SOERE_PRO_2014
soil metagenome
Soil from Colmar, sampled one year after organic waste product apllication
ENA first public
2017-06-01
ENA last update
2016-10-21
External Id
SAMEA4058304
INSDC center alias
INRA-CMSE
INSDC center name
UMR Agroecology, INRA - Burgundy University, Dijon, France
INSDC first public
2017-06-01T17:02:03Z
INSDC last update
2016-10-21T09:34:42Z
INSDC status
public
Submitter Id
B4T1_16S
city
Colmar
collection date
2012-03
common name
SOERE_PRO_2012
depth
0.2
environment (biome)
cropland biome
environment (feature)
microbial feature
environment (material)
arable soil
geographic location (country and/or sea)
France
geographic location (elevation)
175
geographic location (latitude)
48.0833
geographic location (longitude)
7.3667
geographic location (region and locality)
Alsace
history/previous land use
12 years of organic waste application (every 2 years)
horizon
A horizon
investigation type
metagenome
multiplex identifiers
CGCGTATACA
nucleic acid amplification
5ng of DNA were used for a 25µl PCR conducted under the following conditions: initial denaturation: 94degC_2 min; 35 cycles of denaturation: 94degC_30sec; annealing: 52degC_30sec; elongation: 72degC_1min; final elongation: 72degC_7min. A second PCR of 9 cycles was then conducted under similar PCR conditions with purified PCR products and ten base pair multiplex identifiers added to the primers at 5' position to specifically identify each sample and avoid PCR biases.
nucleic acid extraction
DNA was extracted using a procedure slightly modified, developed by the GenoSol platform for application in large-scale soil surveys (Terrat et al., 2012)
organic waste product
Non-composted sewage sludge
pcr conditions
5ng of DNA were used for a 25 µl PCR conducted under the following conditions: initial denaturation:94degC_2.0min;35 cycles of denaturation:94degC_0.5min;annealing:52degC_0.5min;elongation:72degC_1.0min;final elongation:72degC_7.0min
pcr primers
F479:5'-CAGCMGCYGCNGTAANAC-3'; R888:5'CCGYCAATTCMTTTRAGT-3'
project name
SOERE_PRO_2014
sample name
B4T1_16S
sample volume or weight for DNA extraction
1
sequencing method
Illumina
soil environmental package
soil
target gene
16S rRNA gene