The microbial community associated with ascocarps of the ectomycorrhizal fungus Tuber borchii Vittad. was studied by both cultivation and direct extraction of bacterial 16S rRNA gene (rDNA) sequence approaches. The inner part of six T. borchii ascoma collected in North-Central Italy was used to establish a bacterial culture collection and to extract the total genomic DNA to obtain a library of 16S rDNAs representative of the truffle bacterial community. Most of the isolates were affiliated to the gamma-Proteobacteria, mainly Fluorescent pseudomonads; some isolates were members of the Bacteroidetes group and Gram-positive bacteria, mostly Bacillaceae. The majority of the clones from the library were alpha-Proteobacteria showing significant similarity values, of greater than 97%, with members of the Sinorhizobium/Ensifer Group, Rhizobium and Bradyrhizobium spp. not previously identified as Tuber-associated bacteria. Only a few bacterial strains belonging to this bacterial subclass were found in the culture collection and isolated on a medium specific for Rhizobium-like organisms. A few clones were members of the beta- and gamma-Proteobacteria; as well as low and high G+C Gram-positive bacteria. Our findings clearly indicate that a dual approach increases the information obtained on the structural composition of a truffle bacterial community as compared to that derived via cultivation or direct recovery of 16S rDNA sequences alone.

Mycorrhizal ascomycetous fungi are obligate ectosymbionts that colonize the roots of gymnosperms and angiosperms. In this paper we describe a straightforward approach in which a combination of morphological and molecular methods was used to survey the presence of potentially endo-and epiphytic bacteria associated with the ascomycetous ectomycorrhizal fungus Tuber borchii Vittad. Universal eubacterial primers specific for the 5 and 3 ends of the 16S rRNA gene (16S rDNA) were used for PCR amplification, direct sequencing, and phylogenetic analyses. The 16S rDNA was amplified directly from four pure cultures of T. borchii Vittad. mycelium. A nearly full-length sequence of the gene coding for the prokaryotic small-subunit rRNA was obtained from each T. borchii mycelium studied. The 16S rDNA sequences were almost identical (98 to 99% similarity), and phylogenetic analysis placed them in a single unique rRNA branch belonging to the CytophagaFlexibacter-Bacteroides (CFB) phylogroup which had not been described previously. In situ detection of the CFB bacterium in the hyphal tissue of the fungus T. borchii was carried out by using 16S rRNA-targeted oligonucleotide probes for the eubacterial domain and the Cytophaga-Flexibacter phylum, as well as a probe specifically designed for the detection of this mycelium-associated bacterium. Fluorescent in situ hybridization showed that all three of the probes used bound to the mycelium tissue. This study provides the first direct visual evidence of a not-yet-cultured CFB bacterium associated with a mycorrhizal fungus of the genus Tuber.The mycorrhizal ascomycetous fungi belonging to the genus Tuber, commonly called truffles, are obligate ectosymbionts that colonize the roots of gymnosperms and angiosperms (23,39,45). Ectomycorrhizal fungi are present in natural and agricultural ecosystems, provide health benefits to plants, and contribute to soil nutrient cycling. The symbiotic development of mycorrhizal fungi on plant roots has been reported to be influenced by bacteria present in the mycorrhizosphere (10,16,35,47). Although various bacterial populations, such as fluorescent Pseudomonas strains and the spore-forming bacteria Micrococcus spp., Moraxella spp., Corynebacterium spp., and Staphylococcus spp., have been isolated from truffles (3,14,20), no molecular evidence has been found concerning the relationship between these organisms and their specific locations in the Tuber host tissue. There is also no information concerning the endo-and epiphytic bacteria which throughout life or during part of the life cycle may invade the tissues of the living fungus and cause unapparent and asymptomatic infections throughout the fungal life cycle and thus during production of the mycelium, contact with the host root, and development of the ectomycorrhizae and fruit bodies.Since at least 95% of all soil bacteria have not been cultured (2, 25, 36), bacteria isolated from truffles could represent only a fraction of the entire natural bacterial community associated with truffles. For this rea...

This study describes a rapid method to identify different truffle species by analysis of their volatile compound fraction using static headspace solid-phase microextraction gas chromatography/mass spectrometry. The volatile organic compounds (VOCs) were extracted using a new 2-cm 50/30 mm DVB/CAR/PDMS fiber placed for 10 min in the headspace of the truffle sample with the vial maintained at 208C (in a thermostatically controlled analysis room). The mass spectra of the VOC chromatograms were represented as 'fingerprints' of the analysed samples. Next, stepwise factorial discriminant analysis afforded a limited number of characteristic fragment ions that allowed a classification of the truffle species studied. This new method provides an effective approach to rapid quality control and identification of truffle species by analysis of their volatile fraction. Moreover, this method offers the advantage of minimizing thermal, mechanical, and chemical modifications of the truffles, thereby reducing the risk of analytical artifacts.

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Tuber ectomycorrhizae in a Tuber magnatum "truffière", located in Central Italy, were studied using molecular methods. Specifically, RFLP-ITS analyses, ITS sequencing and specific probes hybridization were used to identify 335 Tuber-like ectomycorrhizal morphotypes. Molecular identification was possible even when distinct morphological characteristics were lacking. For the first time, T. magnatum ectomycorrhizae and other coexisting Tuber species collected in the field were analysed using molecular tools for unambiguous identification. Although the "truffière" under investigation yields good harvests of T. magnatum fruiting bodies, the percentage of T. magnatum ectomycorrhizae found was very low (less than 4.4% of the 335 root tips analysed), whereas the percentages of Tuber maculatum and Tuber rufum were considerably higher (48.9% and 19.0%, respectively).

Polymorphisms of a ribosomal DNA region (ITS) have been analysed using a specific pair of primers, in order to type fruitbodies and ectomycorrhizae of different truffle species. The identification of ectomycorrhizae was obtained by digestion of the PCR products using restriction enzymes. The resultsshow that the strategy used is both suitable and sensitive to characterize the symbiotic fungi from few mycorrhized root tips.

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Five species of white truffle were classified using PCR-based techniques. RAPD (random amplified polymorphic DNA) fingerprints and specific pairs of primers were used. A RAPD fragment was constant in Tuber borchii Vittad. isolates and polymorphic among the other species. Two molecular markers specific for T. borchii were developed from the sequence of the non-polymorphic RAPD fragment and from regions flanking the 5h-3h ends of a truffle gene. These markers were applied in the identification of T. borchii fruit bodies, mycelia and mycorrhizas, allowing us to monitor the development of this fungus during its entire life cycle.