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


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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