Biodiversity Exploratories Information System

general

id 10564
versionID 1.1.16
title VIP_data_topsoil_jointsampling_microbiolgroups_2008_Heiko_Nacke
owners
owner1 Heiko Nacke
owner2 Rolf Daniel
projectName Soilomics
datasetManager
datasetManagerName Rolf Daniel
institute University of Göttingen
email rdaniel@gwdg.de

researchObjects

approxNumberOfPlots
noOfGP 57
noOfEP 57
noOfMIP 57
noOfVIP 57
habitats
grassland yes
forest yes
experimentalManipulation no
relativePositionToGround
aboveGround no
belowGround yes
repeatedMeasurement
timeBasedRepetition
numberOfRepetitions 0
plotBasedRepetition
numberOfSubPlots 0
taxa
taxon1 Microbes
processesAndServices
processOrService1 Other
environmentalDescriptors
environmentalDescriptor1 Other
bioticDataTypes
bioticDataType1 Multiple Species
bioticDataType2 Total Abundances
bioticDataType3 Abundances

methodology

introduction In this data file 16S rRNA gene based analysis of forest and grassland soil procaryotic community composition and diversity "Schwaebische Alb" is stored. The data is intended to be used for synthesis of data associated with the joint soil sampling campaign 2008.
measurements
theory 454 pyrosequencing of a partial sequence, V2-V3 region, of the 16S rRNA gene. Starting material was isolated DNA from forest and grassland soil samples (A horizon) of all VIP plots (Schwaebische Alb).
type none
equipment
instruments Roche 454
calibration none
procedures none

description

acronyms
acronymPair1
acronym1
meaning1
keywords
keyword1 soil microbiological groups

time

when
format yyyy-MM-dd
startDate 2008-04-01
endDate 2008-05-31
dateEntry 2010-03-26
dateLastModified 2015-06-08

data

fileType structuredData
manipulations none
errors none
qualityLevel processed
dataStatus incomplete
dataStructure
dataFormat
missingValues NA
NA
matrix
columnName
rowName
contentType
matrixUnit
variables
name typeOfVariable units description block
1 plotID character(16) name of the plot 0
2 horizon character(16) name of horizon 0
3 16S_sequences_from_pyrosequencing integerNumber No of 16S sequences from pyrosequencing 0
4 classifiable_sequences_to_domain_bacteria integerNumber No of sequences classifiable to domain of bacteria 0
5 Alphaproteobacteria realNumber percent Relative abundances calculated from the classifiable sequences 0
6 Acidobacteria realNumber percent Relative abundances calculated from the classifiable sequences 0
7 Unclassified_bacteria realNumber percent Relative abundances calculated from the classifiable sequences 0
8 Actinobacteria realNumber percent Relative abundances calculated from the classifiable sequences 0
9 Unclassified_Proteobacteria realNumber percent Relative abundances calculated from the classifiable sequences 0
10 Betaproteobacteria realNumber percent Relative abundances calculated from the classifiable sequences 0
11 Deltaproteobacteria realNumber percent Relative abundances calculated from the classifiable sequences 0
12 Gammaproteobacteria realNumber percent Relative abundances calculated from the classifiable sequences 0
13 WS3 realNumber percent Relative abundances calculated from the classifiable sequences 0
14 Firmicutes realNumber percent Relative abundances calculated from the classifiable sequences 0
15 TM7 realNumber percent Relative abundances calculated from the classifiable sequences 0
16 Bacteroidetes realNumber percent Relative abundances calculated from the classifiable sequences 0
17 Other_Phyla realNumber percent Relative abundances calculated from the classifiable sequences 0
18 Shannon_Index_3percent realNumber Shannon Index 3% (genetic distance of 3% = species level) 0
19 Shannon_Index_20percent realNumber Shannon Index 20 % (genetic distance of 20% = phylum level) 0

references

database
papers
paper1
relatedDatasets
dataset1
citation Nacke, Heiko; Rolf Daniel (2016): VIP_data_topsoil_jointsampling_microbiolgroups_2008_Heiko_Nacke. v1.1.16. Biodiversity Exploratories Information System. Dataset. https://www.bexis.uni-jena.de/PublicData/PublicData.aspx?DatasetId=10564

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