Alfredo Vizzini

The Faces of Fungi database: fungal names linked with morphology, phylogeny and human impacts

Taxonomic names are key links between various databases that store information on different organisms. Several global fungal nomenclural and taxonomic databases (notably Index Fungorum, Species Fungorum and MycoBank) can be sourced to find taxonomic details about fungi, while DNA sequence data can be sourced from NCBI, EBI and UNITE databases. Although the sequence data may be linked to a name, the quality of the metadata is variable and generally there is no corresponding link to images, descriptions or herbarium material. There is generally no way to establish the accuracy of the names in these genomic databases, other than whether the submission is from a reputable source. To tackle this problem, a new database (FacesofFungi), accessible at www.facesoffungi.org (FoF) has been established. This fungal database allows deposition of taxonomic data, phenotypic details and other useful data, which will enhance our current taxonomic understanding and ultimately enable mycologists to gain better and updated insights into the current fungal classification system. In addition, the database will also allow access to comprehensive metadata including descriptions of voucher and type specimens. This database is user-friendly, providing links and easy access between taxonomic ranks, with the classification system based primarily on molecular data (from the literature and via updated web-based phylogenetic trees), and to a lesser extent on morphological data when molecular data are unavailable. In FoF species are not only linked to the closest phylogenetic representatives, but also relevant data is provided, wherever available, on various applied aspects, such as ecological, industrial, quarantine and chemical uses. The data include the three main fungal groups (Ascomycota, Basidiomycota, Basal fungi) and fungus-like organisms. The FoF webpage is an output funded by the Mushroom Research Foundation which is an NGO with seven directors with mycological expertise. The webpage has 76 curators, and with the help of these specialists, FoF will provide an updated natural classification of the fungi, with illustrated accounts of species linked to molecular data. The present paper introduces the FoF database to the scientific community and briefly reviews some of the problems associated with classification and identification of the main fungal groups. The structure and use of the database is then explained. We would like to invite all mycologists to contribute to these web pages.

Unravelling Soil Fungal Communities from Different Mediterranean Land-Use Backgrounds

Background Fungi strongly influence ecosystem structure and functioning, playing a key role in many ecological services as decomposers, plant mutualists and pathogens. The Mediterranean area is a biodiversity hotspot that is increasingly threatened by intense land use. Therefore, to achieve a balance between conservation and human development, a better understanding of the impact of land use on the underlying fungal communities is needed. Methodology/Principal Findings We used parallel pyrosequencing of the nuclear ribosomal ITS regions to characterize the fungal communities in five soils subjected to different anthropogenic impact in a typical Mediterranean landscape: a natural cork-oak forest, a pasture, a managed meadow, and two vineyards. Marked differences in the distribution of taxon assemblages among the different sites and communities were found. Data analyses consistently indicated a sharp distinction of the fungal community of the cork oak forest soil from those described in the other soils. Each soil showed features of the fungal assemblages retrieved which can be easily related to the above-ground settings: ectomycorrhizal phylotypes were numerous in natural sites covered by trees, but were nearly completely missing from the anthropogenic and grass-covered sites; similarly, coprophilous fungi were common in grazed sites. Conclusions/Significance Data suggest that investigation on the below-ground fungal community may provide useful elements on the above-ground features such as vegetation coverage and agronomic procedures, allowing to assess the cost of anthropogenic land use to hidden diversity in soil. Datasets provided in this study may contribute to future searches for fungal bio-indicators as biodiversity markers of a specific site or a land-use degree.

Is the Perigord black truffle threatened by an invasive species? We dreaded it and it has happened!

Invasive alien species are species introduced deliberately or unintentionally to areas outside their natural habitats. They can cause a significant irreversible environmental and socio-economic impact at genetic, species and ecosystem levels, and as claimed by Moore (2000), ‘throughout the world, exotic aliens are wreaking havoc’. The control of these invasive alien species has been discussed at international conventions, such as the Bern convention in 1979. Research on biological introductions has primarily focused on plant and animal invaders. Until now only a few studies have dealt with the spread of fungi through different continents and countries (Desprez-Loustau et al., 2007), largely because of a lack of scientific knowledge of fungal biodiversity and ecology. Reports have mostly focused on the introduction of agronomically important plant pathogenic fungi (above all, rusts and Ascomycetes) and pseudofungi (Stramenopila and Peronosporomycetes), and their invasion routes (Desprez-Loustau et al., 2007). The most common way of introducing fungal pathogens is through the movement of infected planting stock or infested wood (Coetzee et al., 2001). The success of invasive fungal pathogens in these new environments might be explained by an increased aggressiveness towards new host species that have not had an opportunity to evolve resistance. The ecological impacts of the intentional/unintentional introduction of fungal species, apart from plant pathogens, have been largely ignored (Schwartz et al., 2006). Regarding saprotrophic taxa, in-depth studies have only been carried out with a few species, for example Coprinopsis stangliana (Bougher, 2006), and some woodchip fungi (Shaw et al., 2004). As far as ectomycorrhizal fungi are concerned, the accidental introduction and spread of Amanita phalloides (Pringle & Vellinga, 2006), Boletus edulis s.l. (Hall et al., 1998) and Eucalyptus-associated species, such as Pisolithus spp. (Martin et al., 2002), have been carefully studied and monitored. These symbiotic fungi were accidentally introduced when allochthonous trees were planted for agriculture and reforestation (Hall et al., 1998; Martin et al., 2002). The deliberate movement of nonindigenous mycorrhizal fungal species and strains is a phenomenon occurring with increasing frequency as a consequence of the use of beneficial soil organisms to improve horticulture (Azcon-Aguilar & Barea, 1997), bioremediation (Leyval et al., 2002), reforestation (Duponnois et al., 2005) and edible fruit body production (Hall et al., 1998; Hall et al., 2003). The impact of all these introductions on the overall native resident fungal communities is not well understood, and scant attention has been paid to the ecological impact of transporting nonpathogenic fungi across continents (with a few exceptions, e.g. Selosse et al., 1998). Monitoring efforts are therefore urgently needed to track the spreading pattern of introduced fungi.

Phylogeny of the Pluteaceae (Agaricales, Basidiomycota): taxonomy and character evolution

The phylogeny of the genera traditionally classified in the family Pluteaceae (Agaricales, Basidiomycota) was investigated using molecular data from nuclear ribosomal genes (nSSU, ITS, nLSU) and consequences for taxonomy and character evolution were evaluated. The genus Volvariella is polyphyletic, as most of its representatives fall outside the Pluteoid clade and shows affinities to some hygrophoroid genera (Camarophyllus, Cantharocybe). Volvariella gloiocephala and allies are placed in a different clade, which represents the sister group of Pluteus, and a new generic name, Volvopluteus, is proposed to accommodate these taxa. Characters such as basidiospore size and pileipellis structure can be used to separate Pluteus, Volvariella and Volvopluteus. The genus Pluteus is monophyletic and includes species with partial veil traditionally classified in the genus Chamaeota. The evolution of morphological features used in the infrageneric taxonomy of the genus, such as metuloid cystidia and pileipellis structure, was analyzed. Agreement between the molecular phylogeny and morphological subdivision of Pluteus is, generally speaking, good, though some rearrangements are necessary: (i) species with non-metuloid pleurocystidia and pileipellis as a cutis are placed either in sect. Celluloderma, together with the species characterized by a hymenidermal pipeipellis, or in sect. Pluteus, with the metuloid bearing species; (ii) subdivision of sect. Celluloderma according to the presence/absence of cystidioid elements in the pileipellis is not supported by molecular data.

Molecular phylogeny, morphology, pigment chemistry and ecology in Hygrophoraceae (Agaricales)

Molecular phylogenies using 1–4 gene regions and information on ecology, morphology and pigment chemistry were used in a partial revision of the agaric family Hygro- phoraceae. The phylogenetically supported genera we recognize here in the Hygrophoraceae based on these and previous analyses are: Acantholichen, Ampulloclitocybe, Arrhenia, Cantharellula, Cantharocybe, Chromosera, Chrysomphalina, Cora, Corella, Cuphophyllus, Cyphellostereum, Dictyonema, Eonema, Gliophorus, Haasiella, Humidicutis, Hygroaster, Hygrocybe, Hygrophorus, Lichenomphalia, Neohygrocybe, Porpolomopsis and Pseudoarmillariella. A new genus that is sister to Chromosera is described as Gloioxanthomyces. Revisions were made at the ranks of subfamily, tribe, genus, subgenus, section and subsection. We present three new subfamilies, eight tribes (five new), eight subgenera (one new, one new combination and one stat. nov.), 26 sections (five new and three new combinations and two stat. nov.) and 14 subsections (two new, two stat. nov.). Species of Chromosera, Gliophorus, Humidicutis, and Neohygrocybe are often treated within the genus Hygrocybe; we therefore provide valid names in both classification systems. We used a minimalist approach in transferring genera and creating new names and combinations. Consequently, we retain in the Hygrophoraceae the basal cuphophylloid grade comprising the genera Cuphophyllus, Ampulloclitocybe and Cantharocybe, despite weak phylogenetic support. We include Aeruginospora and Semiomphalina in Hygrophoraceae based on morphology though molecular data are lacking. The lower hygrophoroid clade is basal to Hygrophoraceae s.s., comprising the genera Aphroditeola, Macrotyphula, Phyllotopsis, Pleurocybella, Sarcomyxa, Tricholomopsis and Typhula.

Fungal biodiversity and in situ conservation in Italy.

Abstract A remarkable increase in knowledge of fungal biodiversity in Italy has occurred in the last five years. The authors report up-to-date numbers of fungi (Basidiomycota and Ascomycota) by regions together with distributional and ecological data on hypogeous fungi. Specific case studies such as alpine fungi, orchid mycorrhizas symbionts, invasive species, and the use of macrofungi as food by red squirrels are analyzed. In situ conservation strategies carried out on target species and/or taxonomic groups are also indicated.

Bacterial and fungal communities associated with Tuber magnatum -productive niches

Abstract Truffles are hypogeous ectomycorrhizal fungi of ecological interest for forestry in soils of the northern hemisphere, and of economical relevance for food markets worldwide. The molecular mechanisms that control truffle body formation are largely unknown, as well as the environmental factors that are likely involved. Among the latter, it has been hypothesized that soil‐borne communities may have an impact on truffle production. To address this question, we investigated bacterial and fungal communities resident in productive versus adjacent non‐productive grounds of the white truffle Tuber magnatum by using PCR‐DGGE. Although bacterial communities were generally highly similar across all samples within the grounds, profiles did cluster according to the productivity of circumscribed niches, and a Moraxella osloensis population appeared to be associated with productive sites. Fungal communities revealed several populations, yet showed no obvious patterns in relation to productivity, although Mortierella and Fusarium oxysporum appeared to be more abundant in the productive area. Our results offer a first glimpse into microbial communities thriving in truffle productive niches, and open the question as to whether microbe‐mediated mechanisms may facilitate/inhibit truffle fruiting‐body production or, vice versa, i.e. whether truffle sporocarps have an impact on the microbes living in the rhizosphere.

Tuber borchii versus Tuber maculatum: Neotype studies and DNA analyses

Two similar truffle species described by Vittadini, Tuber borchii and T. maculatum, were compared. We designate neotypes for both species, which were described microscopically and compared with fre...

Macrofungi as ecosystem resources: Conservation versus exploitation

Fungi are organisms of significant importance not only for the crucial roles they undertake in nature but also for many human activities that are strictly dependent on them. Indeed, fungi possess fundamental positions in ecosystems functioning including nutrient cycles and wood decomposition. As concerns human-related activities, edible and non-edible mushrooms are also involved and/or exploited in forestry, pharmaceutical industry and food production; hence, nowadays they represent a major economic source worldwide. In order to maintain and improve their strategic importance, several conservation strategies, such as habitat preservation, are needed. This article reports several contributions inherent to the relationships between wood-decaying fungi, edible and non-edible mushrooms and their potential exploitation as non-timber forest products and genetic resources.

Species recognition in Pluteus and Volvopluteus (Pluteaceae, Agaricales): morphology, geography and phylogeny

The phylogeny of several species-complexes of the genera Pluteus and Volvopluteus (Agaricales, Basidiomycota) was investigated using molecular data (ITS) and the consequences for taxonomy, nomenclature and morphological species recognition in these groups were evaluated. Conflicts between morphological and molecular delimitation were detected in sect. Pluteus, especially for taxa in the cervinus-petasatus clade with clamp-connections or white basidiocarps. Some species of sect. Celluloderma are apparently widely distributed in Europe, North America and Asia, either with (P. aurantiorugosus, P. chrysophlebius, P. fenzlii, P. phlebophorus) or without (P. romellii) molecular differentiation in collections from different continents. A lectotype and a supporting epitype are designated for Pluteus cervinus, the type species of the genus. The name Pluteus chrysophlebius is accepted as the correct name for the species in sect. Celluloderma, also known under the names P. admirabilis and P. chrysophaeus. A lectotype is designated for the latter. Pluteus saupei and Pluteus heteromarginatus, from the USA, P. castri, from Russia and Japan, and Volvopluteus asiaticus, from Japan, are described as new. A complete description and a new name, Pluteus losulus, are given for the African P. cervinus var. ealaensis. The American Volvopluteus michiganensis is described in detail. Taxonomic comments and a morphology-based key to all known species of Volvopluteus are provided.