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characteristic: multiplex identifiers

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characteristic: ENA-CHECKLIST

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text: Yes

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characteristic: miscellaneous parameter

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characteristic: multiplex identifiers

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characteristic: ENA-CHECKLIST

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text: Finland

characteristic: geographic location (latitude)

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text: human-gut

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characteristic: investigation type

text: Yes

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characteristic: miscellaneous parameter

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characteristic: organism

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text: pyrosequencing

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characteristic: multiplex identifiers

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characteristic: miscellaneous parameter

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characteristic: organism

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text: pyrosequencing

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characteristic: title


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characteristic: geographic location (latitude)

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text: Yes

text: TD

characteristic: miscellaneous parameter

text: TCAGTCTC

text: human gut metagenome

characteristic: organism

text: Parkinson's Disease Microbiome

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text: pyrosequencing

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characteristic: title


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characteristic: host subject id

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characteristic: medical history performed

text: PIGD

text: TGTCGAGT

characteristic: multiplex identifiers

text: human gut metagenome

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characteristic: ENA-CHECKLIST

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characteristic: organism

text: Parkinson's Disease Microbiome

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text: pyrosequencing

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text: female

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characteristic: title


text: Res

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text: Crop soil

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unit: m

characteristic: depth

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).

characteristic: description

text: cropland biome

text: farm

text: agricultural soil

text: France

characteristic: geographic location (elevation)

text: mimarks-survey

text: CGTGAGCTGA

characteristic: multiplex identifiers

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.

characteristic: nucleic acid extraction

text: soil metagenome

text: 5ng of DNA were used for a 25µl 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. 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.

characteristic: pcr conditions

text: F479:5-CAGCMGCYGCNGTAANAC-3; R888:5-CCGYCAATTCMTTTRAGT-3

characteristic: pcr primers

characteristic: ph

text: Ecofinders

unit: g

characteristic: sample weight for DNA extraction

text: soil metagenome

text: soil

characteristic: soil environmental package

text: 16S rDNA

characteristic: target gene

unit: % sand/silt/clay

characteristic: texture

unit: g/kg

characteristic: total n

characteristic: total organic carbon


text: Res

characteristic: Acronym of the soil name

text: ISOm

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Number of the biological replicate

characteristic: SRA accession

characteristic: Submitter Id

text: Crop soil

text: cropland biome

characteristic: environment (biome)

text: farm

characteristic: environment (feature)

text: agricultural soil

characteristic: environment (material)

text: France

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: CATCGAGCAG

text: soil metagenome

characteristic: organism

text: Ecofinders

characteristic: project name

text: soil metagenome

characteristic: sequencing method

text: soil

text: 16S rDNA

characteristic: title


text: Chp

characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

text: public

characteristic: collection date

text: Crop soil

characteristic: current land use

characteristic: depth

characteristic: description

text: cropland biome

text: farm

text: agricultural soil

text: France

characteristic: geographic location (elevation)

text: mimarks-survey

text: CGAGCTAGCT

characteristic: multiplex identifiers

text: 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.

characteristic: nucleic acid extraction

text: soil metagenome

characteristic: pcr conditions

characteristic: pcr primers

characteristic: ph

text: Ecofinders

characteristic: sample weight for DNA extraction

text: soil metagenome

text: soil

characteristic: soil environmental package

text: 16S rDNA

characteristic: target gene

characteristic: texture

characteristic: total n

characteristic: total organic carbon


text: Res

characteristic: Acronym of the soil name

text: ISOm

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Number of the biological replicate

characteristic: SRA accession

characteristic: Submitter Id

text: Crop soil

text: cropland biome

characteristic: environment (biome)

text: farm

characteristic: environment (feature)

text: agricultural soil

characteristic: environment (material)

text: France

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: CATAGTGACA

text: soil metagenome

characteristic: organism

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.

text: FR1:5-ANCCATTCAATCGGTANT-3;FF390:5-CGATAACGAACGAGACCT-3

text: Ecofinders

characteristic: project name

text: soil metagenome

characteristic: sequencing method

text: soil

text: 18S rDNA

characteristic: title


text: Res

characteristic: Acronym of the soil name

text: ISOm

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

text: public

characteristic: collection date

text: Crop soil

characteristic: current land use

characteristic: depth

characteristic: description

text: cropland biome

text: farm

text: agricultural soil

text: France

characteristic: geographic location (elevation)

text: mimarks-survey

text: CGCGTATACA

characteristic: multiplex identifiers

characteristic: nucleic acid extraction

text: soil metagenome

characteristic: pcr conditions

characteristic: pcr primers

characteristic: ph

text: Ecofinders

characteristic: sample weight for DNA extraction

text: soil metagenome

text: soil

characteristic: soil environmental package

text: 18S rDNA

characteristic: target gene

characteristic: texture

characteristic: total n

characteristic: total organic carbon


text: Chp

characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Number of the biological replicate

characteristic: SRA accession

characteristic: Submitter Id

text: Crop soil

text: cropland biome

characteristic: environment (biome)

text: farm

characteristic: environment (feature)

text: agricultural soil

characteristic: environment (material)

text: France

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: CGTACTCAGA

text: soil metagenome

characteristic: organism

text: Ecofinders

characteristic: project name

text: soil metagenome

characteristic: sequencing method

text: soil

text: 18S rDNA

characteristic: title


text: Chp

characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

text: public

characteristic: collection date

text: Crop soil

characteristic: current land use

characteristic: depth

characteristic: description

text: cropland biome

text: farm

text: agricultural soil

text: France

characteristic: geographic location (elevation)

text: mimarks-survey

text: CACGCTACGT

characteristic: multiplex identifiers

characteristic: nucleic acid extraction

text: soil metagenome

characteristic: pcr conditions

characteristic: pcr primers

characteristic: ph

text: Ecofinders

characteristic: sample weight for DNA extraction

text: soil metagenome

text: soil

characteristic: soil environmental package

text: 16S rDNA

characteristic: target gene

characteristic: texture

characteristic: total n

characteristic: total organic carbon


text: Chp

characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Number of the biological replicate

characteristic: SRA accession

characteristic: Submitter Id

text: Crop soil

text: cropland biome

characteristic: environment (biome)

text: farm

characteristic: environment (feature)

text: agricultural soil

characteristic: environment (material)

text: France

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: CGCTATCTAT

text: soil metagenome

characteristic: organism

text: Ecofinders

characteristic: project name

text: soil metagenome

characteristic: sequencing method

text: soil

text: 16S rDNA

characteristic: title


text: Epo

characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

text: public

characteristic: collection date

text: Crop soil

characteristic: current land use

characteristic: depth

characteristic: description

text: cropland biome

text: farm

text: agricultural soil

text: France

characteristic: geographic location (elevation)

text: mimarks-survey

text: CATACTCTAC

characteristic: multiplex identifiers

characteristic: nucleic acid extraction

text: soil metagenome

characteristic: pcr conditions

characteristic: pcr primers

characteristic: ph

text: Ecofinders

characteristic: sample weight for DNA extraction

text: soil metagenome

text: soil

characteristic: soil environmental package

text: 16S rDNA

characteristic: target gene

characteristic: texture

characteristic: total n

characteristic: total organic carbon


text: Chp

characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Number of the biological replicate

characteristic: SRA accession

characteristic: Submitter Id

text: Crop soil

text: cropland biome

characteristic: environment (biome)

text: farm

characteristic: environment (feature)

text: agricultural soil

characteristic: environment (material)

text: France

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: CGCGTATACA

text: soil metagenome

characteristic: organism

text: Ecofinders

characteristic: project name

text: soil metagenome

characteristic: sequencing method

text: soil

text: 18S rDNA

characteristic: title


text: Chp

characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

text: public

characteristic: collection date

text: Crop soil

characteristic: current land use

characteristic: depth

characteristic: description

text: cropland biome

text: farm

text: agricultural soil

text: France

characteristic: geographic location (elevation)

text: mimarks-survey

text: CATCGAGCAG

characteristic: multiplex identifiers

characteristic: nucleic acid extraction

text: soil metagenome

characteristic: pcr conditions

characteristic: pcr primers

characteristic: ph

text: Ecofinders

characteristic: sample weight for DNA extraction

text: soil metagenome

text: soil

characteristic: soil environmental package

text: 18S rDNA

characteristic: target gene

characteristic: texture

characteristic: total n

characteristic: total organic carbon


text: Epo

characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Number of the biological replicate

characteristic: SRA accession

characteristic: Submitter Id

text: Crop soil

text: cropland biome

characteristic: environment (biome)

text: farm

characteristic: environment (feature)

text: agricultural soil

characteristic: environment (material)

text: France

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: CGTCGATCTC

text: soil metagenome

characteristic: organism

text: Ecofinders

characteristic: project name

text: soil metagenome

characteristic: sequencing method

text: soil

text: 18S rDNA

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: URMITE

characteristic: INSDC center name

text: public

characteristic: collection date

text: human

characteristic: common name

text: humain

text: gut microbiota

text: gut microbiota

text: France

text: human-gut

characteristic: human gut environmental package

text: mimarks-survey

text: Homo sapiens

text: Enterocolite

text: Homo sapiens

text: pyrosequencing


text: Epo

characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

text: INRA-CMSE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Number of the biological replicate

characteristic: SRA accession

characteristic: Submitter Id

text: Crop soil

characteristic: current land use

characteristic: depth

characteristic: description

text: cropland biome

characteristic: environment (biome)

text: farm

characteristic: environment (feature)

text: agricultural soil

text: France

characteristic: geographic location (elevation)

text: mimarks-survey

text: CGCGACATCT

characteristic: multiplex identifiers

characteristic: nucleic acid extraction

text: soil metagenome

characteristic: pcr conditions

characteristic: pcr primers

characteristic: ph

text: Ecofinders

characteristic: sample weight for DNA extraction

text: soil metagenome

text: soil

characteristic: soil environmental package

text: 16S rDNA

characteristic: target gene

characteristic: texture

characteristic: total n

characteristic: total organic carbon


text: Epo

characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Number of the biological replicate

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Crop soil

characteristic: current land use

text: cropland biome

text: farm

text: agricultural soil

characteristic: environment (material)

text: France

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: CAGTACTGCG

text: soil metagenome

characteristic: organism

text: Ecofinders

characteristic: project name

text: soil metagenome

characteristic: sequencing method

text: soil

text: 16S rDNA

characteristic: title


characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

text: public

text: Forest soil

characteristic: depth

characteristic: description

text: temperate woodland biome

characteristic: environment (biome)

text: planted forest

characteristic: environment (feature)

text: forest soil

text: France

characteristic: geographic location (elevation)

text: mimarks-survey

text: CGTACAGTCA

characteristic: multiplex identifiers

characteristic: nucleic acid extraction

text: soil metagenome

characteristic: pcr conditions

characteristic: pcr primers

characteristic: ph

text: Ecofinders

characteristic: sample weight for DNA extraction

text: soil metagenome

text: soil

characteristic: soil environmental package

text: 16S rDNA

characteristic: target gene

characteristic: texture

characteristic: total n

characteristic: total organic carbon


text: Epo

characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Number of the biological replicate

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Crop soil

characteristic: current land use

text: cropland biome

text: farm

text: agricultural soil

characteristic: environment (material)

text: France

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: CGACACTATC

text: soil metagenome

characteristic: organism

text: Ecofinders

characteristic: project name

text: soil metagenome

characteristic: sequencing method

text: soil

text: 18S rDNA

characteristic: title


text: Epo

characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

text: public

text: Crop soil

characteristic: depth

characteristic: description

text: cropland biome

characteristic: environment (biome)

text: farm

characteristic: environment (feature)

text: agricultural soil

text: France

characteristic: geographic location (elevation)

text: mimarks-survey

text: CGCTATCTAT

characteristic: multiplex identifiers

characteristic: nucleic acid extraction

text: soil metagenome

characteristic: pcr conditions

characteristic: pcr primers

characteristic: ph

text: Ecofinders

characteristic: sample weight for DNA extraction

text: soil metagenome

text: soil

characteristic: soil environmental package

text: 18S rDNA

characteristic: target gene

characteristic: texture

characteristic: total n

characteristic: total organic carbon


characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Number of the biological replicate

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Forest soil

characteristic: current land use

text: temperate woodland biome

text: planted forest

text: forest soil

characteristic: environment (material)

text: France

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: CGATCTGTCG

text: soil metagenome

characteristic: organism

text: Ecofinders

characteristic: project name

text: soil metagenome

characteristic: sequencing method

text: soil

text: 18S rDNA

characteristic: title


characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

text: public

text: Forest soil

characteristic: depth

characteristic: description

text: temperate woodland biome

characteristic: environment (biome)

text: planted forest

characteristic: environment (feature)

text: forest soil

text: France

characteristic: geographic location (elevation)

text: mimarks-survey

text: CACACGATAG

characteristic: multiplex identifiers

characteristic: nucleic acid extraction

text: soil metagenome

characteristic: pcr conditions

characteristic: pcr primers

characteristic: ph

text: Ecofinders

characteristic: sample weight for DNA extraction

text: soil metagenome

text: soil

characteristic: soil environmental package

text: 16S rDNA

characteristic: target gene

characteristic: texture

characteristic: total n

characteristic: total organic carbon


characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Number of the biological replicate

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Forest soil

characteristic: current land use

text: temperate woodland biome

text: planted forest

text: forest soil

characteristic: environment (material)

text: France

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: CATATCTCGT

text: soil metagenome

characteristic: organism

text: Ecofinders

characteristic: project name

text: soil metagenome

characteristic: sequencing method

text: soil

text: 16S rDNA

characteristic: title


text: Lus

characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

text: public

text: Grassland

characteristic: depth

characteristic: description

text: temperate grassland biome

characteristic: environment (biome)

text: farm

characteristic: environment (feature)

text: agricultural soil

text: France

characteristic: geographic location (elevation)

text: mimarks-survey

text: CAGACGTCTG

characteristic: multiplex identifiers

characteristic: nucleic acid extraction

text: soil metagenome

characteristic: pcr conditions

characteristic: pcr primers

characteristic: ph

text: Ecofinders

characteristic: sample weight for DNA extraction

text: soil metagenome

text: soil

characteristic: soil environmental package

text: 16S rDNA

characteristic: target gene

characteristic: texture

characteristic: total n

characteristic: total organic carbon


characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Number of the biological replicate

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Forest soil

characteristic: current land use

text: temperate woodland biome

text: planted forest

text: forest soil

characteristic: environment (material)

text: France

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: CGTGTCTCTA

text: soil metagenome

characteristic: organism

text: Ecofinders

characteristic: project name

text: soil metagenome

characteristic: sequencing method

text: soil

text: 18S rDNA

characteristic: title


characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

text: public

text: Forest soil

characteristic: depth

characteristic: description

text: temperate woodland biome

characteristic: environment (biome)

text: planted forest

characteristic: environment (feature)

text: forest soil

text: France

characteristic: geographic location (elevation)

text: mimarks-survey

text: CAGACGTCTG

characteristic: multiplex identifiers

characteristic: nucleic acid extraction

text: soil metagenome

characteristic: pcr conditions

characteristic: pcr primers

characteristic: ph

text: Ecofinders

characteristic: sample weight for DNA extraction

text: soil metagenome

text: soil

characteristic: soil environmental package

text: 18S rDNA

characteristic: target gene

characteristic: texture

characteristic: total n

characteristic: total organic carbon


text: Lus

characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Number of the biological replicate

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Grassland

characteristic: current land use

text: temperate grassland biome

text: farm

text: agricultural soil

characteristic: environment (material)

text: France

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: CAGTAGACGT

text: soil metagenome

characteristic: organism

text: Ecofinders

characteristic: project name

text: soil metagenome

characteristic: sequencing method

text: soil

text: 18S rDNA

characteristic: title


text: Lus

characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

text: public

text: Grassland

characteristic: depth

characteristic: description

text: temperate grassland biome

characteristic: environment (biome)

text: farm

characteristic: environment (feature)

text: agricultural soil

text: France

characteristic: geographic location (elevation)

text: mimarks-survey

text: CACGTGTCGC

characteristic: multiplex identifiers

characteristic: nucleic acid extraction

text: soil metagenome

characteristic: pcr conditions

characteristic: pcr primers

characteristic: ph

text: Ecofinders

characteristic: sample weight for DNA extraction

text: soil metagenome

text: soil

characteristic: soil environmental package

text: 16S rDNA

characteristic: target gene

characteristic: texture

characteristic: total n

characteristic: total organic carbon


text: Lus

characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Number of the biological replicate

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Grassland

characteristic: current land use

text: temperate grassland biome

text: farm

text: agricultural soil

characteristic: environment (material)

text: France

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: CACGCTACGT

text: soil metagenome

characteristic: organism

text: Ecofinders

characteristic: project name

text: soil metagenome

characteristic: sequencing method

text: soil

text: 16S rDNA

characteristic: title


text: Res

characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

text: public

text: Crop soil

characteristic: depth

characteristic: description

text: cropland biome

characteristic: environment (biome)

text: farm

characteristic: environment (feature)

text: agricultural soil

text: France

characteristic: geographic location (elevation)

text: mimarks-survey

text: CAGTAGACGT

characteristic: multiplex identifiers

characteristic: nucleic acid extraction

text: soil metagenome

characteristic: pcr conditions

characteristic: pcr primers

characteristic: ph

text: Ecofinders

characteristic: sample weight for DNA extraction

text: soil metagenome

text: soil

characteristic: soil environmental package

text: 16S rDNA

characteristic: target gene

characteristic: texture

characteristic: total n

characteristic: total organic carbon


text: Lus

characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Number of the biological replicate

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Grassland

characteristic: current land use

text: temperate grassland biome

text: farm

text: agricultural soil

characteristic: environment (material)

text: France

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: CGACGTGACT

text: soil metagenome

characteristic: organism

text: Ecofinders

characteristic: project name

text: soil metagenome

characteristic: sequencing method

text: soil

text: 18S rDNA

characteristic: title


text: Lus

characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

text: public

text: Grassland

characteristic: depth

characteristic: description

text: temperate grassland biome

characteristic: environment (biome)

text: farm

characteristic: environment (feature)

text: agricultural soil

text: France

characteristic: geographic location (elevation)

text: mimarks-survey

text: CAGACGTCTG

characteristic: multiplex identifiers

characteristic: nucleic acid extraction

text: soil metagenome

characteristic: pcr conditions

characteristic: pcr primers

characteristic: ph

text: Ecofinders

characteristic: sample weight for DNA extraction

text: soil metagenome

text: soil

characteristic: soil environmental package

text: 18S rDNA

characteristic: target gene

characteristic: texture

characteristic: total n

characteristic: total organic carbon


text: Res

characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Number of the biological replicate

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Crop soil

characteristic: current land use

text: cropland biome

text: farm

text: agricultural soil

characteristic: environment (material)

text: France

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: CGACACTATC

text: soil metagenome

characteristic: organism

text: Ecofinders

characteristic: project name

text: soil metagenome

characteristic: sequencing method

text: soil

text: 18S rDNA

characteristic: title


text: Res

characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

text: public

text: Crop soil

characteristic: depth

characteristic: description

text: cropland biome

characteristic: environment (biome)

text: farm

characteristic: environment (feature)

text: agricultural soil

text: France

characteristic: geographic location (elevation)

text: mimarks-survey

text: CACACGATAG

characteristic: multiplex identifiers

characteristic: nucleic acid extraction

text: soil metagenome

characteristic: pcr conditions

characteristic: pcr primers

characteristic: ph

text: Ecofinders

characteristic: sample weight for DNA extraction

text: soil metagenome

text: soil

characteristic: soil environmental package

text: 16S rDNA

characteristic: target gene

characteristic: texture

characteristic: total n

characteristic: total organic carbon


text: Res

characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Number of the biological replicate

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Crop soil

characteristic: current land use

text: cropland biome

text: farm

text: agricultural soil

characteristic: environment (material)

text: France

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: CATAGTAGTG

text: soil metagenome

characteristic: organism

text: Ecofinders

characteristic: project name

text: soil metagenome

characteristic: sequencing method

text: soil

text: 16S rDNA

characteristic: title


text: Chp

characteristic: Acronym of the soil name

text: ISO

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

text: public

text: Crop soil

characteristic: depth

characteristic: description

text: cropland biome

characteristic: environment (biome)

text: farm

characteristic: environment (feature)

text: agricultural soil

text: France

characteristic: geographic location (elevation)

text: mimarks-survey

text: CGATCTGTCG

characteristic: multiplex identifiers

text: This protocol is a version of ISO-11063 standard (Martin-Laurent et al., 2001). Soil was added to a bead beating tube containing 2 g of glass beads of 106 µm diameter and eight glass beads of 2 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 30 s at 1600 rpm in a mini bead-beater cell disruptor (Mikro-Dismembrator, Braun Biotech International) before incubation for 10 min at 70degC and centrifugation at 14,000g for 1 min. 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 (full details are described in Martin-Laurent et al. (2001) and Philippot et al. (2010)).

characteristic: nucleic acid extraction

text: soil metagenome

characteristic: pcr conditions

characteristic: pcr primers

characteristic: ph

text: Ecofinders

characteristic: sample weight for DNA extraction

text: soil metagenome

text: soil

characteristic: soil environmental package

text: 18S rDNA

characteristic: target gene

characteristic: texture

characteristic: total n

characteristic: total organic carbon


text: Res

characteristic: Acronym of the soil name

text: GnS-GII

characteristic: Acronym of the used DNA extraction method

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Number of the biological replicate

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Crop soil

characteristic: current land use

text: cropland biome

text: farm

text: agricultural soil

characteristic: environment (material)

text: France

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: CGTAGACTAG

text: soil metagenome

characteristic: organism

text: Ecofinders

characteristic: project name

text: soil metagenome

characteristic: sequencing method

text: soil

text: 18S rDNA

characteristic: title