Table 1.
Description of the sampling sites and samples.
Table 2.
Fungi isolated by dilution plates.
Table 3.
Morphological and molecular identification of fungal isolates, compared with the 454 reads databases.
Figure 1.
Distribution of the reads within the fungal phyla.
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, [55]).
Figure 2.
(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.
Figure 3.
Shared and site-specific OTUs.
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.
Figure 4.
Phylogenetic analysis of Verticillium sequences.
NJ tree obtained from the ITS2 sequences alignment of 3 Verticillium leptobactrum isolates from Balangero site (BALA IS4 91, BALA IS4 213 and BALA IS4 1), 4 sequences of V. leptobactrum isolates from other serpentine sites (IS1 1C, IS2 4, IS3 5B and IS5 1; [17]), 7 sequences of V. leptobactrum, 17 of Lecanicillium sp. and 4 of Simplicillium sp. from GenBank and 2 sequences retrieved from the dataset obtained by 454 sequencing (representative of two different OTUs). Sequences of Rotipherophtora minutispora, Haptocillium sphaerosporum and Pochonia chlamydosporia from GenBank were included as out-group. The percentage bootstrap support was calculated out of 1000 trials.
Figure 5.
Comparison of the community structure of different serpentine substrates by DNA fingerprinting.
(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.