Bacteria: Relative Abundances of Soil Bacteria
In shearer/simboot: Simultaneous Inference for Diversity Indices
Bacteria R Documentation
Relative Abundances of Soil Bacteria
Description
Relative abundances of soil bacteria from 27 samples collected
in nine forest and 18 grassland sites in Germany. The data set
includes abundances of 18 bacterial phyla (including three
candidate phyla) and five proteobacterial classes.
Usage
data(Bacteria)
Format
A data frame with 27 observations on the following 24 variables.
Land use typea factor with levels forest grassland
Acidobacteriaa numeric vector
Actinobacteriaa numeric vector
Bacteroidetesa numeric vector
Chloroflexia numeric vector
Cyanobacteriaa numeric vector
Deinococcus-Thermusa numeric vector
Fibrobacteresa numeric vector
Firmicutesa numeric vector
Fusobacteriaa numeric vector
Gemmatimonadetesa numeric vector
Nitrospiraa numeric vector
OP11a numeric vector
Planctomycetesa numeric vector
Spirochaetesa numeric vector
Tenericutesa numeric vector
TM7a numeric vector
Verrucomicrobiaa numeric vector
WS3a numeric vector
Alphaproteobacteriaa numeric vector
Betaproteobacteriaa numeric vector
Deltaproteobacteriaa numeric vector
Gammaproteobacteriaa numeric vector
Epsilonproteobacteriaa numeric vector
Details
Relative abundances of 18 bacterial phyla (including three
candidate phyla) and five proteobacterial classes (alpha, beta,
gamma, delta and epsilon) from two ecological metagenomics
studies (Will et al. 2010, Nacke et al. 2011). There are 27
observations altogether, nine of which stem from forest and 18
from grassland plots in Germany.
One goal of these investigations was to unravel differences in
bacterial diversity and community composition between the land
use types forest and grassland.
The bacteria's relative abundances were determined by analyzing
the V2-V3 region of the 16S rRNA gene via pyrosequencing-based
DNA techniques.
Source
Will, C., Thuermer, A., Wollherr, A., et al. (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.
Nacke, H., Thuermer, A., Wollherr, A., et al. (2011) Pyrosequencing-
based assessment of bacterial community structure along different
management types in German forest and grassland soils. PLoS One,
6, e17000.
Examples
data(Bacteria)
str(Bacteria)
### Assess whether there is a difference in biodiversity and
### community composition species richness (Shannon index,
### Simpson index) between grassland and forest.
### Bootstrap times set to 50 due to example time settings
library(simboot)
mcpHill(dataf=Bacteria[,2:24], fact=Bacteria[,1], boots=50, qval=c(0,1,2))
shearer/simboot documentation built on Feb. 13, 2024, 6:58 a.m.
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| Bacteria | R Documentation |
Relative Abundances of Soil Bacteria
Description
Relative abundances of soil bacteria from 27 samples collected in nine forest and 18 grassland sites in Germany. The data set includes abundances of 18 bacterial phyla (including three candidate phyla) and five proteobacterial classes.
Usage
data(Bacteria)Format
A data frame with 27 observations on the following 24 variables.
Land use typea factor with levels
forestgrasslandAcidobacteriaa numeric vector
Actinobacteriaa numeric vector
Bacteroidetesa numeric vector
Chloroflexia numeric vector
Cyanobacteriaa numeric vector
Deinococcus-Thermusa numeric vector
Fibrobacteresa numeric vector
Firmicutesa numeric vector
Fusobacteriaa numeric vector
Gemmatimonadetesa numeric vector
Nitrospiraa numeric vector
OP11a numeric vector
Planctomycetesa numeric vector
Spirochaetesa numeric vector
Tenericutesa numeric vector
TM7a numeric vector
Verrucomicrobiaa numeric vector
WS3a numeric vector
Alphaproteobacteriaa numeric vector
Betaproteobacteriaa numeric vector
Deltaproteobacteriaa numeric vector
Gammaproteobacteriaa numeric vector
Epsilonproteobacteriaa numeric vector
Details
Relative abundances of 18 bacterial phyla (including three candidate phyla) and five proteobacterial classes (alpha, beta, gamma, delta and epsilon) from two ecological metagenomics studies (Will et al. 2010, Nacke et al. 2011). There are 27 observations altogether, nine of which stem from forest and 18 from grassland plots in Germany.
One goal of these investigations was to unravel differences in bacterial diversity and community composition between the land use types forest and grassland.
The bacteria's relative abundances were determined by analyzing the V2-V3 region of the 16S rRNA gene via pyrosequencing-based DNA techniques.
Source
Will, C., Thuermer, A., Wollherr, A., et al. (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.
Nacke, H., Thuermer, A., Wollherr, A., et al. (2011) Pyrosequencing- based assessment of bacterial community structure along different management types in German forest and grassland soils. PLoS One, 6, e17000.
Examples
data(Bacteria)
str(Bacteria)
### Assess whether there is a difference in biodiversity and
### community composition species richness (Shannon index,
### Simpson index) between grassland and forest.
### Bootstrap times set to 50 due to example time settings
library(simboot)
mcpHill(dataf=Bacteria[,2:24], fact=Bacteria[,1], boots=50, qval=c(0,1,2))
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