simboot (version 0.2-8)

Bacteria: 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 type

a factor with levels forest grassland

Acidobacteria

a numeric vector

Actinobacteria

a numeric vector

Bacteroidetes

a numeric vector

Chloroflexi

a numeric vector

Cyanobacteria

a numeric vector

Deinococcus-Thermus

a numeric vector

Fibrobacteres

a numeric vector

Firmicutes

a numeric vector

Fusobacteria

a numeric vector

Gemmatimonadetes

a numeric vector

Nitrospira

a numeric vector

OP11

a numeric vector

Planctomycetes

a numeric vector

Spirochaetes

a numeric vector

Tenericutes

a numeric vector

TM7

a numeric vector

Verrucomicrobia

a numeric vector

WS3

a numeric vector

Alphaproteobacteria

a numeric vector

Betaproteobacteria

a numeric vector

Deltaproteobacteria

a numeric vector

Gammaproteobacteria

a numeric vector

Epsilonproteobacteria

a 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.

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))