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{
"data": {
"type": "samples",
"id": "SRS269064",
"attributes": {
"biosample": "SAMN00744361",
"sample-metadata": [
{
"key": "NCBI sample classification",
"value": "2",
"unit": null
},
{
"key": "instrument model",
"value": "454 GS FLX",
"unit": null
}
],
"latitude": null,
"longitude": null,
"accession": "SRS269064",
"analysis-completed": "2016-10-18",
"collection-date": null,
"geo-loc-name": null,
"sample-desc": "The soil used for this study was collected in October 2009 from the A horizon of a grassland and a forest in the Biodiversity Exploratory Hainich (Germany}, sieved to 2 mm and stored at 4°C. The grassland (latitude N 51° 6' 47.5'', longitude E 10° 26' 10.3'') was a fertilized mown pasture (cattle) of stagnosol soil with a pH of 7.2, whereas the forest (latitude N 51° 6' 10.2'', longitude E 10° 2' 3.1'') was an unmanaged beech forest of luvisol soil with a pH of 5.3. The soil was pre-incubated for 40 days at 15°C in the dark. Microcosms were set up by placing 3 g (dw) of soil into a 100 ml flask. Soil samples were supplemented with sterile water to reach 80% of the maximum water holding capacity. The experiment was started by supplementation of 13C-labelled wheat roots at 5 mg per g (dw) soil. As controls, soil was (i) amended with unlabelled wheat roots or (ii) incubated without any plant material. Each treatment was run in triplicates with static incubation at 20°C in the dark for 168 h. Samples of headspace and soil were removed at different time points of incubation (0, 24, 48, 72, 96 and 168 h) from three flasks of each treatment and soil was stored at -80°C for molecular analysis. Total DNA and RNA were extracted simultaneously from one soil sample (1 g) of each time point using a direct lysis technique. The co-extracted DNA was removed from an aliquot of the RNA by digestion with DNase. Subsequently, RNA was re-extracted and complete removal of DNA from RNA extracts was verified by 16S rRNA gene based PCR using Primers Ba27f (5`-AGAGTTTGATCCTGGCTCAG-3'') and Ba907r (5´-CCGTCAATTCCTTTRAGTTT-3´). Total RNA from the treatments was quantified. RNA extracts (500 ng of RNA) of the labelled treatments were mixed with cesium trifluoroacetate. In order to separate the RNA on the basis of the molecular weight, equilibrium density gradient centrifugation was performed using an ultracentrifuge. Gradients of density-resolved RNA were fractionated and the CsTFA buoyant density of each fraction was determined. Nucleic acids were precipitated over night with 3 M sodium acetate and ethanol for subsequent community analysis. To analyze the taxonomic composition of the soil bacterial community in selected density fractions, the V1-V3 region of the 16S rRNA gene (Escherichia coli positions 8 to 536) was chosen for amplification and subsequent pyrosequencing of the PCR products. The V1-V3 region was amplified with the primer set Ba27f and Ba518r containing the Roche 454 pyrosequencing adaptors (Ba27f: 5'-CGTATCGCCTCCCTCGCGCCATCAGAGAGTTTGATCCTGGCTCAG-3', Ba518r_mod: 5'-CTATGCGCCTTGCCAGCCCGCTCAGCGTATTACCGCGGCTGCTGG-3') in duplicates. Between the Roche 454 pyrosequencing adaptor and the forward primer, 10-bp-barcodes were added to allow the sorting of each sample from the mixed pyrosequencing outcome. PCR products were pooled and purified, quantification of the PCR products was performed using the Quant-iT dsDNA BR assay kit. Equal amounts of ten barcoded samples were pooled and the sequences of the partial 16S rRNA genes determined by employing the Roche GS-FLX 454 pyrosequencer.",
"environment-biome": null,
"environment-feature": null,
"environment-material": null,
"sample-name": "Identification of soil bacteria assimilating carbon from 13C-labelled wheat residue by RNA-based Stable Isotope Probing",
"sample-alias": "SIP 13C wheat - pyrosequencing of gradient fractions",
"host-tax-id": null,
"species": null,
"last-update": "2016-10-18T13:57:04"
},
"relationships": {
"biome": {
"data": {
"type": "biomes",
"id": "root:Environmental:Terrestrial:Soil:Crop:Agricultural land"
},
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Terrestrial:Soil:Crop:Agricultural%20land?format=api"
}
},
"studies": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/samples/SRS269064/studies?format=api"
},
"data": [
{
"type": "studies",
"id": "MGYS00001263",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00001263?format=api"
}
}
]
},
"runs": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/samples/SRS269064/runs?format=api"
}
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/samples/SRS269064?format=api"
}
}
}