PCR blank control
blank sample
PCR blank control with water instead of DNA extract. Treated like the other samples in the subsequent steps.
positive.control.type
Bacterial mock community of the following taxa: Bacillus subtilis (NCBI:txid1423), Chryseobacterium luteum, Clostridium roseum (NCBI:txid421531), Enterobacter mori (NCBI:txid539813), Franconibacter helveticus (NCBI:txid357240), Glycomyces tenuis (NCBI:txid58116), Pseudomonas fluorescens (NCBI:txid294), Pseudomonas putida (NCBI:txid303), Rhizobium endophyticum (NCBI:txid578290), Streptomyces acidiscabies (NCBI:txid42234), Variovorax guangxiensis (NCBI:txid1775474). Amplicons were generated individually for each taxon with the same conditions as for the other samples and pooled in equimolar manner after amplification.
collection date
missing: control sample
geographic.location..latitude.
missing: control sample
geographic.location..region.and.locality.
missing: control sample
plant.body.site
missing: control sample
host.common.name
missing: control sample
host.taxid
missing: control sample
project.name
Rhizo4Bio: RhizoTraits
pcr.conditions
initial denaturation:98degC_120s; denaturation:98degC_10s; annealing:55degC_30s; extension:72degC_30s; final extension:72degC_120s
pcr.primers
515f: 5'-GTGYCAGCMGCCGCGGTAA-3', 806RB: 5'-GGACTACNVGGGTWTCTAAT-3'
target.subfragment
V4
subspecific.genetic.lineage
missing: control sample
target.gene
16S rRNA
rainfall.regimen
missing: control sample
geographic location (country and/or sea)
missing: control sample
sequencing.method
Illumina iSeq 100
elevation
missing: control sample
organism
blank sample
scientific_name
blank sample
environmental.medium
missing: control sample
sample.storage.temperature
missing: control sample
geographic.location..longitude.
missing: control sample
broad.scale.environmental.context
missing: control sample
fertilizer.regimen
missing: control sample
host.life.stage
missing: control sample
local.environmental.context
missing: control sample
negative.control.type
Extraction with water instead of sample and PCR blank control.
herbicide.regimen
missing: control sample
host.age
missing: control sample
sequence.quality.check
none