Volume 14 - 2023 - Issue 1

1. Endophytic fungi in green manure crops; friends or foe?

Authors: Abeywickrama PD, Qian N, Jayawardena RS, Li Y, Zhang W, Guo K, Zhang L, Zhang G, Yan J, Li X, Guo Z, Hyde KD, Peng Y, Zhao W

Recieved: 03 April 2022, Accepted: 10 December 2022, Published: 13 January 2023

Astragalus sinicus and Vicia villosa; are frequently applied green manure plants used in China. However, there is poor knowledge of the fungal endophytic community and the mycobiome of green manure crops. Field surveys were conducted during 2017–2019 in four provinces in China. Asymptomatic plant parts were collected. Using a culture-dependent method, 517 fungal isolates were obtained from Astragalus sinicus and Vicia villosa. These isolates were further identified using a combination of morphological and multi-loci phylogenetic analyses and were differentiated into 30 species in 15 genera in ten families belonging to only Ascomycota. Most isolated strains belonged to Sordariomycetes. The most dominant genus was Fusarium, with 381 isolates from both crops, while all other taxa were isolated less than 40 times. The similarity search on the Fusarium MLST database showed the 370 strains belonged to seven Fusarium complexes and one subclade. Eleven strains could not be assigned to any complex. The remaining 136 isolates were identified and assigned to 23 known and seven novel species. A total of 178 Operational Taxonomic Units (OTUs) were obtained from Illumina analysis and mainly classified into five phyla (Ascomycota, Basidiomycota, Chytridiomycota, Cryptomycota, and Mucoromycota). Overall OTUs were further assigned to 21 classes, 48 orders, 66 families, and 74 genera. Based on overall OTUs, the most abundant species was Alternaria alternata, which was also isolated from the culture-dependent method. Most species and genera recorded from the High Throughput Sequencing (HTS) approach were not obtained in the culture-dependent method (Boeremia, Cladosporium, Filobasidium, Magnoporthe, Mucor, Rhizoctonia, Sporidiobolus). Functional annotation reveals that all Ascomycetes genera obtained in both approaches comprised several plant pathogenic species. Potential beneficial and/or biocontrol strains were also identified. The common green manure crops used in China harbors a hidden, underexplored mycobiome which may comprise potential for application. These results will increase awareness of green manure practices. Precautions need to be in place when incorporating green manure crops in the soil, as these could facilitate inoculum sources for the next disease cycle of the main crop.

Keywords: 7 new taxa – Checklist – Culture dependent – Cover crops – High-throughput sequencing – Taxonomy


2. Morphology and multigene phylogeny reveal ten novel taxa in Ascomycota from terrestrial palm substrates (Arecaceae) in Thailand

Authors: Konta S, Tibpromma S, Karunarathna SC, Samarakoon MC, Steven LS, Mapook A, Boonmee S, Senwanna C, Balasuriya A, Eungwanichayapant PD, Hyde KD

Recieved: 11 August 2022, Accepted: 28 November 2022, Published: 13 January 2023

Arecaceae is one of the important plant families in Thailand, and several of its representative genera are used for food, cosmetics, and energy sources. During the past eight years (2014 to 2022), more than 50 new taxa associated with terrestrial palm substrates have been reported in Thailand. The present study continued the survey of fungi associated with terrestrial palms in Thailand and based on both morphological characteristics and phylogenetic analyses of combined sequence data, fungal taxa belonging to the orders Amphisphaeriales, Diaporthales, Distoseptisporales, Glomerellales, Pleosporales, and Xylariales were identified. A new genus Triseptatospora and nine new species viz., Acremoniisimulans cocois, Acrocalymma arengae, Bartalinia adonidiae, Cytospora calamicola, Distoseptispora licualae, Neopestalotiopsis elaeidis, Pteridiospora arengae, Triseptatospora calami, and Xenoanthostomella calami are described and introduced here. Morphological illustrations, descriptions, and phylogenetic trees which indicate the placement of the new taxa are provided.

Keywords: 10 new taxa – Dothideomycetes – palm fungi – phylogeny – saprobe – Sordariomycetes – taxonomy – Thai fungi


3. Finding correct names for economically important chanterelles (Cantharellus, Hydnaceae, Cantharellales) in southwestern China: a plea for third party annotation of sequences in GenBank

Authors: Wang XH, Hofstetter V, Cao SQ, Liu PG, Buyck B

Recieved: 23 November 2022, Accepted: 10 February 2023, Published: 29 March 2023

One might think that the use of DNA sequences in species recognition will soon have solved all taxonomic confusions. This scenario, however, is not what happened in the taxonomy of chanterelles in the eastern and southern parts of Asia. To solve the name problems associated with chanterelles in southwestern China, we sequenced the loci ITS, LSU, rpb2 and(or) tef1 of 68 Cantharellus specimens collected in China and South Korea, including the holotypes of C. albovenosus, C. tuberculosporus, C. versicolor and C. zangii. We used these sequences to link species described from China, India, Japan and South Korea. We took an in-depth look at available sequence data for Indian Cantharellus that have caused a lot of taxonomic confusions. We found most DNA data related with Asian chanterelles have flaws concerning either wrong sequences, unreliable base pairs, or confusing metadata. These problems, together with over-interpretation of genetic and morphological variation, are responsible for many synonyms. Taxonomically, we reached the following conclusions: C. yunnanensis is a Craterellus; C. tuberculosporus is a very rare Himalayan species close to C. cibarius; C. versicolor is the most common subalpine golden chanterelle in the Himalayas; the earliest available name for the bulk of marketed, yellow, medium-sized chanterelles in temperate and subtropical China is C. applanatus, not C. yunnanensis; Cantharellus anzutake, C. himalayensis and C. natarajanii are all synonyms of C. applanatus; C. sinominor and C. subminor are later synonyms of the Indian C. elongatipes; C. sikkimensis is conspecific with C. zangii; C. albovenosus is merely a white-gilled form of C. phloginus. Allowing third party annotations or comments directly in the nucleotide database of NCBI would constitute a much more efficient way to signal errors or omissions concerning both sequences and their associated metadata deposited in GenBank.

Keywords: Craterellus – holotype – INDELs – ITS – morphology – species recognition


4. Freshwater fungal biology

Authors: Calabon MS, Hyde KD, Jones EBG, Bao DF, Bhunjun CS, Phukhamsakda C, Shen HW, Gentekaki E, Al Sharie AH, Barros J, Chandrasiri KSU, Hu DM, Hurdeal VG, Rossi W, Valle LG, Zhang H, Figueroa M, Raja HA, Seena S, Song HY, Dong W, El-Elimat T, Leonardi M, Li Y, Li YJ, Luo ZL, Ritter CD, Strongman DB, Wei MJ, Balasuriya A

Recieved: 05 July 2022, Accepted: 31 January 2023, Published: 04 April 2023

Research into freshwater fungi has generated a wealth of information over the past decades with various published articles, i.e., reviews, books, and monographs. With the advancement of methodologies used in freshwater fungal research, and numerous mycologists working on this ecological group, our knowledge progress and understanding of freshwater fungi, including novel discoveries and new insights in the ecology of freshwater fungi, has advanced. With this enormous progress, it is timely that an updated account of freshwater fungi be compiled in one volume. Thus, this account is published to give a comprehensive overview of the different facets of freshwater fungal biology. It includes an updated classification scheme based on the latest taxonomic and phylogenetic analysis of freshwater fungal taxa, including their evolutionary history. The biology, diversity, and geographical distribution of higher and basal freshwater fungi are also discussed in the entries. A section on dispersal and adaptation of filamentous freshwater fungi is included in the present work. The ecological importance and role of fungi in the breakdown of wood in freshwater habitats, including their physiology, are discussed in detail. The biotechnological potential of freshwater fungi as producers of bioactive metabolites are reviewed, with methodologies in antimicrobial drug discovery. The present volume also provides an overview of different high throughput sequencing (HTS) platforms for freshwater fungal research highlighting their advantages and challenges, including recent studies of HTS in identification and quantification of fungal communities in freshwater habitats. The present volume also identifies the knowledge gaps and direction of future research in freshwater fungi.

Keywords: Aquatic mycology – biology of microfungi – ecosystem functions – fungal classification – fungal ecology – taxonomy – systematics


5. Phylogenomics and diversification of Sordariomycetes

Authors: Chen YP, Su PW, Hyde KD, Maharachchikumbura SSN

Recieved: 13 February 2023, Accepted: 22 March 2023, Published: 19 April 2023

The Sordariomycetes is a specious, morphologically diverse, and widely distributed class of the phylum Ascomycota that forms a well-supported clade diverged from Leotiomycetes. Aside from their ecological significance as plant and human pathogens, saprobes, endophytes, and fungicolous taxa, species of Sordariomycetes produces a wide range of chemically novel and diverse metabolites used in important fields. Recent phylogenetic analyses derived from a small number of genes have considerably increased our understanding of the family, order, and subclass relationships within Sordariomycetes, but several important groups have not been resolved well. In addition, there are various paraphyletic or polyphyletic groups. Moreover, the criteria used to establish higher ranks remain highly variable across different studies. Therefore, the taxonomy of Sordariomycetes is in constant flux, remains poorly understood, and is subject to much controversy. Here, for the first time, we have assembled a phylogenetic dataset containing 638 genomes representing the 156 genera, 50 families, and 17 orders and 5 subclasses of Sordariomycetes. This data set is based on 1124 genes and results in a well-resolved phylogenomic tree. We further constructed an evolutionary timeline of Sordariomycetes diversification based on the genomic data sets. Our divergence time estimate results are inconsistent with previous studies, suggesting estimates of node ages are less precise and varied. Based on these results, we discuss the higher ranks of Sordariomycetes and empirically propose an unprecedented taxonomic framework for the class.

Keywords: Ascomycota – divergence time – evolution – genomes – tree of life


6. An updated taxonomic framework of Hymenochaetales (Agaricomycetes, Basidiomycota)

Authors: Wang XW, Liu SL, Zhou LW

Recieved: 08 November 2022, Accepted: 01 March 2023, Published: 20 April 2023

Hymenochaetales is one of the fungal orders being mainly composed of wood-inhabiting macrofungi within Agaricomycetes, Basidiomycota. While the species diversity has been well explored, the classification of Hymenochaetales at the family level is still contrary and not fully resolved. In this study, the taxonomic framework of Hymenochaetales is updated with the help of phylogenetic and molecular clock analyses based on six to seven gene regions. Compared with previous papers, the concepts of Hyphodontiaceae and Schizoporaceae are unchanged, while six additional families are emended: the circumscription of the monotypic family Chaetoporellaceae is enlarged by including Echinoporia in this family; a larger concept of Hymenochaetaceae is formally proposed to accommodate members originally in the families Hymenochaetaceae, Neoantrodiellaceae and Nigrofomitaceae, and the genera Basidioradulum and Trichaptum; Repetobasidiaceae and Tubulicrinaceae are reinstated as two monotypic families; the circumscription of Rickenellaceae is reduced to be a monotypic family; and the family name Rigidoporaceae is resurrected to replace its later synonym Oxyporaceae. Besides these eight previously known families, Odonticiaceae is newly erected for Leifia and Odonticium, while five additional monotypic families are also newly erected to make as many genera as possible accommodated at the family level. In addition, Botryodontia, Neoantrodiella and Skvortzoviella are considered to be later synonyms of Rigidoporus, Cyanotrama and Schizocorticium, respectively, and species sampled from these three genera in the current phylogenetic analyses are accordingly transferred. Eventually, a total of 14 families, viz. Chaetoporellaceae, Hymenochaetaceae, Hyphodontiaceae, Odonticiaceae, Peniophorellaceae, Repetobasidiaceae, Resiniciaceae, Rickenellaceae, Rigidoporaceae, Schizocorticiaceae, Schizoporaceae, Sideraceae, Skvortzoviaceae and Tubulicrinaceae accommodating 64 genera, and 19 independent genera are accepted in Hymenochaetales. In conclusion, a more natural taxonomic system of Hymenochaetales is achieved, which is a crucial basis for further exploring species diversity, resource utilization and trait evolution of this fungal order.

Keywords: 11 new taxa – Hymenochaetaceae – molecular clock – six new families – wood-inhabiting fungi


About Mycosphere

Mycosphere publishes reviews, research articles, methodology papers, taxonomic works such as monographs, which are relevant to fungal biology, including lichens. The official journal language is English.


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    Innovative Institute for Plant Health ,
    Zhongkai University of Agriculture and Engineering,
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Zhongkai University of Agriculture and Engineering