqsanger.gz | |||
| SRR2189230_1.fastq.gz | Fastqsanger.gz | |||
| SRR2189230_2.fastq.gz | Fastqsanger.gz | |||
| SRR2189241_1.fastq.gz | Fastqsanger.gz |
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Project description:Nitrogen (N), the primary limiting factor for plant growth and yield in agriculture, has a patchy distribution in soils due to fertilizer application or decomposing organic matter. Studies in solution culture over-simplify the complex soil environment where microbial competition and spatial and temporal heterogeneity challenge roots’ ability to acquire adequate amounts of nutrients required for plant growth. In this study, various ammonium treatments (as 15N) were applied to a discrete volume of soil containing tomato (Solanum lycopersicum) roots to simulate encounters with a localized enriched patch of soil. Transcriptome analysis was used to identify genes differentially expressed in roots 53 hrs after treatment. Results: The ammonium treatments resulted in significantly higher concentrations of both ammonium and nitrate in the patch soil. The plant roots and shoots exhibited increased levels of 15N over time, indicating a sustained response to the enriched environment. Root transcriptome analysis identified 585 genes differentially regulated 53 hrs after the treatments. Nitrogen metabolism and cell growth genes were induced by the high ammonium (65 ug NH4+-N g-1 soil), while stress response genes were repressed. The complex regulation of specific transporters following the ammonium pulse reflects a simultaneous and synergistic response to rapidly changing concentrations of both forms of inorganic N in the soil patch. Transcriptional analysis of the phosphate transporters demonstrates cross-talk between N and phosphate uptake pathways and suggests that roots increase phosphate uptake via the arbuscular mycorrhizal symbiosis in response to N. Conclusion: This work enhances our understanding of root function by providing a snapshot of the response of the tomato root transcriptome to a pulse of ammonium in a complex soil environment. This response includes an important role for the mycorrhizal symbiosis in the utilization of an N patch.
2010-03-24 | GSE21020 | GEO
Project description:Evaluation of different strategies to interpret metaproteomics data acquired on soil samples from a floodplain along the Seine River (France) incorporating sample-specific metagenomics data, soil genome catalogue database, and generic sequence database.
2022-02-17 | PXD026798 | Pride
Project description:Nitrogen (N), the primary limiting factor for plant growth and yield in agriculture, has a patchy distribution in soils due to fertilizer application or decomposing organic matter. Studies in solution culture over-simplify the complex soil environment where microbial competition and spatial and temporal heterogeneity challenge rootsâ ability to acquire adequate amounts of nutrients required for plant growth. In this study, various ammonium treatments (as 15N) were applied to a discrete volume of soil containing tomato (Solanum lycopersicum) roots to simulate encounters with a localized enriched patch of soil. Transcriptome analysis was used to identify genes differentially expressed in roots 53 hrs after treatment. Results: The ammonium treatments resulted in significantly higher concentrations of both ammonium and nitrate in the patch soil. The plant roots and shoots exhibited increased levels of 15N over time, indicating a sustained response to the enriched environment. Root transcriptome analysis identified 585 genes differentially regulated 53 hrs after the treatments. Nitrogen metabolism and cell growth genes were induced by the high ammonium (65 ug NH4+-N g-1 soil), while stress response genes were repressed. The complex regulation of specific transporters following the ammonium pulse reflects a simultaneous and synergistic response to rapidly changing concentrations of both forms of inorganic N in the soil patch. Transcriptional analysis of the phosphate transporters demonstrates cross-talk between N and phosphate uptake pathways and suggests that roots increase phosphate uptake via the arbuscular mycorrhizal symbiosis in response to N. Conclusion: This work enhances our understanding of root function by providing a snapshot of the response of the tomato root transcriptome to a pulse of ammonium in a complex soil environment. This response includes an important role for the mycorrhizal symbiosis in the utilization of an N patch. 9 Total samples were analyzed across 3 treatment groups (3 biological replicates per group). We generated the following pairwise comparisons using JMP Genomics software: Control vs. Low N, Control vs. high N, and low N vs. high N. One way ANOVA was used to determine significantly different expression. Genes with an FDRâ¤10% were presented.
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Project description:Effect of different soil treatments on soil microbial communities
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Project description:Soil water repellency (SWR) (i.e. soil hydrophobicity or decreased soil wettability) is a major cause of global soil degradation and a key agricultural concern. This metabolomics data will support the larger effort measuring soil water repellency and soil aggregate formation caused by microbial community composition through a combination of the standard drop penetration test, transmission electron microscopy characterization and physico-chemical analyses of soil aggregates at 6 timepoints. Model soils created from clay/sand mixtures as described in Kallenbach et al. (2016, Nature Communications) with sterile, ground pine litter as a carbon/nitrogen source were inoculated with 15 different microbial communities known to have significantly different compositions based on 16S rRNA sequencing. This data will allow assessment of the direct influence of microbial community composition on soil water repellency and soil aggregate stability, which are main causes of soil degradation.
The work (proposal:https://doi.org/10.46936/10.25585/60001346) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.
2024-02-14 | MSV000094090 | MassIVE