Heatmap comparison of the microbiomes in croplands (CFS and OFS) and the woodland.

<p>Colors mark the average relative abundance (in number of sequences per sample) of each bacterial genus within the sample. Only identified genera with total counts exceeding 5 sequences per library are presented.</p

The number of bacteria and archaea per gram of soil, estimated by quantitative PCR.

<p>The raw data on the number of 16S rRNA genes per gram of soil, calibrated to the <i>E</i>. <i>coli</i> and <i>H</i>. <i>salinarum</i> 16S rDNA copy number, were translated to the number of prokaryotic cells per gram of soil by use of the information on the average number of 16S rRNA copies in bacterial and archaeal genomes deposited in rrnDB database [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145072#pone.0145072.ref036" target="_blank">36</a>]. Error bars indicate standard deviation (n = 3).</p

OTUs analyzed in a bootstrapped maximum likelihood phylogenetic tree and their abundance presented in a table.

<p>Pairwise tests indicated either an increase (+) or a decrease (–) in abundance between samples of the organic farming system (OFS), the conventional farming system (CFS) and the woodland (Wood). Blank cells indicate insufficient data. The significance of difference was assessed using a permutation test, INS indicates insignificant difference.</p

Abundance ratios of the most common bacterial phyla in the soil in organic (OFS) vs. conventional (CFS) farming systems, and the woodland vs. farmland systems (wood vs. FS; FS combines OFS and CFS samples).

<p>Circle size indicates the average abundance of the phylum.</p

PCoA analysis performed for the weighted unifrac distances of soil microbiomes.

<p>Wood, woodland soil; CFS, conventional farming system; OFS, organic farming system. The axes show the percentage of explained variation in unifrac distances.</p