Biodiversity Exploratories Information System

general

id 21868
versionID 1.1.3
title 16S rRNA gene (V3 region) RNA-based analysis of soil bacterial community composition (Family level) grassland 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 150
noOfEP 150
noOfMIP 75
noOfVIP 27
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 Relative abundances (total is 100%) 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.
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.
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 2017-11-23

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 Family string name of bacterial taxon 0
3 relative_Abundance realNumber relative abundance (%) 0

references

database
papers
paper1 Soliveres, S., van der Plas, F., Manning, P., Prati, D., Gossner, M.M., Renner, S.C. et al. (2016) Biodiversity at multiple trophic levels is needed for ecosystem multifunctionality. Nature 536: 456-459.
relatedDatasets
dataset1
citation Overmann, Jörg; Johannes Sikorski (2018): 16S rRNA gene (V3 region) RNA-based analysis of soil bacterial community composition (Family level) grassland 2011. v1.1.3. Biodiversity Exploratories Information System. Dataset. https://www.bexis.uni-jena.de/PublicData/PublicData.aspx?DatasetId=21868

comment

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