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).

Fungal endophytes have generally been considered as hidden microorganisms that reside asymptomatically within plant tissues and have been exploited for their potential in medicine and plant pathology. They are ubiquitous and associated with nearly all plant species sampled. Even though the exact roles of endophytic fungi within a plant is yet to be established, many speculate that they play important roles in obtaining nutrients and thus improve plant growth, confer plant immunity and promote resistance against biotic and abiotic stresses. It has been postulated that endophytes can exhibit different lifestyles and can even switch lifestyle (i.e., from endophytic to pathogenic or saprobic depending upon plant growth stages). However, there is limited evidence as to whether this switch really happens in vivo. Along the same line, with increasing knowledge of endophytic diversity, defining endophytes has not been easy given their multifaceted functions. The present study provides an updated account with comprehensive knowledge on several aspects including problems with existing definitions, isolation and identification techniques, theoretical and experimental evidence of the role of endophytes, contribution to fungal diversity as well as agenda for future research avenues. For years there has been a number of controversies and debates surrounding as to what exactly is an endophyte. Most of the previous definitions were ephemeral in nature and rather vague and could not realistically define an endophyte. Taking into account numerous biological aspects, we propose herein that endophytes can be defined as “asymptomatic microbial partners that are intimately associated and co-inhabit within healthy internal plant tissues with the ability to confer benefits, co-evolve and alter their lifestyle depending upon plant life stages and adverse conditions”. We also discuss the evolution of endophytes based on fossil data and their co-evolution with their host partners. Studies on fungal endophytes have relied mostly on culture-dependent methods to enable their characterization. However, it is generally well known that these methods suffer drawbacks and there is a need to address the challenges associated with lack of sporulation to enable morphological characterization, slow growth on artificial media, as well as contamination issues. These issues are discussed and addressed in detail here. The molecular mechanisms underlying endophytic colonization, avoidance of plant defense mechanisms, lifestyle changes, as well as their genomics and transcriptomics, are also reviewed. We analyze the possibility of endophytes being host-specific or associated with certain hosts and finally provide an account of their economic importance. This outline of fungal endophytes will provide a more comprehensive understanding of endophytes and can serve for boost research into the exploration and their potential applications in the future.

Pleurotheciales is the largest order in Savoryellomycetidae with a large proportion of species known from freshwater habitats. In order to investigate the phylogenetic relationships of taxa within Pleurotheciales and contribute to their diversity, submerged wood was collected from freshwater habitats in China (Yunnan Province) and Thailand. Two dematiaceous, sporodochial hyphomycetes and one annulatascales-like ascomycete with unusual morphology as compared to extant ones were discovered. They were subjected to DNA-based phylogenetic analyses and the results revealed three distinct lineages in Savoryellomycetidae. This morpho-phylo taxonomic study supports the establishment of five novel taxa including two novel genera, Obliquifusoideum and Saprodesmium, and three novel species, Coleodictyospora muriformis, Obliquifusoideum guttulatum and Saprodesmium dematiosporum. Coleodictyospora muriformis and S. dematiosporum are placed in Pleurotheciales, while O. guttulatum is referred to Savoryellomycetidae genera incertae sedis. The phylogenetic relationships are also presented for Coleodictyospora and Pseudocoleodictyospora, which raises an intriguing taxonomic issue. These two genera are positioned in two different classes, viz Sordariomycetes and Dothideomycetes, although they are quite similar except for the presence of a conidial sheath. This study expands our knowledge of the fungal diversity of freshwater fungi, and also indicates that Pleurotheciales species are mostly found in freshwater habitats.

Apiospora, an ascomycetous genus in Apiosporaceae, comprises saprobes, endophytes, and pathogens of humans and plants. They have a cosmopolitan distribution with a wide range of hosts reported from Asia. In the present study, we collected and isolated Apiospora species from Wurfbainia villosa and grasses in Guangdong and Yunnan provinces in China. Multi-locus phylogeny based on the internal transcribed spacer, the large subunit nuclear rDNA, the partial translation elongation factor 1-α, and β-tubulin was performed to clarify the phylogenetic affinities of the Apiospora species. Based on the distinctive morphological characteristics and molecular evidence, Ap. endophytica, Ap. guangdongensis, Ap. wurfbainiae, and Ap. yunnanensis are proposed. Descriptions, illustrations, and notes for the newly discovered species are provided and compared with closely related Apiospora species. An updated phylogeny of Apiospora is presented, along with a discussion on the phylogenetic affinities of ambiguous taxa.

The health and attractiveness of ornamental plants play key role in gardening and horticulture. They affect both the economical and ornamental value of the plants. In this study, we collected and isolated microfungi associated with dead petioles of dwarf date palm and living leaves of lady palm from Zhongkai University Garden, Guangzhou, China. Phylogenetic relationships were investigated based on multi-locus phylogeny of ITS, LSU, SSU and tef-1α sequence data. The morphology of the new collections was compared with all the relevant species. Based on the morphological comparison and multi-locus phylogeny, we introduce Byssosphaeria phoenicis sp. nov. and Pseudocoleophoma rhapidis sp. nov. in Melanommataceae and Dictyosporiaceae, respectively. Detailed descriptions and illustrations are provided with notes discussing allied species in Byssosphaeria and Pseudocoleophoma. Pathogenicity testing of P. rhapidis causing leaf spots on lady palm was proven and Koch’s postulates fulfilled. This is the first phytopathogenic Pseudocoleophoma species. The pathogenicity does not cause dieback, but the leaf spots reduce the aesthetical value of the plants.

Over the past two decades, numerous novel species have been identified within Dictyosporiaceae, primarily in Dictyocheirospora and Dictyosporium. A recent monograph has revealed that these two genera exhibit a distinct preference for freshwater habitats, particularly in southern China. However, further investigation into the distribution and diversity of the two genera in Guangdong and Guizhou Provinces remains insufficient. In this study, we conducted an analysis of four intriguing cheiroid hyphomycetes collected from flowing rivers in these two regions. Through morphological and phylogenetic analyses incorporating combined LSU, SSU, ITS, and tef1-α sequence data, we have identified them as a novel species in Dictyocheirospora (Dictyoc. submersa sp. nov.), two novel species in Dictyosporium (Dictyos. guangdongense sp. nov. and Dictyos. variabilisporum sp. nov.), and one previously documented species (Dictyos. digitatum). Specifically, the identification of Dictyos. guangdongense is primarily based on its distinct morphology, characterized by complanate, cheiroid, and brown to dark brown conidia, with a hyaline, short, and atrophied appendage arising from the apical cell of the outer row. In addition, the morphological distinctions between Dictyocheirospora and Dictyosporium are further clarified based on our new data. This study also highlights a few phylogenetic matters regarding Dictyosporiaceae.