A comprehensive account of fungal classification from freshwater habitats is outlined and discussed in the present review based on literature of biodiversity studies and recent morpho-phylogenetic analyses. A total of 3,870 freshwater fungal species are listed with additional details on the isolation source, habitat, geographical distribution, and molecular data. The Ascomycota (2,968 species, 1,018 genera) dominated the freshwater fungal taxa wherein Sordariomycetes (823 species, 298 genera) had the largest number, followed by Dothideomycetes (677 species, 229 genera), Eurotiomycetes (276 species, 49 genera), and Leotiomycetes (260 species, 83 genera). Other phyla included in the updated classification of freshwater fungi are: Chytridiomycota (333 species, 97 genera), Rozellomycota (221 species, 105 genera), Basidiomycota (218 species, 100 genera), Blastocladiomycota (47 species, 10 genera), Monoblepharomycota (29 species, 6 genera), Mucoromycota (19 species, 10 genera), Aphelidiomycota (15 species, 3 genera), Entomophthoromycota (6 species, 4 genera), Mortierellomycota (5 species, 3 genera), Olpidiomycota (4 species, 1 genus), Zoopagomycota (3 species, 2 genera), and Sanchytriomycota (2 species, 2 genera). The freshwater fungi belong to 1,361 genera, 386 families and 145 orders. The Pleosporales and Laboulbeniaceae are the largest freshwater fungal order and family comprised of 391 and 185 species, respectively. The most speciose genera are Chitonomyces (87, Laboulbeniomycetes), Verrucaria (50, Eurotiomycetes), Rhizophydium (52, Rhizophydiomycetes), Penicillium (47, Eurotiomycetes), and Candida (42, Saccharomycetes).

Tuber magnatum produces the world's most expensive truffle. This fungus produces very rare ectomycorrhizas which are difficult or even impossible to detect in the field. A “real-time” PCR assay was recently developed to quantify and to track T. magnatum mycelium in soil. Here, this technique was used to investigate the spatial distribution of T. magnatum extra-radical mycelium in soil productive patches and its dynamic across seasons. This study was carried out in four different natural T. magnatum truffle grounds located in different Italian regions. During the fruiting seasons, the amount of T. magnatum mycelium was significantly higher around the fruiting points and decreased going farther away from them. Moreover, T. magnatum mycelium inside the productive patches underwent seasonal fluctuations. In early spring, the amount of T. magnatum mycelium was significantly higher than in summer. In summer, probably due to the hot and dry season, T. magnatum mycelium significantly decreased, whereas in autumn it increased again and was concentrated at the putative fruiting points. These results give new insights on T. magnatum ecology and are useful to plan the most appropriate sampling strategy for evaluating the management of a truffle ground.