Volume 14 - 2023 Issue 1
17. Beyond observation: genomic traits and machine learning algorithms for predicting fungal lifestyles
Chen YP et al. (2023)
16. Mycosphere Notes 413–448: Dothideomycetes associated with woody oil plants in China
Li WL et al. (2023)
15. Diversity of fungal communities associated with grapevine trunk diseases in China
Zhou YY et al. (2023)
14. Lasiodiplodia: Generic revision by providing molecular markers, geographical distribution and haplotype diversity
Rathnayaka AR et al. (2023)
13. The relevance of fungi in astrobiology research – Astromycology
Simões MF et al. (2023)
12. Annotated notes on Diaporthe species
Hongsanan S et al. (2023)
11. Updated systematics of Trichaptum s.l. (Hymenochaetales, Basidiomycota)
Zhou M et al. (2023)
9. New taxa of Boletaceae from China
Wu G et al. (2023)
8. Mycosphere notes 387–412 – novel species of fungal taxa from around the world
Hyde KD et al. (2023)
Volume 13 - 2022 - Issue 1
Authors: Ji X, Zhou JL, Song CG, Xu TM, Wu DM, Cui BK
Recieved: 16 November 2021, Accepted: 21 January 2022, Published: 26 January 2022
Polyporus is a taxonomically controversial genus which includes species belonging to six infrageneric groups. Recently, many species of Polyporus have been transferred into other related genera viz. Cerioporus, Favolus, Lentinus, Neofavolus and Picipes based on the phylogenetic and morphological analyses. To ascertain the relationships of Polyporus and its allied genera, eight DNA fragments viz. the internal transcribed spacers 1 and 2 with the 5.8S rDNA (ITS), the nuclear ribosomal large subunit (nLSU), partial translation elongation factor 1-α gene (EF1-α), the mitochondrial small-subunit (mtSSU), the β-tubulin gene (TUB), the gene for RNA polymerase II largest subunit (RPB1), the gene for RNA polymerase II second largest subunit (RPB2) and the nuclear ribosomal small subunit (nSSU), are used in the molecular systematic studies. Phylogenetic analyses were carried out based on two combined datasets (ITS+nLSU) and (ITS+nLSU+EF1-α+mtSSU+RPB1+RPB2+nSSU+TUB), and the results indicated that species of Polyporus and its related genera fell into six well supported clades: the picipes clade, the favolus calde, the neofavolus clade, the lentinus clade, the core polyporus clade and the squamosus clade. Moreover, the conserved regions of six DNA fragments (5.8S, nLSU, EF1-α, RPB1, RPB2 and nSSU) were used to analyze the divergence times and evolutionary relationships of Polyporus and its related genera by using BEAST v1.8. Bayesian evolutionary analysis revealed that the ancestor of Polyporales split at about 141.81 Mya, while the mean stem ages of the six major clades of Polyporus and its allied genera were 49–63 Mya. Based on the combined analyses of morphology, phylogenies and divergence times, species in the picipes clade formed the genus Picipes by the coriaceous (fresh) to hard (dry) basidiomata and strongly branched skeleto-binding hyphae; species nested in the favolus clade and the neofavolus clade were separately treated as two distinct genera Favolus and Neofavolus; the polyporoid species in the lentinus clade with central and light-colored stipe and inflated hyphae were transferred into Lentinus, and the core polyporus clade was treated as Polyporus s. str. The squamosus clade contained species belonging to several different genera viz. Datronia, Datroniella, Echinochaete, Mycobonia, Neodatronia, Polyporus s. lat. and Pseudofavolus, but there are no enough efficient morphological evidence to combine all species in the squamosus clade into a specific genus. In addition, three new species of Polyporus and seven new species of Picipes are described and illustrated.
Keywords: molecular clock – morphology – multi-gene phylogenies – new species – Polyporaceae
Authors: Wijayawardene NN, Hyde KD, Dai DQ, Sánchez-García M, Goto BT, Saxena RK, Erdoğdu M, Selçuk F, Rajeshkumar KC, Aptroot A, Błaszkowski J, Boonyuen N, da Silva GA, de Souza FA, Dong W4, Ertz D, Haelewaters D, Jones EBG, Karunarathna SC, Kirk PM, Kukwa M, Kumla J, Leontyev DV, Lumbsch HT, Maharachchikumbura SSN, Marguno F, Martínez-Rodríguez P, Mešić A, Monteiro JS, Oehl F, Pawłowska J, Pem D, Pfliegler WP, Phillips AJL, Pošta A, He MQ, Li JX, Raza M, Sruthi OP, Suetrong S, Suwannarach N, Tedersoo L, Thiyagaraja V, Tibpromma S, Tkalčec Z, Tokarev YS, Wanasinghe DN, Wijesundara DSA, Wimalaseana SDMK, Madrid H, Zhang GQ, Gao Y, Sánchez-Castro I, Tang LZ, Stadler M, Yurkov A, Thines M
Recieved: 22 November 2021, Accepted: 25 January 2022, Published: 23 February 2022
This paper provides an updated classification of the Kingdom Fungi (including fossil fungi) and fungus-like taxa. Five-hundred and twenty-three (535) notes are provided for newly introduced taxa and for changes that have been made since the previous outline. In the discussion, the latest taxonomic changes in Basidiomycota are provided and the classification of Mycosphaerellales are broadly discussed. Genera listed in Mycosphaerellaceae have been confirmed by DNA sequence analyses, while doubtful genera (DNA sequences being unavailable but traditionally accommodated in Mycosphaerellaceae) are listed in the discussion. Problematic genera in Glomeromycota are also discussed based on phylogenetic results.
Keywords: Ascomycota – basal fungi – Basidiomycota – Classification – Fossil fungi – Rozellomycota
Authors: Manawasinghe IS, Calabon MS, Jones EBG, Zhang YX, Liao CF, Xiong Y, Chaiwan N, Kularathnage ND, Liu NG, Tang SM, Sysouphanthong P, Du TY, Luo M, Pasouvang P, Pem D, Phonemany M, Ishaq M, Chen JW, Karunarathna SC, Mai ZL, Rathnayaka AR, Samarakoon MC, Tennakoon DS, Wijesinghe SN, Yang YH, Zhao HJ, Fiaz M, Doilom M, Dutta AK, Khalid AN, Liu JW, Thongklang N, Senanayake IC, Tibpromma S, You LQ, Camporesi E, Gafforov YS, Hyde KD
Recieved: 05 November 2021, Accepted: 15 February 2022, Published: 25 April 2022
This is the seventh in a series of Mycosphere notes in which we provide notes on the collection of fungi isolated from various hosts. In this set of notes, we introduce Pseudophialocephala as a new genus, nine new species, 27 new host or country records and five new combinations. The new species are Ceratosphaeria yunnanensis, Cytospora salicis-albae, Gymnopus bunerensis, Kalmusia cordylines, Leucoagaricus croceus, Leucoagaricus laosensis, Neopyrenochaeta shaoguanica, Pseudophialocephala cuneata and Robillarda aquatica. Pseudophialocephala humicola, Pseudophialocephala aquatica, Pseudophialocephala salinicola, Pseudophialocephala terricola and Pseudophialocephala xalapensis are introduced as new combinations. We provide new molecular data for 43 species belonging to two phyla, three classes and 15 orders. Updated phylogenetic trees for 22 families (Agaricaceae, Botryosphaeriaceae, Chaetosphaeriaceae, Coniochaetaceae, Didymosphaeriaceae, Gloeophyllaceae, Glomerellaceae, Hysteriaceae, Lophiostomataceae, Magnaporthaceae, Neopyrenochaetaceae, Omphalotacea, Phaeosphaeriaceae, Phyllostictaceae, Pleosporaceae, Saccotheciaceae, Savoryellaceae, Sporocadaceae, Stachybotryaceae, Torulaceae, Valsaceae, Physalacriaceae) and 32 genera (Alfaria, Aureobasidium, Ceratosphaeria, Collybiopsis, Colletotrichum, Comoclathris, Coniochaeta, Cytospora, Dothiorella, Gymnopus, Gymnopus, Heliocybe, Hysterium, Hysterobrevium, Kalmusia, Leptospora, Letendraea, Leucoagaricus, Mucidula, Neoleptosporella, Neopyrenochaeta, Paraleptospora, Phyllosticta, Pseudophialocephala, Rhytidhysteron, Robillarda, Savoryella, Sporocadus, Thozetella, Torula and Vaginatispora) are given.
Keywords: 9 new taxa – 27 new records – 5 new combinations – Agaricomycetes – Ascomycota – Basidiomycota – Dothideomycetes – Molecular phylogeny – New hosts – New species – Sordariomycetes – Taxonomy
Authors: Marasinghe DS, Hongsanan S, Zeng XY, Jones EGB, Boonmee S, Hyde KD
Recieved: 03 February 2022, Accepted: 30 March 2022, Published: 05 May 2022
Epifoliar fungi are poorly studied symbionts that co-inhabit the surface of living plants. They are relatively understudied and generally lack molecular data thus there is considerable taxonomic confusion in the group as early taxonomic studies were based on morphology. Many taxa are difficult to isolate for obtaining cultures and therefore molecular analysis is a limitation for biotrophic species unless sequenced directly from the fruiting bodies. Epifoliar fungi evolved from diverse ancestors and include mainly members of the Dothideomycetes, Eurotiomycetes, Lecanoromycetes, and Sordariomycetes. The classification of epifoliar fungi is challenging due to taxonomic confusion in historical classifications and insufficient molecular data. In this study, we provide a summary of major epifoliar families (Asterinaceae, Meliolaceae, Micropeltidaceae, Microthyriaceae, Parmulariaceae and Zeloasperisporiaceae). The modes of nutrition of each family are also reviewed. Character analysis of a combined LSU, SSU and rpb2 dataset shows that epifoliar fungi have different taxonomic and evolutionary relationships in Ascomycota. Epifoliar fungi are generally considered to be host-specific, but this needs to be confirmed using molecular data as morphological differences are minor. Therefore, future research should focus on addressing the drawbacks of current studies and use new molecular approaches. To obtain better insights into epifoliar fungi, a combination of taxonomic and ecological studies is needed.
Keywords: Ascomycota – Character analysis – Epiphytes – Nutrition – Symbionts
Authors: Wong PTW, Tan YP, Weese TL, Shivas RG
Recieved: 29 March 2022, Accepted: 10 June 2022, Published: 05 July 2022
Isolates of Magnaporthiopsis (Magnaporthaceae, Magnaporthales) were obtained from turfgrass species with patch disease symptoms in sports fields and golf courses in eastern Australia. Patch disease was characterised by plants with root rot, vascular discolouration and dark, ectotrophic mycelium on the root surfaces. Four new species, Magnaporthiopsis dharug, M. gadigal, M. gumbaynggirr and M. yugambeh, are described based on phylogenetic analysis of concatenated partial DNA sequences of the internal transcribed spacer (ITS) region, RNA polymerase II largest subunit (RPB1) and translation elongation factor 1-alpha (TEF1α). The descriptions of the fungi include morphological characteristics and host associations. Magnaporthiopsis dharug was isolated from diseased roots of Cynodon dactylon (couch grass, Bermudagrass), Festuca rubra ssp. commutata (Chewing’s fescue) and Poa annua (winter grass); M. gadigal from diseased roots of Pennisetum clandestinum (kikuyu grass); M. gumbaynggirr from diseased roots of C. dactylon; and M. yugambeh from diseased roots of P. annua.
Keywords: ectotrophic root-infecting fungi – phylogeny – plant pathogens – Poaceae – taxonomy
Authors: Gomdola D, Bhunjun CS, Hyde KD, Jeewon R, Pem D, Jayawardena RS
Recieved: 27 April 2022, Accepted: 28 June 2022, Published: 06 July 2022
Plant pathogenic fungi and fungus-like taxa (oomycetes) form part of the ecological makeup of healthy natural forest ecosystems. Some help to eliminate unhealthy trees, while others are essential for the conservation of plant species diversity, particularly soil-borne pathogens. However, many fungal pathogens also have devastating effects on forest ecosystems. Disease impacts are more profound when pathogens newly emerge and these can even wipe out an entire tree population. These organisms have developed a plethora of strategies to colonize and infect plants and there are several factors causing pathogens to emerge. Therefore, to prevent emerging diseases, a thorough understanding of the factors causing them is necessary. It is also important to have a comprehensive understanding of the mechanisms of disease development and propagation to design effective control measures. In this review, we describe the phenomenon of emerging and re-emerging pathogens by exemplifying ten important recently emerged forest pathogenic fungi and fungus-like taxa, namely, Ophiostoma novo-ulmi, Ceratocystis fimbriata, Fusarium circinatum, Hymenoscyphus fraxineus, Phyllosticta citricarpa, Neonectria faginata, Sphaerulina musiva, Phytophthora pluvialis, P. agathidicida, and Melampsora × columbiana. They have been listed in order of the most cited to the least cited species based on data obtained from the Web of Science. We provide a review for each species to document its emergence and its negative impact on the host(s). We also revise their taxonomic placement, host and country details, and provide updated phylogenetic trees for each genus. The number of accepted species based on molecular data is also provided.
Keywords: Diseases – Fungus-like pathogens – Phylogeny – Phytopathogenic fungi
7. Cronartium rust (Pucciniales, Cronartiaceae): species delineation, diversity and host alternation
Authors: Zhao P, Liu F, Huang JE, Zhou X, Duan WJ, Cai L
Recieved: 20 February 2022, Accepted: 08 July 2022, Published: 02 August 2022
Cronartium species (Basidiomycota, Pucciniales, Melampsorineae) infect two or five-needle pines, resulting in considerable economic losses and ecological damage. Many species are considered of quarantine importance, however, precise identification is challenging due to the poorly resolved generic boundaries of Cronartium and other members in Melampsorineae, as well as species limits within the genus Cronartium. In this study, species delimitation was carried out based on morphological examination and multi-locus phylogenetic assessment using sequences of rDNA SSU-ITS-LSU regions and CO3 gene. Twenty-six species including seven new species (C. castaneae, C. mongolicum, C. murrayanae, C. myricae, C. peridiatum, C. qinlingense, C. ribis-taedae), and one new combination (C. floridanum) are recognized. Cronartium arizonicum, C. comandrae, C. comptoniae, C. occidentale, and C. pyriforme are epitypified to stabilize the use of names for taxonomy and quarantine significance. In addition, 18 species were revealed for their previously unknown life cycles.
Keywords: pine blister rust – Pucciniales – quarantine pests – species boundary – taxonomy
8. The importance of culture-based techniques in the genomic era for assessing the taxonomy and diversity of soil fungi
Authors: Yasanthika WAE, Wanasinghe DN, Mortimer PE, Monkai J, Farias ARG
Recieved: 22 May 2022, Accepted: 19 August 2022, Published: 06 September 2022
Fungi are a diverse and highly abundant group of organisms found in soils worldwide. Understanding fungi is essential as they are key drivers of below-ground ecosystem functions. Taxonomy is a fundamental discipline, acting as the initial step toward biodiversity, ecology, and biotechnology studies. Both culture-dependent and -independent methods are employed in the taxonomic investigations of soil-dwelling taxa. High-throughput sequencing (HTS) is a genomic-based method widely applied in global studies that has revealed numerous unculturable soil taxa. However, this method is limited by its inability to link physical specimens to species identification. Culturing methods result in specimens that can be used to obtain genetic sequences and morphological data in applied studies. Thus, combining both methods is an important trend in taxonomic studies. This review discusses how culturing is important for soil fungal discovery and describes the main culturing methods. It also briefly addresses the role of HTS in taxonomy and its drawbacks, and the potential to combine both culture-dependent and -independent methods to gain better insights into soil fungi.
Keywords: Culturing methods – fungal taxonomy – fungi – high throughput sequencing – soil
Authors: Norphanphoun C, Gentekaki E, Hongsanan S, Jayawardena R, Senanayake IC, Manawasinghe IS, Abeywickrama PD, Bhunjun CS, Hyde KD
Recieved: 20 May 2022, Accepted: 15 August 2022, Published: 06 September 2022
Diaporthe species have a worldwide distribution and are associated with economically important hosts as pathogens, endophytes, and saprobes. Taxonomic identification of Diaporthe species is challenging due to overlapping morphological traits and host associations. Herein, we have assembled a comprehensive dataset and inferred a phylogenetic tree of Diaporthaceae using combined sequence data of ITS, ef1α, β-tubulin, cal and his3. Diaporthe is not monophyletic and segregates into several phylogenetically distinct clades. We introduce 13 species complexes of Diaporthe to aid the identification of species in the genus and to make communication easier. Nine species were treated as singletons apart from the major clades. Two taxa of Diaporthaceae, Ophiodiaporthe cyatheae and Chiangraiomyces bauhiniae, are synonymized under D. cyatheae (≡ O. cyatheae) and D. pseudobauhiniae (≡ C. bauhiniae), respectively based on phylogenetic analyses and morphological characters. The phylogenetic relationships of Diaporthaceae are reappraised, and suggestions are given for future work.
Keywords: Diaporthaceae – Morphology – Phylogeny – Plant disease – Species complexes
Authors: Marena GD, Carvalho GC, Monazzi LCS, Maschio-Lima T, De Almeida MTG, Da Silva JLM, Fortunato GC, Araújo VHS, Venancio DCV, Chang MR, Chorilli M
Recieved: 30 June 2022, Accepted: 27 September 2022, Published: 18 October 2022
Candida auris, a new emerging yeast that was isolated for the first time in 2009 in the ear canal of a Japanese patient, are increasingly been associated with outbreaks, threatening the whole world. As a highly lethal and contagious microorganism, C. auris can be considered a threat to public health, mainly due to the high death rate in hospital environments and ability to resist to the main first-line antifungal agents (echinocandins, azoles and polyenes), which limits its treatment and infection control. As it is a microorganism with little scientific and clinical knowledge, controlling its infection is still a great challenge. Faced with the worrying situation, this review presents important information concerning the morphology and biology of C. auris, as well as resistance mechanisms, updated epidemiology, virulence, immune response escape mechanisms, pathogenesis and processor involved in the pathogenesis mechanism, clinical manifestations, laboratory diagnosis and sample collection methods, molecular diagnostics, treatment of infection (main drugs used and future therapies) and prophylactic methods, with the objective not only of clarifying doubts of the scientific and medical population, but also of helping to control new outbreaks of C. auris worldwide.
Keywords: antifungal therapy – candidemia – emerging fungus – infectious diseases – resistance
Authors: Liu SL, He SH, Wang XW, May TW, He G, Chen SL, Zhou LW
Recieved: 29 June 2022, Accepted: 04 October 2022, Published: 04 November 2022
Trechisporales, typified by Trechispora and equivalent to Hydnodontales, is a recently introduced order within Agaricomycetes. This order only comprises one family Hydnodontaceae and 16 independent genera, but the relationships among these genera are not fully clarified. Here, via a wider sampling especially from Asia Pacific, careful morphological examinations and comprehensive multilocus-based phylogenetic analyses, the classification of Trechisporales is emended. Sertulicium and Sistotremastrum are segregated from Trechisporales, and placed in the new family Sistotremastraceae within the new order Sistotremastrales. A new genus Allotrechispora segregated from Trechispora is introduced within Hydnodontaceae, Trechisporales, and Boidinella, Litschauerella and Sphaerobasidium are excluded from Trechisporales. Brief summaries to genera accepted in Sistotremastrales and Trechisporales, and a key to all 12 genera accepted in Trechisporales are provided. In addition, Tomentella and Murrilloporus, potential synonyms of Trechispora, are excluded from Trechisporales and of uncertain position, respectively. At the species level, 19 new species are described with one from Allotrechispora, one from Fibrodontia, one from Subulicystidium and 16 from Trechispora, and seven new combinations are proposed with two for Allotrechispora and five for Trechispora. In addition, Trechispora yunnanensis is excluded from Trechispora. A key to all 87 species accepted in Trechispora is provided. In conclusion, an emended classification of Trechisporales within Agaricomycetes is constructed, which will help to further clarify species diversity and explore trait evolution within Trechisporales.
Keywords: 29 new taxa – Hydnodontaceae – Hydnodontales – macrofungi – Sistotremastraceae – Taxonomy
12. Morphology, phylogeny, host association and geography of fungi associated with plants of Annonaceae, Apocynaceae and Magnoliaceae
Authors: de Silva NI, Hyde KD, Lumyong S, Phillips AJL, Bhat DJ, Maharachchikumbura SSN, Thambugala KM, Tennakoon DS, Suwannarach N, Karunarathna SC
Recieved: 30 May 2022, Accepted: 17 October 2022, Published: 18 November 2022
This paper elaborates the advances made in the study of morphology, phylogeny, host association and geography of novel and interesting fungi in China and Thailand. We documented saprobic microfungi from dead twigs of different plant hosts from Annonaceae (Anomianthus dulcis, Cananga odorata and Desmos chinensis), Apocynaceae (Alstonia scholaris) and Magnoliaceae (Magnolia champaca, M. garrettii and M. liliifera) in Yunnan Province, China and northern Thailand. Descriptions, illustrations and discussions on the familial placement of taxa are given based on phylogeny and morphological data. One new genus Muriformispora in Neohendersoniaceae (Dothideomycetes) and twelve new species, Acrocalymma magnoliae, Diaporthe chiangmaiensis, Fuscostagonospora magnoliae, Gyrothrix anomianthi, Hermatomyces anomianthi, Muriformispora magnoliae, Neomassaria alstoniae, N. thailandica, Neoroussoella thailandica, Peroneutypa anomianthi, Pseudochaetosphaeronema magnoliae and Torula canangae are introduced. An amended account of Hermatomyces is provided to include the sexual morph of the genus. New host records or new country records are provided for Acrocalymma pterocarpi, A. walkeri, Amphisphaeria micheliae, Angustimassarina populi, Aurantiascoma minimum, Diaporthe musigena, D. pterocarpi, Eutypella citricola, Gyrothrix oleae, Hermatomyces sphaericus, Lasiodiplodia crassispora, L. exigua, L. ponkanicola, L. pseudotheobromae, L. thailandica, L. theobromae, Magnibotryascoma kunmingense, Memnoniella ellipsoidea, Melomastia clematidis, M. thamplaensis, Neoroussoella entadae, Nectria pseudotrichia, Nigrograna thymi, Periconia byssoides, P. pseudobyssoides, Phaeosphaeria sinensis, Pseudopithomyces chartarum, Pseudofusicoccum adansoniae, Rhytidhysteron neorufulum, Setoapiospora thailandica and Xenoroussoella triseptata.
Keywords: 12 new species – Ascomycota – Dothideomycetes – Multi-locus phylogeny – Sordariomycetes – Systematics