Graphical summary of trait correlations.

<p>Significant (p ≤ 0.05) negative correlations are indicated in red, positive correlations in green, correlations close to significance (p ≤ 0.08) are indicated with dashed lines. Significant differences between treatments of categorical variables are indicated in yellow. Indication of <i>R</i>. <i>solani</i> only <i>and M</i>. <i>hiemalis</i> only implies that the correlation of a trait with mycophagy is only for mycophagous growth of collimonads on either of these fungi.</p

Trait phylogenetic signals.

<p>Trait phylogenetic signals.</p

The effect of field site, year, growth stage and cultivar on soil ascomycete, basidiomycete and glomeromycete diversity for different taxonomic levels.

*<p>Only samples where plant was present are included in the analyses.</p><p>All diversities were calculated using both Shannon H’ and Simpson diversity indexes and presented in the table as Shannon H’/Simpson diversity. If both P-values are the same, only one value is presented. Diversity index for classes was not calculated for basidiomycetes and glomeromycetes due to low numbers or unevenness of classes. Significant P-values are marked with bold.</p

Effect of cultivar, year, growth stage and field on fungal diversity.

<p>Boxplots of changes in diversity of <i>Ascomycota</i> and <i>Basidiomycota</i> between years, growth stages, fields and between baseline, GM and its parental variety. The baseline (all other cultivars combined, n = 16) is marked with green boxplots, the GM-variety (n = 4) with purple and the parental variety ‘Karnico’ (n = 4) with blue markers. Diversity was calculated using Shannon-Wiener index (H’) and statistical comparisons are presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033819#pone-0033819-t005" target="_blank">table 5</a>.</p

Change in fungal biomass.

<p>Boxplots of fungal biomass in the rhizosphere as measured by ergosterol concentrations during 3 years in different growth stages and in both field locations. The baseline (all other cultivars combined, n = 16) is marked with green boxplots, the GM-variety (n = 4) with purple and the parental variety ‘Karnico’ (n = 4) with blue markers. The star indicates a significant cultivar effect at the indicated time point. The values under the graphs are the cultivars with highest and lowest values (on average) colored the same as in the boxplots where ‘D’ = ‘Désirée’, ‘Avk’ = ’Aveka’, ‘Avn’ = ’Aventra’, ‘P’ = ‘Premiere’, ‘K’ = ‘Karnico’ (parental cultivar) and ‘M’ = ’Modena’ (modified cultivar).</p

Statistical analysis of the effects of cultivar and GM-trait on fungal-related parameters in post-harvest soil samples as well as in the rhizosphere of next plant barley.

<p>ANOVA was used as a similarity measure for fungal biomass, enzymatic measurements and diversity and F values are presented in the table. ANOSIM was used for the community data derived from T-REX and R-values are presented in the table. Significant P-values for both ANOVA and ANOSIM are marked with bold.</p

ANOVAs of the effect of cultivar (including all cultivars) and GM-cultivar ‘Modena’ versus parental cultivar ‘Karnico’ on diversity of ascomycetes, basidiomycetes and glomeromycetes in the rhizosphere in both fields, all years and growth stages.

<p>The diversities were estimated using Shannon-H’. The first two columns of each fungal group are performed at the level of OTUs and the third column indicates significance at the level of orders. Significant P-values are marked with bold.</p

ANOSIM comparisons between the fields, years, growth stages, cultivars and GM-trait for <i>Ascomycota</i>, <i>Basidiomycota</i> and <i>Glomeromycota</i>.

*<p>Only samples where plant was present are included in the analyses.</p><p>Significant P-values are marked with bold.</p

ANOVA analysis of effects of cultivar (including all cultivars) and GM-cultivar ‘Modena’ versus parental cultivar ‘Karnico’on fungal biomass, enzymatic activities and fungal richness in the rhizosphere in different fields, years and growth stages.

<p>Significant P-values are marked with bold.</p

Principal component analysis of functioning and diversity of fungal communities in plots cropped with different potato cultivars.

<p>For clarity, the years and field sites are combined. Pre-cropping samples are represented by black circles, young plant stage samples with diamonds, flowering plants stage samples with triangles and senescence stage samples with squares. Green markers and error bars represent baseline cultivars (n = 96), purple markers the GM-variety (n = 24) and blue markers the parental variety ‘Karnico’ (n = 24). The explanatory parameters are mentioned next to the axis. The enzymes measured as functional parameters were laccases, Mn-peroxidases and cellulases.</p