Comparison of the community structure of different serpentine substrates by DNA fingerprinting.

<p>(A) DGGE profiles of amplified ITS1 gene fragments from rocks/soil samples (lanes 1-2-3: MOMP, 4-5-6-7: JOUV, 8-9-10-11: VARA, 12-13-14-15: BALA). The gradient of the urea and formamide ranged from 15% to 50%. (B) Principal Coordinate Analysis based on the presence/absence of the amplicons in the DGGE gel. The chart shows that the subsamples of each substrate do not cluster together.</p

Shared and site-specific OTUs.

<p>Venn diagrams representing the distribution of OTUs (and corresponding number of reads in brackets) in the four sampling sites, calculated both considering all the OTUs, and considering only the non-singletons. (A) ITS1 OTUs. (B) ITS2 OTUs (C) ITS1 non-singletons OTUs (D) ITS2 non-singletons OTUs.</p

Phylogenetic analysis of <i>Verticillium</i> sequences.

<p>NJ tree obtained from the ITS2 sequences alignment of 3 <i>Verticillium leptobactrum</i> isolates from Balangero site (BALA IS4 91, BALA IS4 213 and BALA IS4 1), 4 sequences of <i>V. leptobactrum</i> isolates from other serpentine sites (IS1 1C, IS2 4, IS3 5B and IS5 1; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044233#pone.0044233-Daghino2" target="_blank">[17]</a>), 7 sequences of <i>V. leptobactrum</i>, 17 of <i>Lecanicillium sp.</i> and 4 of <i>Simplicillium sp.</i> from GenBank and 2 sequences retrieved from the dataset obtained by 454 sequencing (representative of two different OTUs). Sequences of <i>Rotipherophtora minutispora</i>, <i>Haptocillium sphaerosporum</i> and <i>Pochonia chlamydosporia</i> from GenBank were included as out-group. The percentage bootstrap support was calculated out of 1000 trials.</p

Distribution of the reads within the fungal phyla.

<p>The diagram shows the distribution of the sequences obtained by 454 pyrosequencing within the fungal phyla for each substrate, according to the BlastN results in NCBI database (data obtained by MEGAN, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044233#pone.0044233-White1" target="_blank">[55]</a>).</p

Rarefaction data analysis.

<p>(A) Left axis: Clustering of OTUs (as % of total OTUs) according to the number of supporting reads. Right axis: % of the total reads included in each category of OTUs. (B) Rarefaction curves at 97% similarity threshold (OTUs/sampling effort) for ITS1 and ITS2 reads. The rarefaction was calculated both with the total pool of OTUs and with only the non-singletons OTUs.</p

Fungi isolated by dilution plates.

a<p>The four dominant morphotypes for each substrate were identified based on their macro- and micro-morphological features and by sequencing of the ITS region of rDNA in the case of sterile mycelia.</p>b<p>For each taxon the values of abundance (abundance %: CFU number/total CFU number) and frequency (frequency %: number of isolation plates containing the species/total number of plates) are reported.</p

Morphological and molecular identification of fungal isolates, compared with the 454 reads databases.

<p>The morphological identification of the twelve dominant species isolated from the four serpentine substrates was complemented by ITS1-5.8S-ITS2 region sequencing and BlastN analysis (second column). Each sequence was used as a query against the 454 datasets (both ITS1 and ITS2) and the lowest rank identification of the corresponding nearest matching OTU is reported in the third and sixth columns (for ITS1 and ITS2 respectively), together with the bp matching (N of identical bp/bp total lenght of the matching fragment) and the number of sequences supporting the OTU. The last column indicates whether or not (+ or −) the species was detected by both the dilution plate technique and 454 pyrosequencing from the same substrate.</p

Description of the sampling sites and samples.

<p>Location, presence of fibrous minerals (including asbestos), brief description of the sites and of the samples, extractable fraction of macro- and micronutrients (µg of ions/g of soil ± standard deviation) C%, N%, C/N (the statistical analysis was performed by ANOVA with Tukey as post-hoc test (P<0.05) in order to compare the results obtained for each element from the four substrates), and average pH of the samples.</p

A PLAC8-containing protein from an endomycorrhizal fungus confers cadmium resistance to yeast cells by interacting with Mlh3p

<p>admium is a genotoxic pollutant known to target proteins that are involved in DNA repair and in antioxidant defence, altering their functions and ultimately causing mutagenic and carcinogenic effects.</p> <p>We have identified a PLAC8 domain-containing protein, named OmFCR, by a yeast functional screen aimed at identifying genes involved in cadmium resistance in the endomycorrhizal fungus Oidiodendron maius. OmFCR shows a remarkable specificity in mediating cadmium resistance. Both its function and its nuclear localization in yeast strictly depend on the interaction with Mlh3p, a subunit of the mismatch repair (MMR) system.</p> <p>Although proteins belonging to the PLAC8 family are widespread in eukaryotes, they are poorly characterized and their biological role still remains elusive. Our work represents the first report about the potential role of PLAC8 protein as an MMR-associated protein that physically couples DNA lesion recognition by the MMR system to appropriate effectors that affect cell cycle checkpoint pathways. On the basis of cell survival assays and yeast growth curves, we hypothesize that, upon cadmium exposure, OmFCR might promote a higher rate in cell division as compared to control cells.</p

<i>A</i>. <i>thaliana</i> development in the presence of different fungi in the bipartite plate system.

<p>(a) Control plants and plant-fungus co-cultures 15 days after inoculation; (b) plant biomass measurements (roots—grey bars—and aboveground portions—open bars) in the presence/absence of fungi. Note the strong plant biomass increase in the presence of some of the fungi tested. Bars represent the mean ±SD, n = 5 (each biological replicate represents the total biomass of 3 <i>A</i>. <i>thaliana</i> seedlings grown in an individual plate). Statistically significant differences (P<0.05) among treatments are indicated by different letters above the bars. Om, <i>Oidiodendron maius</i>; Mb, <i>Meliniomyces bicolor</i>; Mv, <i>Meliniomyces variabilis</i>; Re, <i>Rhizoscyphus ericae</i>; Lb, <i>Laccaria bicolor</i>; Cg, <i>Cenococcum geophilum</i>; Sl, <i>Suillus luteus</i>; Tc, <i>Tulasnella calospora</i>; Tv, <i>Trametes versicolor</i>; Ch, <i>Cladosporium herbarum</i>.</p