Biodiversity Exploratories Information System


CC-BY-NC Dataset Public since: 2018-11-08 Prototype 16S rRNA gene (V3 region) RNA-based analysis of soil bacterial community composition in Hainich, woodland 2011

DOI: No DOI issued.
Citation: Overmann, Jörg; Johannes Sikorski (2018): 16S rRNA gene (V3 region) RNA-based analysis of soil bacterial community composition in Hainich, woodland 2011. v1.1.2. Biodiversity Exploratories Information System. Dataset. https://www.bexis.uni-jena.de/PublicData/PublicData.aspx?DatasetId=21866




general

id 21866
versionID 1.1.2
title 16S rRNA gene (V3 region) RNA-based analysis of soil bacterial community composition in Hainich, woodland 2011
owners
owner1 Jörg Overmann
owner2 Johannes Sikorski
projectName ProFIL
datasetManager
datasetManagerName Jörg Overmann
institute Ludwig-Maximilians-University Munich
email joerg.overmann@dsmz.de

researchObjects

approxNumberOfPlots
noOfGP 49
noOfEP 49
noOfMIP 24
noOfVIP 12
habitats
grassland no
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 Presence or Absence

methodology

introduction Presence of bacterial taxa at genus level, as determined by high-throughput sequencing of the 16S rRNA gene V3 region. Data are based on RNA extracted from soils.
measurements
theory As the absolute number of bacterial cells of a given taxon can not be determined in complex microbial communities, the relative abundance of taxa is determined by the molecular marker of the 16S rRNA gene. The data have then been converted in presence - absence (i.e, presence could not be prooven) converted.
type High-throughput sequencing
equipment
instruments HiSeq2500 and Illumina GAII
calibration -
procedures Forward and reverse reads from V3 Illumina Amplicon sequencing longer than 100 bp were trimmed and dimers filtered out based on detection methods implemented in FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). FASTQ-files were synchronized for those rare cases where only one of both reads has been filtered out. Reads were joined using fastq-join (Aronesty, 2013) allowing 20 percent mismatch and a minimum overlap of 6. Converted FASTA files were checked for chimeras by Uchime integrated in Usearch 5.2.32 (Edgar et al., 2011) applying the GOLD database from ChimeraSlayer (http://drive5.com/otupipe/gold.tz) as reference. Taxonomic-dependent analysis was performed using RDP Multiclassifier 1.1, which is essentially based on RDP classifer (Wang et al., 2007, Cole et al., 2009). A confidence value of 0.5 was applied for short amplicon data.

Aronesty E (2013). Comparison of Sequencing Utility Programs. The Open Bioinformatics Journal 7: 1-8
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ et al (2009). The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis. Nucleic Acids Research 37: D141-D145.
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011). UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 15:2194-2200.
Wang Q, Garrity GM, Tiedje JM, Cole JR (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-5267.

description

acronyms
acronymPair1
acronym1 -
meaning1 -
keywords
keyword1 soil microbiological groups

time

when
format dd.MM.yyyy
startDate 02.05.2011
endDate 13.05.2011
dateEntry 2017-08-08
dateLastModified 2017-08-08

data

fileType structuredData
manipulations
errors
qualityLevel processed
dataStatus complete
dataStructure
dataFormat
missingValues
NA
matrix
columnName
rowName
contentType
matrixUnit
variables
name typeOfVariable units description block
1 Plot_ID string name of plot 0
2 Genus string name of bacterial taxon 0

references

database
papers
paper1 Schall, P., Gossner, M.M., Heinrichs, S., Fischer, M., Boch, S., Prati, D. et al. The impact of even-aged and uneven-aged forest management on regional biodiversity of multiple taxa in European beech forests. Journal of Applied Ecology: doi: 10.1111/1365-2664.12950.
relatedDatasets
dataset1
citation Overmann, Jörg; Johannes Sikorski (2018): 16S rRNA gene (V3 region) RNA-based analysis of soil bacterial community composition in Hainich, woodland 2011. v1.1.2. Biodiversity Exploratories Information System. Dataset. https://www.bexis.uni-jena.de/PublicData/PublicData.aspx?DatasetId=21866

comment

comment If the data does not list a distinct genus in a distinct EP plot then this does not necessarily indicate absence of that genus in that plot. It merely shows that it has not been possible to detect the genus in that plot.