The global diversity of fungi has been estimated using several different approaches. There is somewhere between 2–11 million estimated species, but the number of formally described taxa is around 150,000, a tiny fraction of the total. In this paper, we examine 12 ascomycete genera as case studies to establish trends in fungal species descriptions, and introduce new species in each genus. To highlight the importance of traditional morpho-molecular methods in publishing new species, we introduce novel taxa in 12 genera that are considered to have low species discovery. We discuss whether the species are likely to be rare or due to a lack of extensive sampling and classification. The genera are Apiospora , Bambusicola , Beltrania , Capronia , Distoseptispora , Endocalyx , Neocatenulostroma , Neodeightonia , Paraconiothyrium , Peroneutypa , Phaeoacremonium and Vanakripa . We discuss host-specificity in selected genera and compare the number of species epithets in each genus with the number of ITS (barcode) sequences deposited in GenBank and UNITE. We furthermore discuss the relationship between the divergence times of these genera with those of their hosts. We hypothesize whether there might be more species in these genera and discuss hosts and habitats that should be investigated for novel species discovery.

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).

This study deals with an extensive taxonomic reevaluation focusing on phylogenetic relationships and morphological characterization of Tubeufiales, especially those helicosporous hyphomycetes which are difficult to identify. Based on evidence from DNA sequence data and morphology, we introduce 13 new genera in the family Tubeufiaceae, viz. Acanthotubeufia, Dematiohelicoma, Dematiohelicomyces, Dematiohelicosporum, Dematiotubeufia, Helicoarctatus, Helicohyalinum, Helicotruncatum, Neochlamydotubeufia, Neohelicoma, Pleurohelicosporium, Pseudohelicomyces and Pseudohelicoon; transfer Chaetosphaerulina from Dothideomycetes genera incertae sedis, and Artocarpomyces and Helicodochium from Ascomycetes genera incertae sedis into Tubeufiaceae; introduce 52 new species, viz. Berkleasmium fusiforme, B. longisporum, Chlamydotubeufia cylindrica, Dematiohelicosporum guttulatum, Helicoarctatus aquaticus, Helicodochium aquaticum, Helicohyalinum infundibulum, Helicoma aquaticum, H. brunneisporum, H. cocois, H. rufum, H. fusiforme, H. longisporum, H. multiseptatum, H. rubriappendiculatum, H. septoconstrictum, H. tectonae, Helicomyces hyalosporus, Helicosporium aquaticum, H. flavisporum, H. setiferum, H. vesicarium, H. viridiflavum, Neochlamydotubeufia fusiformis, Neohelicomyces hyalosporus, Neohelicosporium acrogenisporum, N. astrictum, N. ellipsoideum, N. irregulare, N. krabiense, N. laxisporum, N. ovoideum, Pleurohelicosporium parvisporum, Pseudohelicomyces aquaticus, P. hyalosporus, Tubeufia abundata, T. bambusicola, T. brevis, T. brunnea, T. chlamydospora, T. dictyospora, T. eccentrica, T. fangchengensis, T. hechiensis, T. inaequalis, T. krabiensis, T. rubra, T. sessilis, T. sympodihylospora, T. sympodilaxispora, T. taiwanensis and T. tratensis; provide 43 new combinations, viz. Acanthohelicospora guianensis, Acanthotubeufia filiforme, Berkleasmium aquatica, B. guangxiense, B. latisporum, B. thailandicum, Dematiohelicoma perelegans, D. pulchrum, Dematiohelicomyces helicosporus, Dematiotubeufia chiangraiensis, Helicohyalinum aquaticum, Helicoma elinorae, H. gigasporum, H. hongkongense, H. linderi, H. nematosporum, H. pannosum, H. serpentinum, Helicomyces chiayiensis, Helicotruncatum palmigenum, Neochlamydotubeufia khunkornensis, Neohelicoma fagacearum, Neohelicomyces pallidus, Neohelicosporium abuense, N. aurantiellum, N. griseum, N. morganii, N. myrtacearum, N. nizamabadense, N. sympodiophorum, N. taiwanense, N. vesiculiferum, Pseudohelicomyces indicus, P. paludosus, P. talbotii, Pseudohelicoon gigantisporum, P. subglobosum, Tubeufia dentophora, T. geniculata, T. lilliputea, T. machaerinae, T. sympodiophora and T. xylophila; introduce 16 new records, viz. Dictyospora thailandica, Helicomyces colligatus, H. torquatus, Neohelicosporium guangxiense, N. hyalosporum, N. parvisporum, Thaxteriellopsis lignicola, Tubeufia aquatica, T. chiangmaiensis, T. cylindrothecia, T. filiformis, T. guangxiensis, T. laxispora, T. parvispora, T. roseohelicospora and T. tectonae. The taxonomy of Helicoma, Helicomyces and Helicosporium is revisited based on phylogenetic analyses and morphological evidence. Neorhamphoria is transferred to Bezerromycetaceae. Three species are excluded from the genus Chlamydotubeufia, twelve species from Helicoma, four species from Helicomyces, 25 species from Helicosporium, six species from Neoacanthostigma and one species from Tubeufia. A multi-gene phylogenetic tree based on maximum likelihood and Bayesian analyses of ITS, LSU, RPB2 and TEF1α sequence data of species of Tubeufiales is provided. Detailed descriptions and illustrations are provided, as well as the morphological comparison with similar taxa are explored. The checklist of accepted Tubeufiales species and re-organised Tubeufiales species are provided.

Hypocreomycetidae is a highly diverse group with species from various habitats. This subclass has been reported as pathogenic, endophytic, parasitic, saprobic, fungicolous, lichenicolous, algicolous, coprophilous and insect fungi from aquatic and terrestrial habitats. In this study, we focused on freshwater fungi of Hypocreomycetidae which resulted 41 fresh collections from China and Thailand. Based on morphological and phylogenetic analyses, we identified 26 species that belong to two orders ( Hypocreales and Microascales ) and six families ( Bionectriaceae , Halosphaeriaceae , Microascaceae , Nectriaceae , Sarocladiaceae and Stachybotryaceae ). Ten new species are introduced and 13 new habitats and geographic records are reported. Mariannaea superimposita, Stachybotrys chartarum and S. chlorohalonatus are recollected from freshwater habitats in China. Based on phylogenetic analysis of combined LSU, ITS, SSU, rpb 2 and tef 1-α sequences data, Emericellopsis is transferred to Hypocreales genera incertae sedis ; Pseudoacremonium is transferred to Bionectriaceae ; Sedecimiella is placed in Nectriaceae ; Nautosphaeria and Tubakiella are excluded from Halosphaeriaceae and placed in Microascales genera incertae sedis ; and Faurelina is excluded from Hypocreomycetidae . Varicosporella is placed under Atractium as a synonym of Atractium . In addition, phylogenetic analysis and divergence time estimates showed that Ascocodina , Campylospora , Cornuvesica and Xenodactylariaceae form distinct lineages in Hypocreomycetidae and they evolved in the family/order time frame. Hence, a new order ( Xenodactylariales ) and three new families ( Ascocodinaceae , Campylosporaceae and Cornuvesicaceae ) are introduced based on phylogenetic analysis, divergence time estimations and morphological characters. Ancestral character state analysis is performed for different habitats of Hypocreomycetidae including freshwater, marine and terrestrial taxa. The result indicates that marine and freshwater fungi evolved independently from terrestrial ancestors. The results further support those early diverging clades of this subclass, mostly comprising terrestrial taxa and freshwater and marine taxa have been secondarily derived, while the crown clade ( Nectriaceae ) is represented in all three habitats. The evolution of various morphological adaptations towards their habitual changes are also discussed.

Yunnan Province is one of the rich biodiversity hotspots with abundant resources of lignicolous freshwater fungi. A total of 281 species of lignicolous freshwater fungi from 1986 to the present in Yunnan Province. They are mostly distributed in the classes Dothideomycetes and Sordariomycetes, a few species in the Eurotiomycetes and Leotiomycetes, and rarely reported in Orbiliomycetes and Pezizomycetes. Lignicolous freshwater fungi can decompose lignocellulose substrates and release energy and nutrients, and thus playing an important role in freshwater environment. This study briefly reviewed the biodiversity and taxonomic status of lignicolous freshwater fungi in Yunnan, the ecological functions of lignicolous freshwater fungi, factors affecting community distribution, application status, and research difficulties.