characteristics.text: Epo
characteristics.characteristic: Acronym of the soil name
characteristics.text: ISOm
characteristics.characteristic: Acronym of the used DNA extraction method
characteristics.text: ERC000022
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2014-07-31T17:01:03Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2016-10-21T09:33:03Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA2242649
characteristics.characteristic: External Id
characteristics.text: INRA-CMSE
characteristics.characteristic: INSDC center name
characteristics.text: 2014-07-31T17:01:03Z
characteristics.characteristic: INSDC first public
characteristics.text: 2016-10-21T09:33:03Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: 2
characteristics.characteristic: Number of the biological replicate
characteristics.text: ERS363400
characteristics.characteristic: SRA accession
characteristics.text: ISOm_Epo_18S_02
characteristics.characteristic: Submitter Id
characteristics.text: 2011
characteristics.characteristic: collection date
characteristics.text: Crop soil
characteristics.characteristic: current land use
characteristics.text: 0.1
characteristics.unit: m
characteristics.characteristic: depth
characteristics.text: Five different soils representing forest, grassland and arable biomes were collected from across France. All necessary permits were obtained from the respective land owners (INRA, ADEME, and private owners) for the described field studies. Five individual cores (20 cm depth) were sampled at each site using an unaligned sampling design within a defined area. Replicate soil cores were then bulked to obtain a composite sample for each site. After sieving soil samples to <4 mm, aliquots of 50 g were stored at -40degC prior to DNA extraction. Several physico-chemical parameters were measured for each soil: texture, pH, CaCO3, and total C and N. Physical and chemical analyses were performed by the Soil Analysis Laboratory of INRA (Arras, France, http://www.lille.inra.fr/las) using standard procedures (Plassart et al., 2012 - PLOS ONE).
characteristics.characteristic: description
characteristics.text: cropland biome
characteristics.characteristic: environment (biome)
characteristics.text: farm
characteristics.characteristic: environment (feature)
characteristics.text: agricultural soil
characteristics.characteristic: environment (material)
characteristics.text: France
characteristics.characteristic: geographic location (countryand/orsea,region)
characteristics.text: 208
characteristics.unit: m
characteristics.characteristic: geographic location (elevation)
characteristics.text: 47.231706
characteristics.unit: DD
characteristics.characteristic: geographic location (latitude)
characteristics.text: 5.103217
characteristics.unit: DD
characteristics.characteristic: geographic location (longitude)
characteristics.text: mimarks-survey
characteristics.characteristic: investigation type
characteristics.text: CGTACAGTCA
characteristics.characteristic: multiplex identifiers
characteristics.text: This protocol is a modified version of ISO-11063 standard standard which includes a different mechanical lysis step (FastPrep bead-beating instead of the recommended bead-beating). 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) polyvinylpyrrolidone (40 g/mol) and 2% (w/v) sodium dodecyl sulfate. Tubes were then shaken for 3x30s at 4 m/sec in a FastPrep-24 (MP-Biomedicals, NY, USA) before incubation for 10 min at 70degC and centrifugation at 14,000g for 1 min. 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.
characteristics.characteristic: nucleic acid extraction
characteristics.text: soil metagenome
characteristics.characteristic: organism
characteristics.text: 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.
characteristics.characteristic: pcr conditions
characteristics.text: FR1:5-ANCCATTCAATCGGTANT-3;FF390:5-CGATAACGAACGAGACCT-3
characteristics.characteristic: pcr primers
characteristics.text: 7
characteristics.characteristic: ph
characteristics.text: Ecofinders
characteristics.characteristic: project name
characteristics.text: 1
characteristics.unit: g
characteristics.characteristic: sample weight for DNA extraction
characteristics.text: soil metagenome
characteristics.characteristic: scientific_name
characteristics.text: 454-Pyrosequencing
characteristics.characteristic: sequencing method
characteristics.text: soil
characteristics.characteristic: soil environmental package
characteristics.text: 18S rDNA
characteristics.characteristic: target gene
characteristics.text: 6/55/39
characteristics.unit: % sand/silt/clay
characteristics.characteristic: texture
characteristics.text: ISO_soil_bacteria_fungi_diversity_study
characteristics.characteristic: title
characteristics.text: 1.7
characteristics.unit: g/kg
characteristics.characteristic: total n
characteristics.text: 16.5
characteristics.unit: g/kg
characteristics.characteristic: total organic carbon