Biodiversity Exploratories Information System


CC-BY-NC Dataset Public since: 2016-04-22 Prototype 16S analysis (pyrosequencing), Hainich grassland VIPs 2008

DOI: No DOI issued.
Citation: Fischer, Christiane; Heiko Nacke; Rolf Daniel (2017): 16S analysis (pyrosequencing), Hainich grassland VIPs 2008. v10.1.19. Biodiversity Exploratories Information System. Dataset. https://www.bexis.uni-jena.de/PublicData/PublicData.aspx?DatasetId=10202




general

id 10202
versionID 10.1.19
title 16S analysis (pyrosequencing), Hainich grassland VIPs 2008
owners
owner1 Christiane Fischer
owner2 Heiko Nacke
owner3 Rolf Daniel
projectName Soilomics
datasetManager
datasetManagerName Rolf Daniel
institute University of Göttingen
email rdaniel@gwdg.de

researchObjects

approxNumberOfPlots
noOfGP 9
noOfEP 9
noOfMIP 9
noOfVIP 9
habitats
grassland yes
forest no
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 16S analysis of the diversity in Hainich grassland
measurements
theory 16S analysis of the diversity in Hainich grassland. Soil samples were collected within the joint soil sampling campaign 2008.
type none
equipment
instruments Roche 454
calibration none
procedures none

description

acronyms
acronymPair1
acronym1
meaning1
keywords
keyword1 16S analysis
keyword2 16S rRNA
keyword3 pyrosequencing
keyword4 taxonomy

time

when
format yyyyMMdd
startDate 20080401
endDate 20080531
dateEntry 2010-02-22
dateLastModified 2017-05-30

data

fileType structuredData
manipulations none
errors none
qualityLevel validated
dataStatus complete
dataStructure
dataFormat
missingValues N/A
NA
matrix
columnName
rowName
contentType
matrixUnit
variables
name typeOfVariable units description block
1 Plot_ID character(16) none 0
2 Horizon character(16) none 0
3 Number_of_sequences_per_sample realNumber none Nukber of sequences in that resp. sample 0
4 Acidobacteria realNumber none number of sequences that were classified as this phylum/class in the resp. sample 0
5 Actinobacteria realNumber none number of sequences that were classified as this phylum/class in the resp. sample 0
6 Bacteroidetes realNumber none number of sequences that were classified as this phylum/class in the resp. sample 0
7 Chloroflexi realNumber none number of sequences that were classified as this phylum/class in the resp. sample 0
8 Cyanobacteria realNumber none number of sequences that were classified as this phylum/class in the resp. sample 0
9 Deinococcus_Thermus realNumber none number of sequences that were classified as this phylum/class in the resp. sample 0
10 Fibrobacteres realNumber none number of sequences that were classified as this phylum/class in the resp. sample 0
11 Firmicutes realNumber none number of sequences that were classified as this phylum/class in the resp. sample 0
12 Fusobacteria realNumber none number of sequences that were classified as this phylum/class in the resp. sample 0
13 Gemmatimonadetes realNumber none number of sequences that were classified as this phylum/class in the resp. sample 0
14 Nitrospira realNumber none number of sequences that were classified as this phylum/class in the resp. sample 0
15 OP11 realNumber none number of sequences that were classified as this phylum/class in the resp. sample 0
16 Planctomycetes realNumber none number of sequences that were classified as this phylum/class in the resp. sample 0
17 Proteobacteria realNumber none number of sequences that were classified as this phylum/class in the resp. sample 0
18 Spirochaetes realNumber none number of sequences that were classified as this phylum/class in the resp. sample 0
19 Tenericutes realNumber none number of sequences that were classified as this phylum/class in the resp. sample 0
20 TM7 realNumber none number of sequences that were classified as this phylum/class in the resp. sample 0
21 unclassified_bacteria realNumber none number of sequences that were classified as this phylum/class in the resp. sample 0
22 Verrucomicrobia realNumber none number of sequences that were classified as this phylum/class in the resp. sample 0
23 WS3 realNumber none number of sequences that were classified as this phylum/class in the resp. sample 0
24 Alphaproteobacteria realNumber none number of sequences that were classified as this phylum/class in the resp. sample 0
25 Betaproteobacteria realNumber none number of sequences that were classified as this phylum/class in the resp. sample 0
26 Gammaproteobacteria realNumber none number of sequences that were classified as this phylum/class in the resp. sample 0
27 Deltaproteobacteria realNumber none number of sequences that were classified as this phylum/class in the resp. sample 0
28 Epsilonproteobacteria realNumber none number of sequences that were classified as this phylum/class in the resp. sample 0
29 unclassified_Proteobacteria realNumber none number of sequences that were classified as this phylum/class in the resp. sample 0

references

database
papers
paper1 Will C, Thürmer A, Wollherr A, Nacke H, Herold N, Schrumpf M, Gutknecht J, Wubet T, Buscot F, Daniel R (2010). Horizon-specific bacterial community composition of German grassland soils, as revealed by pyrosequencing-based analysis of 16S rRNA genes. Applied and Environmental Microbiology 76: 6751-6759.
paper2 Birkhofer K, Schöning I, Alt F, Herold N, Klarner B, Maraun M, Marhan S, Oelmann Y, Wubet T, Yurkov A, Begerow D, Berner D, Buscot F, Daniel R, Dietkötter T, Ehnes RB, Erdmann G, Fischer C, Foesel B, Groh J, Gutknecht J, Kandeler E, Lang C, Lohaus G, Meyer A, Nacke H et al. (2012). General relationships between abiotic soil properties and soil biota across spatial scales and different land-use types. PLoS ONE 7: e43292.
paper3 Pallmann P, Schaarschmidt F, Hothorn LA, Fischer C, Nacke H, Priesnitz KU, Schork NJ (2012). Assessing group differences in biodiversity by simultaneously testing a user-defined selection of diversity indices. Molecular Ecology Resources 12: 1068-1078.
relatedDatasets
dataset1
citation Fischer, Christiane; Heiko Nacke; Rolf Daniel (2017): 16S analysis (pyrosequencing), Hainich grassland VIPs 2008. v10.1.19. Biodiversity Exploratories Information System. Dataset. https://www.bexis.uni-jena.de/PublicData/PublicData.aspx?DatasetId=10202

comment

comment