Recent Papers

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

7. Culturable mycota on bats in central and southern Yunnan Province, China

Authors: Liu XF, Tibpromma S, Hughes AC, Chethana KWT, Wijayawardene NN, Dai DQ, Du TY, Elgorban AM, Stephenson SL, Suwannarach N, Xu JC, Lu L, Xu RF, Maharachchikumbura SSN, Zhao CL, Bhat DJ, Sun YM, Karunarathna SC, Mortimer PE

Recieved: 10 December 2022, Accepted: 12 May 2023, Published: 07 June 2023

Bats represent the second largest mammal group, with over 1400 known species dispersed across six continents. Bats are unique in many ways. Notably, their incredible longevity, with a life span of up to ten times longer than what might be expected from their body size and a unique ability to tolerate viruses without displaying any symptoms, means they provide an area of particular importance from a disease risk perspective. In addition, the warm, humid environments in which bats occur provide ideal habitats for fungi to grow, and the bats potentially carry various pathogens that can threaten plants, animals, and humans. Whilst the role of bats as reservoir of viruses is well known, their role as a host to various fungi has been largely neglected. To explore this gap, we investigated the culturable mycota isolated from bats in the diverse Yunnan Province, China. In total, 164 samples from 104 bats were collected, and 164 fungal strains, representing 25 species, were isolated using the dilution plate method. The majority of these species were discovered for the first time from bats, and 14 new species and 11 new records are described in this paper. Some species were previously known from other environments, as pathogens of plants, animals, or humans. Based on morphology and multigene phylogeny, we conclude that bats host a high fungal diversity, including a number of previously unknown species. Novel species described in this paper include Amphichorda yunnanensis, Apiospora xishuangbannaensis, Clonostachys rhinolophicola, Fusarium hipposidericola, F. menglaense, F. rhinolophicola, F. yunnanense, F. xishuangbannaense, Neopestalotiopsis xishuangbannaensis, Phialemoniopsis hipposidericola, Ph. xishuangbannaensis, Trichoderma hipposidericola, T. rhinolophicola and T. xishuangbannaense.

Keywords: 11 new records – 14 new species –Ascomycota – Bat fungi – Caves – Microfungi – Morphology – Phylogeny – Plant pathogens

8. Mycosphere notes 387–412 – novel species of fungal taxa from around the world

Authors: Hyde KD, Norphanphoun C, Ma J, Yang HD, Zhang JY, Du TY, Gao Y, Gomes de Farias AR, He SC, He YK, Li CJY, Li JY, Liu XF, Lu L, Su HL, Tang X, Tian XG, Wang SY, Wei DP, Xu RF, Xu RJ, Yang YY, Zhang F, Zhang Q, Bahkali AH, Boonmee S, Chethana KWT, Jayawardena RS, Lu YZ, Karunarathna SC, Tibpromma S, Wang Y, Zhao Q

Recieved: 22 March 2023, Accepted: 23 May 2023, Published: 08 June 2023

This is the eighth of the series Mycosphere notes wherein we provide descriptions and notes on various fungal genera. In this compilation, we introduce Neophaeosphaeriopsis (Phaeosphaeriaceae) as a new genus, and 25 new species. The new species are Acrodictys bambusae (Acrodictyaceae), Acrogenospora guizhouensis (Acrogenosporaceae), Aureobasidium xishuangbannaensis (Saccotheciaceae), Conlarium guizhouense (Conlariaceae), Dactylellina dulongensis (Orbiliaceae), Diaporthe araliae-chinensis (Diaporthaceae), Dibaeis jingdongensis (Icmadophilaceae), Dictyosporella yunnanensis (Annulatascaceae), Distoseptispora phragmiticola (Distoseptisporaceae), Fusarium camelliae (Nectriaceae), Helminthosporium lignicolum, Helminthosporium shangrilaense (Massarinaceae), Kirschsteiniothelia puerensis (Kirschsteiniotheliaceae), Melomastia septata (Pleurotremataceae), Montagnula aquilariae (Didymosphaeriaceae), Neophaeosphaeriopsis triseptatispora (Phaeosphaeriaceae), Neoroussoella chiangmaiensis (Roussoellaceae), Nigrograna heveae (Nigrogranaceae), Pestalotiopsis ficicrescens (Sporocadaceae), Pleurothecium hainanense (Pleurotheciaceae), Rhodoveronaea hainanensis (Sordariomycetidae), Roussoella chinensis (Roussoellaceae), Torula calceiformis (Torulaceae), Trichoglossum ailaoense (Geoglossaceae) and Zeloasperisporium spartii (Zeloasperisporiaceae). We provide new sequence data for 25 species and updated phylogenetic trees for 24 genera (Acrodictys, Acrogenospora, Aureobasidium, Conlarium, Dactylellina, Diaporthe, Dibaeis, Dictyosporella, Distoseptispora, Fusarium, Helminthosporium, Kirschsteiniothelia, Melomastia, Montagnula, Neophaeosphaeriopsis, Neoroussoella, Nigrograna, Pestalotiopsis, Pleurothecium, Rhodoveronaea, Roussoella, Torula, Trichoglossum, Zeloasperisporium).

Keywords: 26 new taxa – Ascomycota – Molecular phylogeny – New genus – New species – Phylogenetic – Taxonomy

9. New taxa of Boletaceae from China

Authors: Wu G, Li H-J, Horak E, Wu K, Li G-M, Yang Z-L

Recieved: 13 January 2023, Accepted: 10 May 2023, Published: 12 June 2023

China possesses a remarkably rich fungal diversity, particularly among boletes, which can be attributed to its heterogeneous plant communities and varied topography and geography. Despite significant taxonomic efforts, the diversity of bolete species remains inadequately characterized in China, and it is expected that many unexplored taxa are yet to be discovered. Through a combination of morphological observations and molecular phylogenetic analyses, this work identified 12 new taxa of Boletaceae in China, including two new genera (Acyanoboletus and Hongoboletus), nine new species (Acyanoboletus controversus, Acyanoboletus dissimilis, Cyanoboletus fagaceophilus, Neoboletus brunneorubrocarpus, Rubroboletus flavus, Rubroboletus serpentiformis, Suillellus flaviporus, Suillellus pinophilus, Suillellus yunnanensis) and one new combination (Hongoboletus ventricosus). Detailed illustrations and comparisons with other related species were provided to aid in identification. This study can significantly contribute to our understanding of bolete species diversity in China and allied regions.

Keywords: 12 new taxa – bolete – East Asia – molecular phylogeny – taxonomy

10. New insights into the classification and evolution of Favolaschia (Agaricales, Basidiomycota) and its potential distribution, with descriptions of eight new species

Authors: Zhang QY, Liu HG, Papp V, Zhou M, Dai YC, Yuan Y

Recieved: 13 January 2023, Accepted: 26 May 2023, Published: 20 June 2023

Favolaschia is a genus of poroid fungi in the order Agaricales with a worldwide distribution. Most studies of Favolaschia so far have characterized samples from South America and little information is available on samples from other areas. In this study, species diversity, phylogenetic relationships, divergence time, potential geographic distribution, and the environmental factors that determine the distribution of Favolaschia are investigated using a large number of samples covering a wide geographic range in China. Additionally, eight species, viz., Favolaschia bannaensis, F. crassipora, F. flabelliformis, F. rigida, F. semicircularis, F. subpustulosa, F. tenuissima, and F. tephroleuca, are described as new species based on morphology and molecular phylogenetic analyses inferred from a multi-gene dataset (ITS + nLSU + mtSSU + nuSSU + tef1). Morphological descriptions, field photographs, and an identification key are provided. Molecular clock analyses suggest that the common ancestor of Favolaschia originated in East Asia, and South and Central America and emerged in the Paleogene period with full support and a mean crown age of 32.0 Mya (95% highest posterior density of 24.9–41.7 Mya), with most species occurring in the Neogene period. The maximum entropy model (Maxent) is applied here to map the potential distribution of Favolaschia in the present and in the future, i.e., the 2050s, under four different climate change scenarios in China. The resulting model shows that the precipitation of the warmest quarter has the most important impact on the potential distribution of Favolaschia species. The suitability distribution areas of Favolaschia species markedly change in the 2050s under different climate change scenarios. Compared to current conditions, the extent of suitable areas for Favolaschia species in China are expected to increase in the future with lower greenhouse gas emissions.

Keywords: 8 new taxa – Evolution – Maxent – Phylogeny – Taxonomy – Wood-decaying fungi

11. Updated systematics of Trichaptum s.l. (Hymenochaetales, Basidiomycota)

Authors: Zhou M, Dai YC, Vlasák J, Liu HG, Yuan Y

Recieved: 03 March 2023, Accepted: 30 May 2023, Published: 07 August 2023

Trichaptum sensu lato is a widespread wood-decay fungal group important for the transfer of energy and recycling of nutrients in forest ecosystems. The taxonomy of Trichaptum s.l. was previously mostly based on morphology, and phylogenetic relationships among taxa of Trichaptum s.l. are poorly known. The systematics of Trichaptum s.l. was revised using morphology, and molecular study which analysed the combined datasets of ITS+nLSU+mt-SSU+nuc-SSU+TEF1 from 256 samples. Maximum Likelihood (ML) and Bayesian Inference (BI) were employed to perform phylogenetic analyses of these datasets. The traditional Trichaptum s.l. is polyphyletic. Two main clades, distantly related, are recognized and two new families, Hirschioporaceae and Trichaptaceae, are proposed to represent these two clades. All analyzed samples formed seven independent clades representing seven genera, among them five newly proposed. 38 independent lineages are nested in the seven genera, and 10 of them are described as new species. In addition, a total of 49 taxa are identified by phylogenetic analyses and morphological examination of 625 specimens from 19 countries, and 28 new combinations are proposed. To support our results, divergence time estimation and historical biogeography of Trichaptum s.l. are analyzed. Photos and illustrations for ten new species are presented, and a full description for each new species is given. This study recognizes 49 taxa in seven genera belonging to Hymenochaetales and provides a modern global treatment of Trichaptum s.l. Keys to families and genera are provided, and identification keys to accepted species worldwide are given.

Keywords: 38 new taxa – divergence time estimation – phylogeny – polypore – taxonomy

12. Annotated notes on Diaporthe species

Authors: Hongsanan S, Norphanphoun C, Senanayake IC, Jayawardena RS, Manawasinghe IS, Abeywickrama PD, Khuna S, Suwannarach N, Senwanna C, Monkai J, Hyde KD, Gentekaki E, Bhunjun CS

Recieved: 02 June 2023, Accepted: 04 July 2023, Published: 07 August 2023

Diaporthe is a large and taxonomically complex genus, with over a thousand epithets listed in Index Fungorum. The placement of many Diaporthe species remains confusing, and there is a lack of consensus on their taxonomy and phylogeny. In this study, we provide annotated notes on accepted or presumed species of Diaporthe up to 2023. Our notes cover 832 species and include information on their morphology, ecology, geographic distribution, molecular data, and pathogenicity, where available. Diaporthe cyatheae comb. nov., D. pseudobauhiniae nom. nov., D. xishuangbannaensis nom. nov., D. krabiensis sp. nov., and D. pseudobiguttulata nom. nov. are introduced in this paper. In addition, we list 331 species that were previously classified as Diaporthe but are no longer accepted as members of the genus. Our comprehensive review of Diaporthe species provides a resource for researchers and taxonomists, enabling accurate identification and classification, and enhancing our understanding ecological roles of these fungi.

Keywords: Diaporthaceae – Morphology – Plant disease – Species complexes

13. The relevance of fungi in astrobiology research – Astromycology

Authors: Simões MF, Cortesão M, Azua-Bustos A, Bai F-Y, Canini F, Casadevall A, Cassaro A, Cordero RJB, Fairén AG, González-Silva C, Gunde-Cimerman N, Koch S, Liu X-Z, Onofri S, Pacelli C, Selbmann L, Tesei D, Waghmode A, Wang T, Zucconi L, Antunes A

Recieved: 27 April 2023, Accepted: 07 July 2023, Published: 07 August 2023

Since the very first steps of space exploration, fungi have been recorded as contaminants, hitchhikers, or as part of missions’ crews and payloads. Because fungi can cause human disease and are highly active decomposers, their presence in a space-linked context has been a source of major concern given their possible detrimental effects on crews and space structures. However, fungi can also be beneficial and be used for many space applications. The exact effects on fungi are not always clear as they possess high adaptability and plasticity, and their phenotypes and genotypes can undergo several changes under the extreme conditions found in space, thus leading to different results than those we would have on Earth. Understanding and analysing these aspects is the subject of astromycology, a research field within astrobiology.

The impending situation of a resurgent space race is expected to boost astromycology’s visibility and importance. However, researchers lack both a framework and a solid base of knowledge from which to contextualise their work. This critical review addresses this gap by conceptualising the field of astromycology, covering key research and current questions pertaining to the field, and providing a relevant research instrument for future work.

Keywords: Fungi – Mycology – Planetary Protection – Space Exploration – Space Microbiology

14. Lasiodiplodia: Generic revision by providing molecular markers, geographical distribution and haplotype diversity

Authors: Rathnayaka AR, Chethana KWT, Manawasinghe IS, Wijesinghe SN, de Silva NI, Tennakoon DS, Phillips AJL, Liu JK, Jones EBG, Wang Y, Hyde KD

Recieved: 03 April 2023, Accepted: 08 June 2023, Published: 06 September 2023

Lasiodiplodia (Botryosphaeriaceae, Botryosphaeriales) has a global distribution and occurs on a wide range of monocotyledonous, dicotyledonous, and gymnospermous hosts. Most Lasiodiplodia species are pathogens that cause various diseases, such as stem cankers, stem and branch gummosis, shoot blight, and fruit rot. In addition, Lasiodiplodia species occur as endophytes and saprobes. This study presents one of the most reliable molecular markers for Lasiodiplodia. The combination of four loci, the internal transcribed spacer region (ITS), the partial translation elongation factor 1-α gene (tef1-α), beta-tubulin (tub2), and RNA polymerase II second largest subunit (rpb2), provided a more reliable resolution for this genus at the species level. Geographical studies showed that Lasiodiplodia species are distributed in tropical and temperate regions, but not in the polar regions. Among its species, L. theobromae has a worldwide distribution on a wide range of hosts, including economically important crops. Combining the morphology and molecular phylogeny is necessary for accurate taxonomic identification of Lasiodiplodia species and is being used in this study. Multigene phylogenetic analyses were performed based on maximum likelihood and Bayesian inference analyses using combined ITS, tef1-α, tub2, and rpb2 sequence data. In addition, the main morphological characteristics of holotype specimens of Lasiodiplodia species are provided. The current study introduced 25 new host and geographical records of saprobic Lasiodiplodia species from Taiwan province, China and Thailand. Based on the herbarium study, two Lasiodiplodia species, L. avicenniarum and L. krabiensis are synonymized under L. brasiliensis. Our analyses revelaed that Lasiodiplodia theobromae as the most common species in this genus, which occurs in a wide range of hosts in tropical and subtropical regions. The present study has led to the expansion of the taxonomic framework of Lasiodiplodia by revealing new host and geographical records. Furthermore, the haplotype networks generated using ITS, tef1-α, tub2, and rpb2 sequence data for 520 isolates of L. theobromae from 44 host families and 35 countries display that none of the L. theobromae isolates grouped according to their host family or country, suggesting that L. theobromae is a less genetically diverse, globally distributed species.

Keywords: Botryosphaeriaceae – Lasiodiplodia theobromae – new geographical records – new host records

15. Diversity of fungal communities associated with grapevine trunk diseases in China

Authors: Zhou YY, Zhang W, Wu LN, Zhang J, Tan HY, Chethana KWT, Manawasinghe IS, Liu M, Li XH, Hyde KD, Yan JY

Recieved: 03 April 2023, Accepted: 08 June 2023, Published: 18 September 2023

Grapevine trunk diseases (GTDs) are one kind of the most common and destructive diseases worldwide which challenge the sustainable development of the grape industry and cause serious economic loss. From 2020 to 2022, grapevine trunk disease samples were collected from eight provinces in China and associated fungi were identified based on phylogenetic analyses and morphological observations. A total of 199 isolates were obtained, representing 40 species belonging to 21 genera in 10 families. Twenty-one species are reported as the first records in China and 13 as the first records on grapevine worldwide. Diaporthe, Botryosphaeriaceae, Cylindrocarpon-like and Fusarium-like genera were the most frequently isolated taxa. Bartalinia, Botryosphaeria and Dactylonectria species were widely distributed in China. The study provides an insight into the diversity of fungal species on the diseased grapevine, among which some may play the role of common or potential pathogens, endophytes, and saprobes. Relevant results provide the basis for further research on the interactions among fungal communities and strategies for managing grapevine trunk diseases.

Keywords: diversity – grapevine trunk diseases – morphology – new records – phylogenetic analyses

16. Mycosphere Notes 413–448: Dothideomycetes associated with woody oil plants in China

Authors: Li WL, Liang RR, Dissanayake AJ, Liu JK

Recieved: 09 May 2023, Accepted: 29 August 2023, Published: 19 September 2023

This is the ninth in a series of Mycosphere notes wherein we provide notes on various fungal taxa in Dothideomycetes. In this set of notes, we focus on species associated with woody oil plants, which are important in terms of food security, ecology, agriculture and for industrial manufacturing. Eighty-five fungal taxa were identified in three orders (Muyocopronales, Pleosporales and Valsariales). Thirty-four species (belonging to 16 families) were identified in Pleosporales, one species was classified in Valsariales and one species was recognized in Muyocopronales. We introduce two new genera Oleaginea (Lophiostomataceae) and Neobrevicollum (Neohendersoniaceae) and 16 new species, Acrocalymma paeoniae, Corynespora idesiae, Flabellascoma pistaciae, Loculosulcatispora paeoniae, Lophiostoma oleae, Montagnula verniciae, Neobrevicollum oleae, Neocucurbitaria pistaciicola, Nigrograna acericola, Ni. oleae, Ni. sichuanensis, Ni. verniciae, Oleaginea sichuanensis, Palmiascoma acericola, Paramonodictys paeoniae, Pseudothyridariella idesiae. New host/country records are provided for Acrocalymma pterocarpi, Angustimassarina kunmingense, Austropleospora ochracea, Crassiparies quadrisporus, Loculosulcatispora hongheensis, Lophiotrema hydei, Lophiotrema neoarundinaria, Lophiostoma chiangraiense, Lophiostoma japonica, Lophiostoma montanae, Montagnula donacina, Muyocopron lithocarpi, Neokalmusia aquibrunnea, Neovaginatispora fuckelii, Nigrograna hydei, Ni. locuta-pollinis, Ni. magnoliae, Pseudochaetosphaeronema chiangraiense, P. magnoliae, and Valsaria insitiva. Three new asexual/sexual morph connections were made for Acrocalymma pterocarpi, Austropleospora ochracea and Loculosulcatispora hongheensis. A morphological description of one known species, Nigrograna locuta-pollinis, is provided. All taxa are described and illustrated, and phylogenetic trees are presented to show their phylogenetic placements.

Keywords: 2 new genera – 16 new species – 20 new records – molecular phylogeny – multi-gene – taxonomy

17. Beyond observation: genomic traits and machine learning algorithms for predicting fungal lifestyles

Authors: Chen YP, Su PW, Stadler M, Xiang R, Hyde KD, Tian WH, Maharachchikumbura SSN

Recieved: 12 July 2023, Accepted: 22 August 2023, Published: 19 September 2023

Economically and agriculturally important fungal species exhibit various lifestyles, and they can switch their life modes depending on the habitat, host tolerance, and resource availability. Traditionally, fungal lifestyles have been determined based on observation at a particular host or habitat. Therefore, potential fungal pathogens have been neglected until they cause devastating impacts on human health, food security, and ecosystem stability. This study focused on the class Sordariomycetes to explore the genomic traits that could be used to determine the lifestyles of fungi and the possibility of predicting fungal lifestyles using machine learning algorithms. A total of 638 representative genomes encompassing 5 subclasses, 17 orders, and 50 families were selected and annotated. Through an extensive literature survey, the lifestyles of 553 genomes were determined, including plant pathogens, saprotrophs, entomopathogens, mycoparasites, endophytes, human pathogens and nematophagous fungi. We first tried to examine the relationship between fungal lifestyles and transposable elements. We unexpectedly discovered that second-generation sequencing technologies tend to result in reduced size of transposable elements while having no discernible impact on the content of protein-coding genes. Then, we constructed three numerical matrices: 1) a basic genomic feature matrix including 25 features; 2) a functional protein matrix including 24 features; 3) and a combined matrix. Meanwhile, we reconstructed a genome-scale phylogeny, across which comprehensive comparative analyses were conducted. The results indicated that basic genomic features reflected more on phylogeny rather than lifestyle, but the abundance of functional proteins exhibited relatively high discrimination not only in differentiating taxonomic groups at the higher levels but also in differentiating lifestyles. Among these lifestyles including plant pathogens, saprotrophs, entomopathogens, mycoparasites, endophytes, and human pathogens, plant pathogens exhibited the largest secretomes, while entomopathogens had the smallest secretomes. The abundance of secretomes served as a valuable indicator for differentiating plant pathogens from mycoparasites, saprotrophs, and entomopathogens, as well as for discriminating endophytes from entomopathogens. Effectors have long been considered disease determinants, and indeed, we observed a higher presence of effectors in plant pathogens than in saprotrophs and entomopathogens. However, surprisingly, endophytes also exhibited a similar abundance of effectors, challenging their role as a reliable indicator for pathogenic fungi. A single functional protein group could not differentiate all lifestyles, but their combinations resulted in accurate differentiation for most lifestyles. Furthermore, models of six machine learning algorithms were trained, optimized, and evaluated based on the labeled genomes. The best-performance model was used to predict the lifestyle of 83 unlabeled genomes. Although insufficient genome sampling for several lifestyles and inaccurate lifestyle assignments for some genomes, the predictive model still obtained a high degree of accuracy in differentiating plant pathogens. The predictive model can be further optimized with more sequenced genomes in the future and provide a more reliable prediction. It can serve as an early warning system, enabling the identification of potentially devastating fungi and facilitating the implementation of appropriate measures to prevent their spread.

Keywords: CAZymes – FCWDEs – Genomics – genomic profile – PCWDEs – secretome – TEs

18. Global diversity, molecular phylogeny and divergence times of the brown‑rot fungi within the Polyporales

Authors: Liu S, Shen LL, Xu TM, Song CG, Gao N, Wu DM, Sun YF, Cui BK

Recieved: 10 July 2023, Accepted: 12 September 2023, Published: 04 October 2023

Brown-rot fungi are an important group of wood-decaying fungi, aside from the ecological significance as decomposer and plant pathogens in forest ecosystems, some species are edible and medicinal fungi, which have important economic value. Recent taxonomic and phylogenetic studies shown that Polyporales contains the majority of brown-rot fungi and forms 14 family-level lineages. However, its species composition and divergence time are not fully understood. In this study, we inferred phylogeny and divergence times of the brown‑rot fungi within the Polyporales. The phylogenetic relationships of the brown‑rot fungi within the Polyporales are reconstructed based on DNA sequences of multiple loci including the internal transcribed spacer regions (ITS), the large subunit of nuclear ribosomal RNA gene (nLSU), the small subunit of mitochondrial rRNA gene (mtSSU), the small subunit of nuclear ribosomal RNA gene (nuSSU), the largest subunit of RNA polymerase II gene (RPB1), the second largest subunit of RNA polymerase II gene (RPB2) and the translation elongation factor 1-α gene (TEF1). Molecular clock analysis for the divergence time of the brown‑rot fungi within the Polyporales is performed using BEAST based on the seven DNA fragments (ITS, nLSU, mtSSU, nuSSU, RPB1, RPB2, TEF1). Phylogenetic and molecular clock analyses showed that Polyporales appeared in the early Cretaceous (about 141.55 Mya); species of brown-rot fungi within Polyporales gathered and formed 14 family-level lineages, and the differentiation with white-rot fungi occurred in the early Cretaceous (about 119.25 Mya); the brown-rot families of Polyporales were centralized differentiation in the middle Cretaceous (about 81.48–99.54 Mya). Through years of extensive field trip investigations, combined with relevant literature and databases, we concluded that there are 383 brown-rot fungi species within the Polyporales worldwide. Based on the evidence of morphological characters and molecular phylogenetic analyses, 383 brown-rot fungi species within Polyporales belonging to 14 families and 69 genera are recognized, including two new genera, viz., Eucalyptoporia and Resupinopostia; nine new species, viz., Daedalea submodesta, D. vinacea, Eucalyptoporia tasmanica, Fuscopostia avellaneus, F. persicinus, F. tomentosa, Niveoporofomes orientalis, Rhodoantrodia subtropica and Resupinopostia sublateritia; and five new combinations, viz., Cystidiopostia simanii, Osteina subundosa, Resupinopostia lateritia, Spongiporus japonica and S. persicinus. Additionally, an annotated checklist of the species composition, geographical distribution, host trees and some morphological characteristics of brown-rot fungi within Polyporales is given, based on the field trip investigations and published papers.

Keywords: 16 new taxa – brown-rot fungi – macro-fungi – molecular clock – multi-gene phylogeny

19. A multi‑gene phylogeny clarifies species diversity, taxonomy, and divergence times of Ceriporia and other related genera in Irpicaceae (Polyporales, Basidiomycota)

Authors: Wang CG, Zhao H, Liu HG, Zeng GY, Yuan Y, Dai YC

Recieved: 03 July 2023, Accepted: 25 September 2023, Published: 24 October 2023

Phylogenetic and morphological analyses on Ceriporia and other related genera in Irpicaceae were carried out. Ceriporia, Gloeoporus, and Meruliopsis characterised as resupinate, effused-reflexed or pileate polypores with poroid and smooth hymenophore, a monomitic hyphal structure, crystals, and an oily substance are contained in the Irpicaceae. Ceriporia and Meruliopsis are phylogenetically related as sister genera. They share resupinate to rarely effused-reflexed basidiomata with a white, buff to brightly colored hymenophore, a monomitic hyphal structure with simple septa on the generative hyphae, and ellipsoid, cylindrical to allantoid basidiospores. However, hymenial cystidia are present in most Meruliopsis species, while they are absent in most Ceriporia species. Gloeoporus is distinguished from Ceriporia and Meruliopsis by having a gelatinous hymenophore and generative hyphae, sometimes with clamp connections. Phylogenies on Ceriporia and other related genera were reconstructed using multiple loci DNA sequences, including the internal transcribed spacer regions (ITS), the large subunit of nuclear ribosomal RNA gene (nLSU), the largest subunit of RNA polymerase II (RPB1), the translation elongation factor 1-α gene (TEF1) and the small subunit of nuclear ribosomal RNA gene (nSSU), as well as two combined datasets (ITS+nLSU) and (ITS+nLSU+RPB1+TEF1+nSSU). Eleven new species in Ceriporia are described and illustrated, four new combinations in the genus are proposed. Two new species in Gloeoporus and three in Meruliopsis are described and illustrated. Moreover, the evolutionary times of Ceriporia and other related genera in Irpicaceae were revealed based on conserved regions of five DNA fragments (ITS+nLSU+RPB1+TEF1+nSSU). Bayesian evolutionary analysis shows the divergence time of Irpicaceae emerged with a mean stem age of 169.1 Mya [95 % highest posterior density (HPD) of 124.66–231.04 Mya], which occurred during the middle Jurassic. Ceriporia and Meruliopsis grouped and the initial diversification occurred during the early of the Cretaceous with a mean stem age of 113.99 Mya [95% highest posterior density (HPD) of 81.53–153.07 Mya]. Gloeoporus emerged earlier with a mean stem age of 142.84 Mya [95% highest posterior density (HPD) of 102.39–196.41 Mya], which occurred during the early Cretaceous.

Keywords: Molecular clock – multi-marker analyses – polypore – taxonomy – wood-decaying fungi

20. OFPT: a one-stop software for fungal phylogeny

Authors: Zeng XY, Tan TJ, Tian FH, Wang Y, Wen TC

Recieved: 13 July 2023, Accepted: 25 September 2023, Published: 24 October 2023

DNA-based phylogeny is indispensable in modern fungal taxonomy. However, the procedure of conducting phylogenetic analysis is pretty complicated, and mistakes are commonplace leading to results among different researchers with low reliability and reproducibility. On top of that, obtaining robust phylogenetic trees is also very time-consuming, which may cost researchers lots of time performing mostly repetitive operations. There is software offering functions to perform part or complete procedure of the phylogenetic analysis, but they are either too multi-functional or have limited functions. Therefore, we developed a click-and-run software named ‘One-click Fungal Phylogenetic Tool’ (https://ofpt.guhongxin.com), which automates and standardizes the repetitive process of constructing phylogenetic trees and does not require any additional operations while running. This software offers users a step-by-step process and requires only an Excel file with DNA sequence information to automatically generate phylogenetic trees, which will improve the efficiency of phylogenetic study and the reliability of resulting phylogenetic trees.

Keywords: – Bayesian inference – maximum likelihood – Python – sequence data – standardized process

21. Species diversity of Hygrophorus in China and a phylogenetic study of the genus

Authors: Wang CQ, Zhang M, He XL, Liu JW, Wei TZ, Liu TZ, Wang K, Adamčík S, Li TH, Deng WQ

Recieved: 21 July 2023, Accepted: 12 September 2023, Published: 02 November 2023

Hygrophorus is among the most species rich and frequent ectomycorrhizal genera of Agaricales, and several species are popular wild edible mushrooms in northern and southwestern China. In the past two decades, there has been an increasing number of taxonomic and phylogenetic studies of the genus, however, the comprehensive studies on the species diversity and phylogenetic relationship of Hygrophorus in China were lacking. In this study, an extensive survey on the species diversity of Hygrophorus in China was conducted. In total, 62 Chinese Hygrophorus taxa were included in this study. Fifty-five of them are described, illustrated and discussed, including 26 new species; in addition, two recently described species (H. habaensis and H. viridiflavidus) and 5 insufficiently known species are listed with notes. A large-scale phylogenetic study of Hygrophorus was conducted based on the newly obtained sequences and the available internal transcribed spacer (ITS) sequences in the international public databases; and a multi-gene (ITS-LSU-rpb2-tef1-α) phylogeny was also conducted. The species boundaries of Hygrophorus delimited by morphological data are broadly congruent with those based on the ITS phylogenetic analysis. In general, the multi-locus dataset could resolve a section-level phylogeny of the genus; and a new section, i.e. sect. Vividi, is proposed based on both phylogenetic and morphological evidences. However, the subgenera classified by morphology are not supported well by molecular phylogenetic analysis.

Keywords: Hygrophoraceae – Novel taxa – Phylogeny – Taxonomy – Waxcap

22. Fungalpedia, an illustrated compendium of the fungi and fungus-like taxa

Authors: Hyde KD, Amuhenage TB, Apurillo CCS, Asghari R, Aumentado HD, Bahkali AH, Bera I, Bhunjun CS, Calabon MS, Chandrasiri S, Chethana KWT, Doilom M, Dong W, Fallahi M, Gajanayake AJ, Gomdola D, Gunarathne A, Hongsanan S, Huanraluek N, Jayawardena RS, Kapov SA, Khyaju S, Le L, Li CJY, Li QR, Li YX, Lin CG, Linn MM, Liu JK, Liu NG, Luangharn T, Madagammana AD, Manawasinghe IS, Marasinghe DS, McKenzie EHC, Meakala N, Meng QF, Mukhopadhyay S, Norphanphoun C, Pem D, Phukhamsakda C, Sarma VV, Selcuk F, Senanayake IC, Shah S, Shu YX, Silva HVS, Su HL, Tavakol M, Thakshila SAD, Thiyagaraja V, Thongklang N, Tian Q, Tibpromma S, Tun ZL, Ulukapi M, Wang Y, Wannasawang N, Wijayawardene NN, Wimalasena SDMK, Xiao Y, Xiong YR, Yasanthika WAE, Li Q, Dai DQ

Recieved: 17 August 2023, Accepted: 20 October 2023, Published: 08 December 2023

Fungalpedia is an online illustrated compendium of the fungi and fungus-like taxa. In this database we provide notes on the genera and higher taxa of fungi and definitions and descriptions of terms generally used in mycology. Where possible the notes are enhanced with plates and drawings to make the terms easier to understand. In the case of genera, we provide 1) notes on habit, host and lifestyle, 2) higher level classification, 3) genes and other evidence to support the genus, 4) main characters, 5) a critical assessment of the genus and its placement, and 6) photographic plates and/or drawings of the main characters of the genus. For higher taxa we give similar information but a drawing will not be provided. For the various terms we provide definitions and explanations and diagrams to facilitate understanding. We also provide accounts of eminent mycologists both living and deceased. We also provide notes on methodology and biotechnology. Although many of the entries are by invited authors and published in scientific papers, other interested persons are welcome to contribute to entries and/or modify existing entries. Those interested should contact the lead author.

Keywords: Achrochaeta – Agaricus – Alveariospora – Anastomitrabeculia – Aphelidiales – Applied mycology – Ascagilis – Asterosporium – Austropleospora – Basal fungi – Beltraniella – Blastocladiomyceta – Brunneofissura – Bryostigma – Borderline fungi – Castanedomyces – Chaetomella – Clitopaxillus – Coelomycetes – Colletotrichum – Coniella – Comoclathris – Conioscypha – Coprotaceae – Databases – Definitions – Dematiaceous hyphomycetes – Diaporthomycetidae – Dicephalospora – Discomycetes – Dothideomycetes – Epifoliar fungi – Eurotiomycetes – Eminent mycologists – Forest pathology – Freshwater fungi – Fungicolous fungi – Fusarium – Fusasporis – Genera – Grass fungi – Halodiatrype – Higher taxa – Hypocreomycetidae – Hypomyces – Invertebrate fungi – Lichenicolous fungi – Juxtiphoma – Online database – Marine fungi – Megacoelomyces – Moheitospora – Mushrooms – Mycoprotein – Nematocenator – Naevia – Neoamphisphaeria – Obruspora – Oxydothis – Palm fungi – Palmiascoma – Pandanaceomyces – Parameliola – Pararoussoella – pileus – Pirozynskiomyces – Plant pathology – Pleopunctum – Polycephalomyces – Pseudoalternaria – Purpureocorticium – Quixadomyces – Salmacisia – Sanchytriomycota – Savitreea – Setoapiospora – Soil fungi – Sordariomycetidae – Synchaetomella – Towyspora – Wetland fungi – Willeya – Xylariomycetidae – Yeasts

23. Global consortium for the classification of fungi and fungus-like taxa

Authors: Hyde KD, Abdel-Wahab MA, Abdollahzadeh J, Abeywickrama PD, Absalan S, Afshari N, Ainsworth AM, Akulov OY, Aleoshin VV, Al-Sadi AM, Alvarado P, Alves A, Alves-Silva G, Amalfi M, Amira Y, Amuhenage TB, Anderson J, Antonín V, Aouali S, Aptroot A, Apurillo CCS, Araújo JPM, Ariyawansa HA, Armand A, Arumugam E, Asghari R, Assis DMA, Atienza V, Avasthi S, Azevedo E, Bahkali AH, Bakhshi M, Banihashemi Z, Bao DF, Baral HO, Barata M, Barbosa F, Barbosa RN, Barreto RW, Baschien C, Belamesiatseva DB, Bennett Reuel M, Bera I, Bezerra JDP, Bezerra JL, Bhat DJ, Bhunjun CS, Bianchinotti MV, Błaszkowski J, Blondelle A, Boekhout T, Bonito G, Boonmee S, Boonyuen N, Bregant C, Buchanan P, Bundhun D, Burgaud G, Burgess T, Buyck B, Cabarroi-Hernández M, Cáceres MES, Caeiro MF, Cai L, Cai MF, Calabon MS, Calaça FJS, Callalli M, Camara MPS, Cano-Lira JF, Cantillo T, Cao B, Carlavilla JR, Carvalho A, Castañeda-Ruiz RF, Castlebury L, Castro-Jauregui O, Catania MDV, Cavalcanti LH, Cazabonne J, Cedeño-Sanchez ML, Chaharmiri-Dokhaharani S, Chaiwan N, Chakraborty N, Chaverri P, Cheewangkoon R, Chen C, Chen CY, Chen KH, Chen J, Chen Q, Chen WH, Chen YP, Chethana KWT, Coleine C, Condé TO, Corazon-Guivin MA, Cortés-Pérez A, Costa-Rezende DH, Courtecuisse R, Crouch JA, Crous PW, Cui BK, Cui YY, da Silva DKA, da Silva GA, da Silva IR, da Silva RMF, da Silva Santos AC, Dai DQ, Dai YC, Damm U, Darmostuk V, Daroodi Zoha, Das K, Das K, Davoodian N, Davydov EA, Dayarathne MC, Decock C, de Groot MD, De Kesel A, dela Cruz TEE, De Lange R, Delgado G, Denchev CM, Denchev TT, de Oliveira NT, de Silva NI, de Souza FA, Dentinger B, Devadatha B, Dianese JC, Dima B, Diniz AG, Dissanayake AJ, Dissanayake LS, Doğan HH, Doilom M, Dolatabadi S, Dong W, Dong ZY, Dos Santos LA, Drechsler-Santos ER, Du TY, Dubey MK, Dutta AK, Egidi E, Elliott TF, Elshahed MS, Erdoğdu M, Ertz D, Etayo J, Evans HC, Fan XL, Fan YG, Fedosova AG, Fell J, Fernandes I, Firmino AL, Fiuza PO, Flakus A, Fragoso de Souza CA, Frisvad JC, Fryar SC, Gabaldón T, Gajanayake AJ, Galindo LJ, Gannibal PB, García D, García-Sandoval SR, Garrido-Benavent I, Garzoli L, Gautam AK, Ge ZW, Gené DJ, Gentekaki E, Ghobad-Nejhad M, Giachini AJ, Gibertoni TB, Góes-Neto A, Gomdola D, Gomes de Farias AR, Gorjón SP, Goto BT, Granados-Montero MM, Griffith GW, Groenewald JZ, Groenewald M, Grossart HP, Gueidan C, Gunarathne A, Gunaseelan S, Gusmão LFP, Gutierrez AC, Guzmán-Dávalos L, Haelewaters D, Halling R, Han YF, Hapuarachchi KK, Harder CB, Harrington TC, Hattori T, He MQ, He S, He SH, Healy R, Herández-Restrepo M, Heredia G, Hodge KT, Holgado-Rojas M, Hongsanan S, Horak E, Hosoya T, Houbraken J, Huang SK, Huanraluek N, Hur JS, Hurdeal VG, Hustad VP, Iotti M, Iturriaga T, Jafar E, Janik P, Jayalal RGU, Jayasiri SC, Jayawardena RS, Jeewon R, Jerônimo GH, Jesus AL, Jin J, Johnston PR, Jones EBG, Joshi Y, Justo A, Kaishian P, Kakishima M, Kaliyaperumal M, Kang GP, Kang JC, Karimi O, Karpov SA, Karunarathna SC, Kaufmann M, Kemler M, Kezo K, Khyaju S, Kirchmair M, Kirk PM, Kitaura MJ, Klawonn I, Kolarik M, Kong A, Kuhar F, Kukwa M, Kumar S, Kušan I, Lado C, Larsson KH, Latha KPD, Lee HB, Leonardi M, Leontyev DL, Lestari AS, Li CJY, Li DW, Li H, Li HY, Li L, Li QR, Li WL, Li Y, Li YC, Liao CF, Liimatainen K, Lim YW, Lin CG, Linaldeddu BT, Linde CC, Linn MM, Liu F, Liu JK, Liu NG, Liu S, Liu SL, Liu XF, Liu XY, Liu XZ, Liu ZB, Lu L, Lu YZ, Luangharn T, Luangsa-ard JJ, Lumbsch HT, Lumyong S, Luo L, Luo M, Luo ZL, Ma J, Machado AR, Madagammana AD, Madrid H, Magurno F, Magyar D, Mahadevan N, Maharachchikumbura SSN, Maimaiti Y, Malosso E, Manamgoda DS, Manawasinghe IS, Mapook A, Marasinghe DS, Mardones M, Marin-Felix Y, Márquez R, Masigol H, Matočec N, May T, McKenzie EHC, Meiras-Ottoni A, Melo RFR, Mendes ARL, Mendieta S, Meng QF, Menkis A, Menolli N Jr, Mešić A, Meza Calvo JG, Mikhailov KV, Miller SL, Moncada B, Moncalvo JM, Monteiro JS, Monteiro M, Mora-Montes HM, Moreau PA, Mueller GM, Mukhopadyay S, Murugadoss R, Nagy LG, Najafiniya M, Nanayakkara CM, Nascimento CC, Nei Y, Neves MA, Neuhauser S, Niego AGT, Nilsson RH, Niskanen T, Niveiro N, Noorabadi MT, Noordeloos ME, Norphanphoun C, Nuñez Otaño NB, O’Donnell RP, Oehl F, Olariaga I, Orlando FP, Pang KL, Papp V, Pawłowska J, Peintner U, Pem D, Pereira OL, Perera RH, Perez-Moreno J, Perez-Ortega S, Péter G, Phillips AJL, Phonemany M, Phukhamsakda, Phutthacharoen K, Piepenbring M, Pires-Zottarelli CLA, Poinar G, Pošta A, Prieto M, Promputtha I, Quandt CA, Radek R, Rahnama K, Raj KNA, Rajeshkumar KC, Rämä T, Rambold G, Ramírez-Cruz V, Rasconi S, Rathnayaka AR, Raza M, Ren GC, Robledo GL, Rodriguez-Flakus P, Ronikier A, Rossi W, Ryberg M, Ryvarden LR, Salvador‑Montoya CA, Samant B, Samarakoon BC, Samarakoon MC, Sánchez-Castro I, Sánchez-García M, Sandoval-Denis M, Santiago ALCMA, Santamaria B, Santos ACS, Sarma VV, Savchenko A, Savchenko K, Saxena RK, Scholler M, Schoutteten N, Seifollahi E, Selbmann L, Selcuk F, Senanayake IC, Seto K, Shabashova TG, Shen HW, Shen YM, Silva-Filho AGS, Simmons DR, Singh R, Sir EB, Song Chang-Ge, Souza-Motta CM Sruthi OP, Stadler M, Stchigel AM, Stemler J, Stephenson SL, Strassert JFH, Su HL Su L, Suetrong S, Sulistyo B, Sun YF, Sun YR, Svantesson Sten, Sysouphanthong P, Takamatsu S, Tan TH, Tanaka K, Tang AMC, Tang X, Tanney JB, Tavakol NM, Taylor JE, Taylor PWJ, Tedersoo L, Tennakoon DS, Thamodini GK, Thines M, Thiyagaraja V, Thongklang N, Tiago PV, Tian Q, Tian WH, Tibell L, Tibell S, Tibpromma S, Tkalčec Z, Tomšovský M, Toome-Heller M, Torruella G, Tsurykau A, Udayanga D, Ulukapi M, Untereiner WA, Uzunov BA, Valle LG, Van Caenegem W, Van den Wyngaert S, Van Vooren N, Velez P, Verma RK, Vieira LC, Vieira WAS, Vizzini A, Walker A, Walker AK, Wanasinghe DN, Wang CG, Wang K, Wang SX, Wang XY, Wang Y, Wannasawang N, Wartchow F, Wei DP, Wei XL, White JF, Wijayawardene NN, Wijesinghe SN, Wijesundara DSA, Wisitrassameewong K, Worthy FR, Wu F, Wu G, Wu HX, Wu N, Wu WP, Wurzbacher C, Xiao YP, Xiong YR, Xu LJ, Xu R, Xu RF, Xu RJ, Xu TM, Yakovchenko L, Yan JY, Yang H, Yang J, Yang ZL, Yang YH,Yapa N, Yasanthika E, Youssef NH, Yu FM, Yu Q, fD, Yu YX, Yu ZF, Yuan HS, Yuan Y, Yurkov A, Zafari D, Zamora JC, Zare R, Zeng M, Zeng NK, Zeng XY, Zhang F, Zhang H, Zhang JF, Zhang JY, Zhang QY, Zhang SN, Zhang W, Zhang Y, Zhang YX, Zhao CL, Zhao H, Zhao Q, Zhao RL, Zhou LW, Zhou M, Zhurbenko MP, Zin HH, Zucconi L

Recieved: 05 October 2023, Accepted: 07 December 2023, Published: 12 December 2023

The Global Consortium for the Classification of Fungi and fungus-like taxa is an international initiative of more than 550 mycologists to develop an electronic structure for the classification of these organisms. The members of the Consortium originate from 55 countries/regions worldwide, from a wide range of disciplines, and include senior, mid-career and early-career mycologists and plant pathologists. The Consortium will publish a biannual update of the Outline of Fungi and fungus-like taxa, to act as an international scheme for other scientists. Notes on all newly published taxa at or above the level of species will be prepared and published online on the Outline of Fungi website (https://www.outlineoffungi.org/), and these will be finally published in the biannual edition of the Outline of Fungi and fungus-like taxa. Comments on recent important taxonomic opinions on controversial topics will be included in the biannual outline. For example, ‘to promote a more stable taxonomy in Fusarium given the divergences over its generic delimitation’, or ‘are there too many genera in the Boletales?’ and even more importantly, ‘what should be done with the tremendously diverse ‘dark fungal taxa?’ There are undeniable differences in mycologists’ perceptions and opinions regarding species classification as well as the establishment of new species. Given the pluralistic nature of fungal taxonomy and its implications for species concepts and the nature of species, this consortium aims to provide a platform to better refine and stabilise fungal classification, taking into consideration views from different parties. In the future, a confidential voting system will be set up to gauge the opinions of all mycologists in the Consortium on important topics. The results of such surveys will be presented to the International Commission on the Taxonomy of Fungi (ICTF) and the Nomenclature Committee for Fungi (NCF) with opinions and percentages of votes for and against. Criticisms based on scientific evidence with regards to nomenclature, classifications, and taxonomic concepts will be welcomed, and any recommendations on specific taxonomic issues will also be encouraged; however, we will encourage professionally and ethically responsible criticisms of others’ work. This biannual ongoing project will provide an outlet for advances in various topics of fungal classification, nomenclature, and taxonomic concepts and lead to a community-agreed classification scheme for the fungi and fungus-like taxa. Interested parties should contact the lead author if they would like to be involved in future outlines.

Keywords: classification – nomenclature – scientific criticism – taxonomy

24. Boletaceae from Shanxi Province of northern China with descriptions of ten new species

Authors: Mao N, Zhao TY, Zhang YX, Li T, Lv JC, Fan L

Recieved: 31 May 2023, Accepted: 25 October 2023, Published: 13 December 2023

The Boletaceae is a highly diverse group of organisms with both ecological and edible values. There are many studies on Boletaceae in China, but the area investigated is generally the region of sourthwestern and southern China. The knowledge of Boletaceae in northern China is limited. In this study, we surveyed the species diversity of Boletaceae in Shanxi Province, northern China. Molecular phylogenetic analyses were performed using a concatenated internal transcribed spacer of the nuc rDNA (ITS), the large subunit of nuclear ribosomal RNA gene (nrLSU), the translation elongation factor 1-α gene (tef1), and the second largest subunit of RNA polymerase II gene (rpb2) dataset (totally including 1 140 sequences from 409 collections). Our phylogenetic tree revealed 24 Boletaceae species from our collections, which are distributed in 16 genera, i.e. Boletus, Butyriboletus, Caloboletus, Chalciporus, Cyanoboletus, Hemileccinum, Hortiboletus, Leccinum, Neoboletus, Retiboletus, Rubroboletus, Strobilomyces, Suillellus, Tylopilus, Villoboletus, and Xerocomus. Of these species, 14 are identified as known species, including three new to China, and 10 are described and illustrated as new species in this paper. Accordingly, 15 species documented from Shanxi before this study are briefly discussed.

Keywords: 10 new taxa – Basidiomycetes – Boletales – ectomycorrhizal fungi – molecular analysis – taxonomy

25. Endophytic Fusarium and allied fungi from Rosa roxburghii in China

Authors: Zhang H, Zeng Y, Wei TP, Jiang YL, Zeng XY

Recieved: 17 July 2023, Accepted: 20 October 2023, Published: 13 December 2023

Fusarium usually implies plant pathogens. However, endophytic Fusarium and allied fungi, the non-pathogenic species, share equal importance due to their excellent biosynthetic capacity and wide range of biological activities. Rosa roxburghii is an economically important source of medicine and food. We have previously reported on the diversity and antimicrobial activity of endophytic fungi from this plant. Finding several Fusarium species that may represent new taxa requires further confirmation using multi-locus phylogenetic analyses combined with morphology. In this study, 60 related isolates were obtained and identified from healthy R. roxburghii. Eleven novel species and four new combinations are described and illustrated based on multi-gene phylogenetic analyses of Fusarium and thirteen allied genera and morphological comparisons. The new species described herein are Albonectria guizhouensis, Fusarium arbusti, F. caulendophyticum, F. caulicola, F. cili, F. qiannanense, F. radicigenum, F. rosae-roxburghii, F. rosendophyticum, F. rosiradicicola, and Neocosmospora liupanshuiensis, whereas N. gannanensis, N. passiflorae, N. populicola, and N. tumidisperma were introduced as new combinations. In addition, pathogenic and endophytic Fusarium and allied fungi associated with Rosaceae are summarized. The results of this study have important implications for accurately identifying Fusarium-linked fungi and developing potential applications for these endophytic fungi.

Keywords: Multi-gene phylogeny – Morphology – New taxa – Rosaceae-associated fungi – Taxonomy

26. Mycosphere notes 449–468: saprobic and endophytic fungi in China, Thailand, and Uzbekistan

Authors: Dong W, Hyde KD, Jeewon R, Liao CF, Zhao HJ, Kularathnage ND, Li H, Yang YH, Pem D, Shu YX, Gafforov Y, Manawasinghe IS, Doilom M

Recieved: 28 August 2023, Accepted: 11 November 2023, Published: 21 December 2023

This is the tenth of the series Mycosphere Notes, wherein we present newly discovered saprobic and endophytic fungi isolated from various hosts in China, Thailand, and Uzbekistan. In this compilation, we introduce three new genera, viz., Conicotenuis (Phomatosporaceae), Irregularispora (Stictidaceae) and Minimispora (Phomatosporaceae), and 14 new species, viz., Clonostachys artemisiae (Bionectriaceae), Conicotenuis fusiformis (Phomatosporaceae), Irregularispora olivacea (Stictidaceae), Melomastia loropetalicola (Pleurotremataceae), Minimispora superficialis (Phomatosporaceae), Montagnula agaves (Didymosphaeriaceae), Neodendryphiella brassaiopsidis (Dictyosporiaceae), Paramicrosphaeropsis sexualis (Didymellaceae), Pestalotiopsis camelliae-japonicae (Sporocadaceae), Pestalotiopsis pyrrosiae-linguae (Sporocadaceae), Pestalotiopsis zhaoqingensis (Sporocadaceae), Pseudocoleophoma heteropanacicola (Dictyosporiaceae), Pseudopaucispora heteropanacis (Lophiostomataceae) and Torula longan (Torulaceae). In addition, two species Melomastia phetchaburiensis and M. sinensis are reviewed, and their illustrations are provided based on the holotype. A new host record of Torula phytolaccae is described from Phytolacca americana. We describe the sexual morph of Paramicrosphaeropsis for the first time and revise its generic concept herein.

Keywords: 17 new taxa – dematiaceous – Dothideomycetes – freshwater – hyaline-spored – Lecanoromycetes – molecular phylogeny – Sordariomycetes – taxonomy

27. Medical Fusarium: novel species or uncertain identifications?

Authors: Song Y, Hu S, de Hoog GS, Liu X, Meng X, Xue R, van Diepeningen AD, Fokkens L, Li RY, Gao S

Recieved: 31 August 2023, Accepted: 29 November 2023, Published: 27 December 2023

Fungal infections increasingly threaten human health, particularly in immunocompromised patients. Identification of etiologic agents of infection is important for effective treatment. Here, we study a set of 48 Fusarium strains, most of which had been collected from Chinese hospitals over two decades. Sequences of cam, rpb2, tub2, and tef1-α, singly or multilocus, did not entirely match with the described taxa; therefore, the species problem and correctness of identification became a research question. Blast searches in multiple dedicated databases did not always provide identical species assignments. Results remained variable when compared with phylogeny with 636 sequences identified in recent literature, including sequences from 41 type strains. Assignment to specific species within a species complex based on > 1000 single-copy orthologs was also variable for some species. Previously published MALDI-ToF data provided identification that matched sequence-based identification at the species complex level, but performed poorly with lineages within the complexes. Different methods of identification yielded dissimilar results. Some previously identified strains in earlier publications deviated more from the reference than our clinical strains. We further tested species boundaries using levels of admixture and found high admixture levels between F. fujikuroi, F. nisikadoi and F. oxysporum species complexes. It is concluded that species complexes can be recognised phylogenetically by BLAST and by MALDI-ToF, but the high intra-specific diversity of these fungi interferes with the unequivocal assignment of individual isolates to particular lineages. At a higher taxonomic level, most clinical strains were found to belong to F. fujikuroi, F. oxysporum and F. solani (Neocosmospora) complexes, irrespective of the method used for identification. To determine whether these complexes were particularly overrepresented in clinical strains, we compared this data in a larger dataset of 216 clinical isolates to those in environmental samples. We found that clinical strains are enriched for the F. solani complex (Neocosmospora) and less for F. oxysporum and F. fujikuroi complexes, suggesting that among these opportunistic human pathogens, F. solani is particularly equipped to survive in clinical settings.

Keywords: admixture – China – Fusarium – identification – species complex – trans-kingdom

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Volume 15 - 2024 Issue 1