Ka-Lai Pang

Families of Dothideomycetes

Dothideomycetes comprise a highly diverse range of fungi characterized mainly by asci with two wall layers (bitunicate asci) and often with fissitunicate dehiscence. Many species are saprobes, with many asexual states comprising important plant pathogens. They are also endophytes, epiphytes, fungicolous, lichenized, or lichenicolous fungi. They occur in terrestrial, freshwater and marine habitats in almost every part of the world. We accept 105 families in Dothideomycetes with the new families Anteagloniaceae, Bambusicolaceae, Biatriosporaceae, Lichenoconiaceae, Muyocopronaceae, Paranectriellaceae, Roussoellaceae, Salsugineaceae, Seynesiopeltidaceae and Thyridariaceae introduced in this paper. Each family is provided with a description and notes, including asexual and asexual states, and if more than one genus is included, the type genus is also characterized. Each family is provided with at least one figure-plate, usually illustrating the type genus, a list of accepted genera, including asexual genera, and a key to these genera. A phylogenetic tree based on four gene combined analysis add support for 64 of the families and 22 orders, including the novel orders, Dyfrolomycetales, Lichenoconiales, Lichenotheliales, Monoblastiales, Natipusillales, Phaeotrichales and Strigulales. The paper is expected to provide a working document on Dothideomycetes which can be modified as new data comes to light. It is hoped that by illustrating types we provide stimulation and interest so that more work is carried out in this remarkable group of fungi.

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.

Fungal diversity notes 1–110: taxonomic and phylogenetic contributions to fungal species

This paper is a compilation of notes on 110 fungal taxa, including one new family, 10 new genera, and 76 new species, representing a wide taxonomic and geographic range. The new family, Paradictyoarthriniaceae is introduced based on its distinct lineage in Dothideomycetes and its unique morphology. The family is sister to Biatriosporaceae and Roussoellaceae. The new genera are Allophaeosphaeria (Phaeosphaeriaceae), Amphibambusa (Amphisphaeriaceae), Brunneomycosphaerella (Capnodiales genera incertae cedis), Chaetocapnodium (Capnodiaceae), Flammeascoma (Anteagloniaceae), Multiseptospora (Pleosporales genera incertae cedis), Neogaeumannomyces (Magnaporthaceae), Palmiascoma (Bambusicolaceae), Paralecia (Squamarinaceae) and Sarimanas (Melanommataceae). The newly described species are the Ascomycota Aliquandostipite manochii, Allophaeosphaeria dactylidis, A. muriformia, Alternaria cesenica, Amphibambusa bambusicola, Amphisphaeria sorbi, Annulohypoxylon thailandicum, Atrotorquata spartii, Brunneomycosphaerella laburni, Byssosphaeria musae, Camarosporium aborescentis, C. aureum, C. frutexensis, Chaetocapnodium siamensis, Chaetothyrium agathis, Colletotrichum sedi, Conicomyces pseudotransvaalensis, Cytospora berberidis, C. sibiraeae, Diaporthe thunbergiicola, Diatrype palmicola, Dictyosporium aquaticum, D. meiosporum, D. thailandicum, Didymella cirsii, Dinemasporium nelloi, Flammeascoma bambusae, Kalmusia italica, K. spartii, Keissleriella sparticola, Lauriomyces synnematicus, Leptosphaeria ebuli, Lophiostoma pseudodictyosporium, L. ravennicum, Lophiotrema eburnoides, Montagnula graminicola, Multiseptospora thailandica, Myrothecium macrosporum, Natantispora unipolaris, Neogaeumannomyces bambusicola, Neosetophoma clematidis, N. italica, Oxydothis atypica, Palmiascoma gregariascomum, Paraconiothyrium nelloi, P. thysanolaenae, Paradictyoarthrinium tectonicola, Paralecia pratorum, Paraphaeosphaeria spartii, Pestalotiopsis digitalis, P. dracontomelon, P. italiana, Phaeoisaria pseudoclematidis, Phragmocapnias philippinensis, Pseudocamarosporium cotinae, Pseudocercospora tamarindi, Pseudotrichia rubriostiolata, P. thailandica, Psiloglonium multiseptatum, Saagaromyces mangrovei, Sarimanas pseudofluviatile, S. shirakamiense, Tothia spartii, Trichomerium siamensis, Wojnowicia dactylidicola, W. dactylidis and W. lonicerae. The Basidiomycota Agaricus flavicentrus, A. hanthanaensis, A. parvibicolor, A. sodalis, Cantharellus luteostipitatus, Lactarius atrobrunneus, L. politus, Phylloporia dependens and Russula cortinarioides are also introduced. Epitypifications or reference specimens are designated for Hapalocystis berkeleyi, Meliola tamarindi, Pallidocercospora acaciigena, Phaeosphaeria musae, Plenodomus agnitus, Psiloglonium colihuae, P. sasicola and Zasmidium musae while notes and/or new sequence data are provided for Annulohypoxylon leptascum, A. nitens, A. stygium, Biscogniauxia marginata, Fasciatispora nypae, Hypoxylon fendleri, H. monticulosum, Leptosphaeria doliolum, Microsphaeropsis olivacea, Neomicrothyrium, Paraleptosphaeria nitschkei, Phoma medicaginis and Saccotheciaceae. A full description of each species is provided with light micrographs (or drawings). Molecular data is provided for 90 taxa and used to generate phylogenetic trees to establish a natural classification for species.

Towards a natural classification and backbone tree for Sordariomycetes

Sordariomycetes is one of the largest classes of Ascomycota and is characterised by perithecial ascomata and inoperculate unitunicate asci. The class includes many important plant pathogens, as well as endophytes, saprobes, epiphytes, and fungicolous, lichenized or lichenicolous taxa. The class includes freshwater, marine and terrestrial taxa and has a worldwide distribution. This paper provides an updated outline of the Sordariomycetes and a backbone tree incorporating asexual and sexual genera in the class. Based on phylogeny and morphology we introduced three subclasses; Diaporthomycetidae, Lulworthiomycetidae and Meliolomycetidae and five orders; Amplistromatales, Annulatascales, Falcocladiales, Jobellisiales and Togniniales. The outline is based on literature to the end of 2014 and the backbone tree published in this paper. Notes for 397 taxa with information, such as new family and genera novelties, novel molecular data published since the Outline of Ascomycota 2009, and new links between sexual and asexual genera and thus synonymies, are provided. The Sordariomycetes now comprises six subclasses, 28 orders, 90 families and 1344 genera. In addition a list of 829 genera with uncertain placement in Sordariomycetes is also provided.

Families of Sordariomycetes

Sordariomycetes is one of the largest classes of Ascomycota that comprises a highly diverse range of fungi characterized mainly by perithecial ascomata and inoperculate unitunicate asci. The class includes many important plant pathogens, as well as endophytes, saprobes, epiphytes, coprophilous and fungicolous, lichenized or lichenicolous taxa. They occur in terrestrial, freshwater and marine habitats worldwide. This paper reviews the 107 families of the class Sordariomycetes and provides a modified backbone tree based on phylogenetic analysis of four combined loci, with a maximum five representative taxa from each family, where available. This paper brings together for the first time, since Barrs’ 1990 Prodromus, descriptions, notes on the history, and plates or illustrations of type or representative taxa of each family, a list of accepted genera, including asexual genera and a key to these taxa of Sordariomycetes. Delineation of taxa is supported where possible by molecular data. The outline is based on literature to the end of 2015 and the Sordariomycetes now comprises six subclasses, 32 orders, 105 families and 1331 genera. The family Obryzaceae and Pleurotremataceae are excluded from the class.

Fungal endophytes associated with Kandelia candel (Rhizophoraceae) in Mai Po Nature Reserve, Hong Kong

We examined the endophytic fungi associated with the dominant mangrove plant, Kandelia candel, in Mai Po Nature Reserve, Hong Kong. Bark, woody tissue and leaves from four mature healthy trees were sampled for fungal endophytes in April and June, 2001. A total of 880 isolates was obtained, 595 from the June sampling. The highest number of fungal endophytes was cultured from bark (674 isolates) with only 63 from leaves. Three taxa of ascomycetes, 18 of anamorphic fungi and 29 mycelial morphotypes were identified. These results indicate a degree of tissue recurrence with similar endophytic fungal assemblages in bark and wood, and a different assemblage in the leaf samples. Dominant sporulating fungi of K. candel were Phomopsis sp., Pestalotiopsis sp., Guignardia sp. and Xylaria sp., which are cosmopolitan and common endophytic species.

Marine fungi and fungal-like organisms

Understanding how higher fungi with their spectrum of cellulolytic and ligninolytic enzymes degrade wood tissue, while labyrinthuloids and thraustochytrids further contribute to the dissolved organic matter entering the open ocean is essential to marine ecology. This work provides an overview of marine fungi including morphology and ultrastructure, phylogeny and biogeography. Biotechnology is also turning to these organisms to develop new bioactive compounds and to address problems such as decomposition of materials in the ocean and bioremediation of oil spills.

Multi-gene phylogeny of the Halosphaeriaceae: its ordinal status, relationships between genera and morphological character evolution

The halosphaeriaceous fungi constitute the largest group of marine Ascomycota found predominantly in marine environments, with few transitional species found in freshwater and brackish water habitats. It has been one of the most intensively studied groups of marine fungi, with 126 species in 53 genera. The classification of the halosphaeriaceous fungi is contentious with one school maintaining that they should be regarded as a family in the Microascales, while others continue to retain the order Halosphaeriales. To refine the phylogenetic inter-relationships among the halosphaeriaceous fungi, 36 taxa were sequenced and analysed based on three loci [nuclear small and large subunit (SSU, LSU), the second largest RNA polymerase II subunit (RPB2)]. The halosphaeriaceous fungi constitute a monophyletic group and share a common ancestor with the Microascaceae however, they share few morphological characters. In the Halosphaeriaceae the centrum tissue comprises catenophyses; asci are clavate to fusiform; ascospores are hyaline, unicellular to many septate, usually with appendages, and most are saprobic in aquatic habitats. Whereas, the peridium of the Microascaceae is carbonaceous, frequently bearing hyphal appendages or setae; asci are globose or ovoid; ascospores are reniform, often bear ornamenting ridges or wings. Genera in the Microascaceae are mainly saprobic from soil to rotting vegetation and occasionally found as pathogens, and primarily terrestrial. Based on morphological data the halosphaeriaceous taxa might be considered as a group warranting ordinal status (Halosphaeriales) and this issue is discussed in this study. Sequence data also show clearly that the genera Remispora and Ceriosporopsis are polyphyletic and we propose the erection of three new genera to accommodate C. tubulifera (Toriella), R. crispa (Kochiella) and R. galerita (Tubakiella). Bovicornua intricata is referred to the genus Ceriosporopsis. The molecular data indicate that different phylogenies based on DNA sequences support a hypothesis that ascospore appendage developments e.g. unfurling bipolar appendages, have evolved and been lost several times.

Screening Mangrove Endophytic Fungi for Antimalarial Natural Products

We conducted a screening campaign to investigate fungi as a source for new antimalarial compounds. A subset of our fungal collection comprising Chinese mangrove endophytes provided over 5000 lipophilic extracts. We developed an accelerated discovery program based on small-scale cultivation for crude extract screening and a high-throughput malaria assay. Criteria for hits were developed and high priority hits were subjected to scale-up cultivation. Extracts from large scale cultivation were fractionated and these fractions subjected to both in vitro malaria and cytotoxicity screening. Criteria for advancing fractions to purification were developed, including the introduction of a selectivity index and by dereplication of known metabolites. From the Chinese mangrove endophytes, four new compounds (14–16, 18) were isolated including a new dimeric tetrahydroxanthone, dicerandrol D (14), which was found to display the most favorable bioactivity profile.

Tropical aquatic fungi

This paper reports on the distribution of fungal communities in aquatic habitats in tropical regions and highlights differences in the taxa observed in freshwater and marine habitats. Ascomycetes are dominant on substrata in marine environments, with few basidiomycetes and discomycetes. Equally, few freshwater basidiomycetes and discomycetes have been reported from the tropics. In marine habitats, Dothideomycetes dominate on mangrove substrata, and halosphaeriaceous species are most numerous on submerged woody substrata in coastal waters, while yeasts are common in seawater and estuarine habitats. In freshwater, Ingoldian anamorphic fungi are most numerous on decaying leaves, while ascomycetes (Dothideomycetes, Sordariomycetes) are prevalent on submerged/exposed woody substrata. Unique fungi are found in tropical waters and differ from those in temperate locations.