HTTP 200 OK
Allow: GET, HEAD, OPTIONS
Content-Type: application/json
Vary: Accept
{
"data": {
"type": "samples",
"id": "SRS400304",
"attributes": {
"biosample": "SAMN01974501",
"sample-metadata": [
{
"key": "NCBI sample classification",
"value": "256318",
"unit": null
},
{
"key": "instrument model",
"value": "454 GS FLX Titanium",
"unit": null
}
],
"latitude": null,
"longitude": null,
"accession": "SRS400304",
"analysis-completed": "2016-04-20",
"collection-date": null,
"geo-loc-name": null,
"sample-desc": "Changes of microbial communities and abundances were investigated in rice paddy soil transplanted with Korean rice cultivar Nampyeongbyeo (Oryza sativa, Japonica type) using barcoded pyrosequencing and quantitative PCR, respectively. Methane emission rates were measured using a closed chamber method every thirty days and soil properties such as pH, total organic carbon (TOC), total nitrogen(TN), available phosphate, and sulfate were also periodically monitored during the rice cultivation, which showed that methane emission rate from the rice paddy were well correlated with pH and TOC concentration. CH4 emission rate gradually increased with the rice growth and the maximum methane emission was observed during the flowering and heading stage (approximately 90 days), and then gradually decreased after water irrigation was stopped. Microbial community analysis showed that the phyla Proteobacteria, Chloroflexi, Acidobacteria, and Actinobacteria were dominant to approximately 75.4% in Bacteria during the all cultivation period, while the phylum Euryarchaeota dominated in Archaea and its abundance gradually increased during the rice cultivation. Approximately only 1% of bacteria were classified as methanotrophs, whereas methanogens comprised approximately 67% of archaeal population and their abundances increased until 90 days of rice cultivation. Among methanogens, Methanosaeta was dominant and significantly increased during the rice cultivation. Statistical analyses showed that the microbial communities were clearly changed during the rice cultivation. Copy numbers transcriptional levels of pmoA as well as mcrA genes gradually increased during the rice cultivation and their maxima were observed at approximately 90 days of rice cultivation, which were well in accordance with the methane emission rates. Canonical correspondence analysis suggests that Methylocaldum, Methanobacterium and Methanosaeta are positively correlated with methane emission rates.",
"environment-biome": null,
"environment-feature": null,
"environment-material": null,
"sample-name": "Investigation of Methane Emission and Bacterial and Archaeal Communities in Rice Paddy Soil during Rice Cultivation",
"sample-alias": "Rice paddy soil",
"host-tax-id": null,
"species": null,
"last-update": "2016-04-20T21:03:21"
},
"relationships": {
"biome": {
"data": {
"type": "biomes",
"id": "root:Environmental:Terrestrial:Soil"
},
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Terrestrial:Soil?format=api"
}
},
"studies": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/samples/SRS400304/studies?format=api"
},
"data": [
{
"type": "studies",
"id": "MGYS00000745",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000745?format=api"
}
}
]
},
"runs": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/samples/SRS400304/runs?format=api"
}
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/samples/SRS400304?format=api"
}
}
}