Observed and estimated (Chao1 and ACE) fungal richness across the three study regions, Schwäbische Alb (A), Hainich-Dün (H) and Schorfheide Chorin (S) presented using box plots for: (a) the fungal kingdom, (b) the phylum Basidiomycota, (c) the subphylum Agaricomycotina, (d) the phylum Ascomycota and (e) the subphylum Pezizomycotina.

<p>Different letters above bars indicate significant differences between the sites (<i>p</i>≤0.05) based on a Tukey <i>post hoc</i> pairwise comparison.</p

Relationships between the dominant ectomycorrhizal fungal genera and soil and vegetation parameters determined using Spearman’s rank correlation ^a.

a<p>significant correlations with <i>p</i><0.05 are in Bold.</p><p>Tree cover 1: Cover of 5–10 m high trees; Tree cover 2: Cover of >10 m high trees; Tree cover 1 and 2: cumulative tree cover of all trees.</p

Relationships among the ten dominant ectomycorrhizal (ECM) fungal genera determined using Spearman’s rank correlation ^a.

a<p>significant correlations with <i>p</i><0.05 are in bold.</p

Geographic location, main environmental characteristics, soil physical and geochemical parameters of the three regions.

<p>MAT – Mean annual temperature, MAP – Mean annual precipitation.</p

Goodness of fit statistics or squared coefficients ^a of study sites, soil and understory vegetation parameters fitted to the Nonmetric Multi-dimensional Scaling (NMDS) ordination space of the fungal, Basidiomycotan, Ascomycotan, Agaricomycotan, Pezizomycotan, and Ectomycorrhizal (ECM) fungal communities.

a<p>significant squared root correlations are presented in bold (* p<0.05, ** p<0.01, *** p<0.001).</p>b<p>the effect of study regions on the fungal community composition regardless of the management type.</p>c<p>the effect of study region on the fungal community considering the management type.</p><p>Tree cover 1: Cover of 5–10 m high trees; Tree cover 2: Cover of >10 m high trees; Tree cover 1 and 2: cumulative tree cover of all trees.</p

Relative distribution of the four dominant ectomycorrhizal fungal families <i>Russulaceae</i>, <i>Inocybaceae</i>, <i>Sebacinaceae</i> and Thelophoraceae among the three study regions and their relationships with soil pH, C:N ratio and Sand content determined using Box plots and linear regression analysis respectively.

<p>Different letters above bars in the box plots indicate significant differences between the sites (<i>p</i>≤0.05) based on a Tukey HSD <i>post hoc</i> pairwise comparison. Significant regression lines are presented with <i>p-</i>values.</p

Ectomycorrhizal fungal community structure across the three study regions (a) NMDs ordination plot of the study regions Schwäbische Alb (A), Hainich-Dün (H), and Schorfheide Chorin (S), based on the ectomycorrhizal fungal community composition identified in this study (Stress = 11.34).

<p>Soil and vegetation parameters used as an explanatory variable and found to be significant (<i>p</i>≤0.05) are represented as vectors. Management types are abbreviated as AC for age-class and NF for unmanaged natural forests followed by the respective study site. ECM fungal community assembly is nonrandom: C-score distribution (b) and checkerboard indices (c) for observed and randomized ECM fungal OTU occurrence.</p

Relative distribution of the fungal phyla found in this study in the age-class (AC) and unmanaged natural (NF) forests in the Schorfheide-Chorin (S), Hainich-Dün (H), and Schwäbische Alb (A) study regions.

<p>Relative distribution of the fungal phyla found in this study in the age-class (AC) and unmanaged natural (NF) forests in the Schorfheide-Chorin (S), Hainich-Dün (H), and Schwäbische Alb (A) study regions.</p

Fungal community structure across the three study regions: (a) NMDs ordination plot of the study regions Schwäbische Alb (A), Hainich-Dün (H), and Schorfheide Chorin (S), based on the fungal community composition identified as members of the fungal kingdom (Stress = 8.17).

<p>In each diagram soil and vegetation parameters used as an explanatory variable and found to be significant (<i>p</i>≤0.05) are represented as vectors. Management types are abbreviated as AC for age-class and NF for unmanaged natural forests followed by the respective study site. (b) Hierarchical cluster based on the most abundant fungal OTUs identified at least in four of the study plots where the fungal OTUs clearly separated the three regions. Fungal community assembly is nonrandom: C-score distribution (c) and checkerboard indices (d) for observed and randomized fungal OTU occurrence.</p

δ¹³C abundances in soil of a) organic vs. conventional grasslands and b) organic grasslands in relation to the time since certification (<i>r</i>_s = −0.70; <i>p</i><0.001).

<p>Letters indicate significant group differences according to ANOVA analyses (for details see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078134#pone-0078134-t001" target="_blank">Table 1</a> & <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078134#pone-0078134-t002" target="_blank">2</a>).</p