Establishment of the mycorrhizal symbiosis.

<p>An AMF contacts the surface of a legume root, by producing swollen structures called hyphopodia (in yellow) (A). Evident defence reactions are not detectable, and the epidermal cells appear alive, with the nuclei visible as blue spots. Once inside the root, the AMF colonizes the inner cortical cells, producing highly branched structures called arbuscules. Notwithstanding the massive colonization, the plant cells remain alive (B). Pictures kindly provided by Andrea Genre and Mara Novero, University of Torino.</p

Principal Coordinate Analysis (PCoA) of most abundant fungal OTUs.

<p>Ordination on axes 1 and 2 of soils on the basis of the ITS1 OTU presence (PCoA). High-abundance OTUs (>1% in at least one soil) are considered for the statistical analysis (list of these OTUs is reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034847#pone.0034847.s001" target="_blank">table S1</a>). Low-abundance OTUs (including singletons) are excluded. TV, tilled vineyard; CV, covered vineyard; MM, managed meadow; PA, pasture; CO, cork-oak formation.</p

Rarefaction curves describing observed fungal richness.

<p>Rarefaction curves indicating the observed number of operational taxonomic units (OTUs) at a genetic distance of 3% related to the number of sequences retrieved in each of the five different soils with ITS1 (<b>a</b>) and ITS2 (<b>b</b>) primer set, respectively. TV, tilled vineyard; CV, covered vineyard; MM, managed meadow; PA, pasture; CO, cork-oak formation. X-axis  =  sequences number; Y-axis  =  OTUs number.</p

Main features of the five investigated Sardinian soils.

<p>Modified from Pastorelli et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034847#pone.0034847-Pastorelli1" target="_blank">[30]</a>. TV, tilled vineyard; CV, covered vineyard; MM, managed meadow; PA, pasture; CO, cork-oak formation. CEC, Cation-Exchange Capacity.</p

Taxonomic distribution of sequences and OTUs retrieved with the ITS1F-ITS2 (ITS1 region) and ITS3-ITS4 (ITS2 region) primer set in the five Sardinian soils.

<p>Asco/Basidiomycota ratios are reported for each of the fungal communities retrieved with both primer sets in all the soils. TV, tilled vineyard; CV, covered vineyard; MM, managed meadow; PA, pasture; CO, cork-oak formation.</p

Dendrogram showing distribution of fungal assemblages.

<p>Classification analysis (UPGMA, chord distance as the resemblance measure) on the basis of OTU relative abundances data. Numbers on branches represent the bootstrap confidence percentage (100 replicates). TV, tilled vineyard; CV, covered vineyard; MM, managed meadow; PA, pasture; CO, cork-oak formation.</p

Taxonomical distribution of retrieved fungi.

<p>Proportion of the (<b>a</b>) 240 ITS1 and (<b>b</b>) 326 ITS2 fungal operational taxonomic units (OTUs) assigned to the different fungal phyla. Ascomycota were dominant (64.5% of total ITS1 OTUs and 68.0% of total ITS2 OTUs), followed by Basidiomycota (30.3% and 25.4%), Zygomycota (4.5% and 6.5%), and Chytridiomycota (0.6% and 0%).</p

Heat map of <i>Medicago truncatula</i> cytokinin signaling gene expression in roots exposed to various environmental conditions.

<p>Selected Affymetrix array data corresponding to roots under various abiotic and biotic conditions were retrieved from the <i>M. truncatula</i> Gene Expression Atlas (MtGEA) database: “myc.”, mycorrhized roots [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116819#pone.0116819.ref070" target="_blank">70</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116819#pone.0116819.ref071" target="_blank">71</a>]; salt stress, two independent experiments (exp. 1 and exp. 2 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116819#pone.0116819.ref072" target="_blank">72</a>]); <i>Phymatotrichopsis omnivora</i> and <i>Aphanomyces euteiches</i> pathogens (respectively [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116819#pone.0116819.ref068" target="_blank">68</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116819#pone.0116819.ref073" target="_blank">73</a>]). All probes corresponding to cytokinin signaling genes were included in the heat map, which was constructed with logarithmic gene expression ratio between the different conditions and their respective controls, based on Euclidean distance and average clustering probes across the experimental conditions included, using the MeV software. Color scale ranges from eight time fold-repression in green (log2 = −3) to eight time fold-induction in red (log2 = 3). Accession numbers correspond to Affymetrix probes (correspondence with gene ID in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116819#pone.0116819.s005" target="_blank">S2 Table</a>), and multiple probes corresponding to a single gene are indicated by a vertical black bar on the right. Colors indicate cytokinin signaling gene families: in blue, CHKs (CHASE domain containing Histidine Kinases); in green, HPTs (Histidine PhosphoTranfert proteins); in orange, RRBs (Type-B Response Regulators); in violet, RRAs (Type-A Response Regulators). MtCRE1, MtCHK2/HK2, MtCHK3/HK3, MtRR1 to MtRR5 gene names were defined in [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116819#pone.0116819.ref013" target="_blank">13</a>]; MtRR8 in [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116819#pone.0116819.ref046" target="_blank">46</a>]; MtRR11 in [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116819#pone.0116819.ref045" target="_blank">45</a>]. For other IDs, no gene name is available in the literature.</p

<i>cre1</i> mutants show defects in vascular bundle differentiation.

<p><b>A-B</b>. Transversal sections of 7 day-old roots in the Wild-Type (WT) and in the <i>cre1</i> mutant (<i>cre1-1</i> and <i>cre1-2</i> alleles). Sections (80 μm) were made at a 1 cm distance from the root tip. <b>A</b>, bright field images; <b>B</b>, images obtained under UV excitation, revealing the autofluorescence of xylem poles. Bars = 50 μm. <b>C.</b> Number of xylem poles in the Wild-Type (WT) and in the <i>cre1</i> mutant (<i>cre1-1</i> and <i>cre1-2</i> alleles) quantified based on previous sections. <b>D.</b> Stele/root width ratio in the Wild-Type (WT) and in the <i>cre1</i> mutant (<i>cre1-1</i> and <i>cre1-2</i> alleles) quantified based on previous sections. In C and D, error bars represent standard deviation and a Kruskal-Wallis test was used to assess significant differences (letters, α<0.05; n>6).</p

Truffle Brûlés Have an Impact on the Diversity of Soil Bacterial Communities

<div><p>Background</p><p>The development of <i>Tuber melanosporum</i> mycorrhizal symbiosis is associated with the production of an area devoid of vegetation (commonly referred to by the French word ‘brûlé’) around the symbiotic plants and where the fruiting bodies of <i>T. melanosporum</i> are usually collected. The extent of the ecological impact of such an area is still being discovered. While the relationship between <i>T. melanosporum</i> and the other fungi present in the brûlé has been assessed, no data are available on the relationship between this fungus and the bacteria inhabiting the brûlé.</p> <p>Methodology/Principal Findings</p><p>We used DGGE and DNA microarrays of 16S rRNA gene fragments to compare the bacterial and archaeal communities inside and outside of truffle brûlés. Soil samples were collected in 2008 from four productive <i>T. melanosporum/Quercus pubescens</i> truffle-grounds located in Cahors, France, showing characteristic truffle brûlé. All the samples were analyzed by DGGE and one truffle-ground was analyzed also using phylogenetic microarrays. DGGE profiles showed differences in the bacterial community composition, and the microarrays revealed a few differences in relative richness between the brûlé interior and exterior zones, as well as differences in the relative abundance of several taxa.</p> <p>Conclusions/Significance</p><p>The different signal intensities we have measured for members of bacteria and archaea inside <i>versus</i> outside the brûlé are the first demonstration, to our knowledge, that not only fungal communities, but also other microorganisms are affected by <i>T. melanosporum</i>. <i>Firmicutes</i> (e.g., <i>Bacillus</i>), several genera of <i>Actinobacteria</i>, and a few <i>Cyanobacteria</i> had greater representation inside the brûlé compared with outside, whereas <i>Pseudomonas</i> and several genera within the class <i>Flavobacteriaceae</i> had higher relative abundances outside the brûlé. The findings from this study may contribute to future searches for microbial bio-indicators of brûlés.</p> </div