simboot (version 0.2-0)

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)

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.

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))