Two-dimensional non-metric multidimensional scaling (NMDS) biplots based on Bray-Curtis distances displaying differences of A) the total fungal community in the ITS dataset, B) yeasts and dimorphics in the ITS dataset and C) AMF from SSU rDNA dataset in relation to compartment.

<p>Bars represent one standard deviation along both NMDS axes. Only C is labeled with individual MOTUs for readability. Stress value was for A) 0.15, for B) 0.16 and for C) 0.12.</p

Fungal community. Venn diagram showing ratios of sequences occurring in (a) soil 0-10 cm, (b) soil 40–50 cm, (c) soil 60–70 cm and (d) roots and in their overlaps.

<p>Piecharts indicate the ecological composition of the compartmental communities. Relative contribution of compartments or their overlaps to the total number of sequences is also given by a heat map. Within each compartment/overlap, the largest MOTUs are shown. The size of MOTU labels within each compartment/overlap reflects relative sizes by sequence membership (from IBM ManyEyes), green MOTU labels = Basidiomycota, black = Ascomycota.</p

Excel in-cell chart of most abundant fungal MOTUs (≥ 25 sequences) and their distribution in (a) soil 0-10 cm, (b) soil 40–50 cm, (c) soil 60–70 cm and (d) roots.

<p>Red bars represent relative abundance of respective MOTU in the sample, smallest bars are 1 sequence. Sample names contain the year (09 = 2009, 10 = 2010, 11 = 2011), abbreviated month (Jul = July, Sep = September, Dec = December, Jan = January) and depth (S10 = Soil 0–10 cm, S50 = Soil 40–50 cm, S70 = Soil 60–70 cm). n = number of quality checked sequences.</p

Ratio of yeast/dimorphic sequences and MOTUs to complete ITS dataset across the four compartments a-d for all sampling dates.

<p>Sample names contain the year (09 = 2009, 10 = 2010, 11 = 2011), abbreviated month (Jul = July, Sep = September, Dec = December, Jan = January) and depth (S10 = Soil 0–10 cm, S50 = Soil 40–50 cm, S70 = Soil 60–70 cm).</p

SSU rDNA AMF MOTUs and their distribution in (a) soil 0-10 cm, (b) soil 40–50 cm, (c) soil 60–70 cm and (d) roots.

<p>SMOTU = singleton MOTU. Sample names contain the year (09 = 2009, 10 = 2010, 11 = 2011), abbreviated month (Jul = July, Sep = September, Dec = December, Jan = January) and depth (S10 = Soil 0–10 cm, S50 = Soil 40–50 cm, S70 = Soil 60–70 cm). n = number of quality checked AMF sequences.</p

Fungal community structure of the ITS dataset by subphyla across the four compartments a-d for all sampling dates.

<p>Sample names contain the year (09 = 2009, 10 = 2010, 11 = 2011), abbreviated month (Jul = July, Sep = September, Dec = December, Jan = January) and depth (S10 = Soil 0–10 cm, S50 = Soil 40–50 cm, S70 = Soil 60–70 cm).</p

Network Analysis Reveals Ecological Links between N-Fixing Bacteria and Wood-Decaying Fungi

<div><p>Nitrogen availability in dead wood is highly restricted and associations with N-fixing bacteria are thought to enable wood-decaying fungi to meet their nitrogen requirements for vegetative and generative growth. We assessed the diversity of <i>nifH</i> (dinitrogenase reductase) genes in dead wood of the common temperate tree species <i>Fagus sylvatica</i> and <i>Picea abies</i> from differently managed forest plots in Germany using molecular tools. By incorporating these genes into a large compilation of published <i>nifH</i> sequences and subsequent phylogenetic analyses of deduced proteins we verified the presence of diverse pools corresponding to functional <i>nifH</i>, almost all of which are new to science. The distribution of <i>nifH</i> genes strongly correlated with tree species and decay class, but not with forest management, while higher fungal fructification was correlated with decreasing nitrogen content of the dead wood and positively correlated with <i>nifH</i> diversity, especially during the intermediate stage of wood decay. Network analyses based on non-random species co-occurrence patterns revealed interactions among fungi and N-fixing bacteria in the dead wood and strongly indicate the occurrence of at least commensal relationships between these taxa.</p></div

Distribution of the 7,730 <i>nifH</i> MOTUs according to the environments where they have been detected, and whether described as originating from an isolate in GenBank.

<p>168 of the 176 MOTUs derived from this dead wood study have been exclusively identified in wood samples. The integrated heatmap displays proportions of rare sequence types (singletons).</p

Results of perMANOVA analysis of Bray-Curtis dissimilarities in <i>nifH</i> MOTU community structure in relation to tree species, decay class (based on remaining mass after decay) and management type and their interactions, Df = degrees of freedom; SS = sum of squares; MS = mean sum of squares; Pseudo-F = F value by permutation, boldface indicates statistical significance at p<0.05, p-values based on 999 permutations (lowest p-value possible is 0.001).

<p>Results of perMANOVA analysis of Bray-Curtis dissimilarities in <i>nifH</i> MOTU community structure in relation to tree species, decay class (based on remaining mass after decay) and management type and their interactions, Df  =  degrees of freedom; SS  =  sum of squares; MS  =  mean sum of squares; Pseudo-F  =  F value by permutation, boldface indicates statistical significance at p<0.05, p-values based on 999 permutations (lowest p-value possible is 0.001).</p

ANOVA table of effects of the indicated factors on fungal fructification ability.

<p>Complete model summary representing <i>R², F, P</i> statistics. Abbreviations of the depicted ANOVA table Df  =  degrees of freedom, SS  =  sum of squares, MS  =  mean sum of squares. The summary model is as follows: <i>R²</i>, <i>F</i>, and <i>p</i> were 0.5208,</p><p>8.476 and <0.001 (significant), respectively. Boldface indicates statistical significance.</p