RESACOR_soil_bacteria_fungi_diversity_study
soil metagenome
Cd (mg/kg)
2.49
Cu (mg/kg)
147
ENA-FIRST-PUBLIC
2016-06-07T17:01:14Z
ENA-LAST-UPDATE
2018-03-09T13:25:28Z
External Id
SAMEA3444907
INSDC center name
INRA-CMSE
INSDC first public
2016-06-07T17:01:14Z
INSDC last update
2018-03-09T13:25:28Z
INSDC status
public
Pb (mg/kg)
265
Submitter Id
2009_P8_11_18_18S
Zn (mg/kg)
528
collection date
2009
depth
0.2
environment (biome)
cropland biome
environment (feature)
farm
environment (material)
agricultural soil
geographic location (country and/or sea)
France
geographic location (elevation)
32
geographic location (latitude)
49.0166667
geographic location (longitude)
2.16666667
investigation type
mimarks-survey
multiplex identifiers
MID057
nucleic acid extraction
This DNA extraction procedure was initially developed and optimized by the GenoSol platform (Terrat et al., 2012). Soil was added to a 15 mL Falcon tube containing 2.5 g of 1.4 mm diameter ceramic beads, 2 g of 106 µm diameter silica beads and and four glass beads of 4 mm diameter. Each soil sample was mixed with a solution of 100 mM Tris-HCl (pH 8), 100 mM EDTA (pH8), 100 mM NaCl, 2% (w/v) and 2% (w/v) sodium dodecyl sulfate. Tubes were then shaken for 3x30 s at 4 m/sec in a FastPrep-24 (MP-Biomedicals, NY, USA) before incubation for 30 min at 70degC and centrifugation at 7,000g for 5 min at 20degC. After removing the supernatant, proteins were precipitated with 1/10 volume of 3 M sodium acetate prior to centrifugation (14,000g for 5 min at 4degC). Finally, nucleic acids were precipitated by adding 1 volume of ice-cold isopropanol. The DNA pellets obtained after centrifugation (14,000g for 5 min at 4degC) were washed with 70% ethanol
pcr conditions
5ng of DNA were used for a 25µl PCR conducted under the following conditions: initial denaturation: 94degC_3.0min; 35 cycles of denaturation: 94degC_1.0min; annealing: 52degC_1.0min;elongation: 72degC_1.0min;final elongation:72degC_5.0min. 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
pcr primers
FR1:5-ANCCATTCAATCGGTANT-3 ; FF390:5-CGATAACGAACGAGACCT-3
ph
7.6
project name
RESACOR
sample name
2009_P8_11_18_18S
sample volume or weight for DNA extraction
1
scientific_name
soil metagenome
sequencing method
454-Pyrosequencing
soil environmental package
soil
target gene
18S rDNA
texture
80/10.9/7.9
total nitrogen
1.6
total organic carbon
38.3