Polyphasic Identification of Fungi 3.0

A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Fungal Evolution, Biodiversity and Systematics".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 11641

Special Issue Editors


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Guest Editor
Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
Interests: fungal taxonomy; fungal phylogeny; fungal pathogens; Ascomycota; Basidiomycota
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
Interests: fungal taxonomy; fungal phylogeny; fungal pathogens; fungal endophytes; Ascomycota
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Fungi are the second-most species-rich group after insects. Thus, it is more challenging to estimate the total number of extant fungi species than that of plants and animals. Fungi play key roles in ecosystems as decomposers, endophytes, mutualists, and pathogens. However, in most cases, the roles of individual fungi in nature are still unknown. Describing and understanding the natural roles of fungal species can help humankind to overcome fungal diseases and better utilize fungal resources. Identification can be a long and seemingly never-ending process, with frequent revisions of the taxonomic schemes, and it is gradually becoming clearer that fungal identification and authentication require a multiple-step approach in order to generate accurate and useful data. This means that it is necessary to combine more traditional phenotypic and physiological approaches with modern molecular biology. Restriction fragment length polymorphism (RFPL), random amplification of polymorphic DNA (RAPD), amplified fragment length polymorphism-PCR (AFLP-PCR), next-generation sequencing (NGS), DNA barcoding, and whole genome sequencing have all been used to distinguish fungal taxa that are difficult to identify using traditional morphological methods. It is assumed that the genotype of a fungal species is only an indirect indication of its phenotype and ecological adaptations. In other words, a fungal species can be defined as the smallest aggregation of populations with a common lineage that share unique diagnosable phenotypic features.

Recently, a so-called polyphasic approach has been developed for the consistent identification and characterization of fungi. The polyphasic approach consists of the use of different techniques based on the systematization of scientific knowledge. Different methodologies used in this approach include micro- and macro-morphology, biochemical analyses, and molecular biology. These methods assist taxonomists in establishing a consolidated species concept.

This Special Issue will focus on the polyphasic identification of fungi. Studies covering the taxonomy, ecology, physiology, and phylogeny of fungi and fungal biodiversity estimates are welcome.

Prof. Dr. Samantha C. Karunarathna
Prof. Dr. Saowaluck Tibpromma
Guest Editors

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Keywords

  • epitypification
  • fungal diversity
  • fungal taxonomy
  • fungal phylogeny
  • fungal ecology
  • fungal physiology

Published Papers (8 papers)

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Research

29 pages, 44592 KiB  
Article
Four New Fungal Species in Forest Ecological System from Southwestern China
by Yinglian Deng, Jinfa Li, Changlin Zhao and Jian Zhao
J. Fungi 2024, 10(3), 194; https://doi.org/10.3390/jof10030194 - 02 Mar 2024
Viewed by 920
Abstract
Four new wood-inhabiting fungi were found in Southwestern China within the genera Phanerochaete, Phlebiopsis, Asterostroma, and Vararia of the families Phanerochaetaceae and Peniophoraceae, belonging to the orders Polyporales and Russulales individually. Combined with their morphological characteristics and molecular biological evidence, [...] Read more.
Four new wood-inhabiting fungi were found in Southwestern China within the genera Phanerochaete, Phlebiopsis, Asterostroma, and Vararia of the families Phanerochaetaceae and Peniophoraceae, belonging to the orders Polyporales and Russulales individually. Combined with their morphological characteristics and molecular biological evidence, the present study describes them as new fungal taxa. Asterostroma yunnanense is characterized by the resupinate, membranaceous to pellicular basidiomata with a cream to salmon-buff hymenial surface, hyphal system dimitic bearing simple-septa, thin- to thick-walled, yellowish brown asterosetae with acute tips, and thin-walled, echinulate, amyloid, globose basidiospores. Phanerochaete tongbiguanensis is characterized by the resupinate basidiomata with a white to cream hymenial surface, a monomitic hyphal system with simple-septa generative hyphae, the presence of subclavate cystidia covered with a lot of crystals, and oblong ellipsoid basidiospores (6–9 × 3–4.5 µm). Phlebiopsis fissurata is characterized by the membranaceous, tuberculate basidiomata with a buff to slightly brown hymenial surface, a monomitic hyphal system with simple-septa, conical cystidia, and broadly ellipsoid. Vararia yingjiangensis is characterized by a corky basidiomata with a pinkish buff to cinnamon-buff hymenial surface, cracking, yellowish dichohyphae with slightly curved tips, subulate gloeocystidia, and thick-walled, ellipsoid basidiospores (6.5–11.5 × 5–7 µm). The phylogenetic analyses of ITS + nLSU revealed that the two new species were nested into the genera Phanerochaete and Phlebiopsis within the family Phanerochaetaceae (Polyporales), in which Phanerochaete tongbiguanensis was sister to P. daliensis; Phlebiopsis fissurata was grouped with P. lamprocystidiata. Two new species were clustered into the genera Asterostroma and Vararia within the family Peniophoraceae (Russulales), in which Asterostroma yunnanense was sister to A. cervicolor; Vararia yingjiangensis formed a single branch. Full article
(This article belongs to the Special Issue Polyphasic Identification of Fungi 3.0)
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39 pages, 12983 KiB  
Article
Broadening the Knowledge of Mexican Boletes: Addition of a New Genus, Seven New Species, and Three New Combinations
by Olivia Ayala-Vásquez, Jesús Pérez-Moreno, Juan Pablo Pinzón, Roberto Garibay-Orijel, Jesús García-Jiménez, Javier Isaac de la Fuente, Crystian Sadiel Venegas-Barrera, Magdalena Martínez-Reyes, Leticia Montoya, Víctor Bandala, Celia Elvira Aguirre-Acosta, César Ramiro Martínez-González and Juan Francisco Hernández-Del Valle
J. Fungi 2023, 9(12), 1126; https://doi.org/10.3390/jof9121126 - 21 Nov 2023
Cited by 1 | Viewed by 2090
Abstract
Boletes are one of the most common groups of fungi in temperate, subtropical, and tropical ecosystems. In Mexico, the northern region has mainly been explored in terms of bolete diversity. This study describes a new genus and seven new species based on macromorphological, [...] Read more.
Boletes are one of the most common groups of fungi in temperate, subtropical, and tropical ecosystems. In Mexico, the northern region has mainly been explored in terms of bolete diversity. This study describes a new genus and seven new species based on macromorphological, micromorphological, molecular, phylogenetic, and ecological data. Garcileccinum gen. nov. is typified with G. salmonicolor based on multigene phylogenetic analysis of nrLSU, RPB2, and TEF1, and it is closely related to Leccinum and Leccinellum. Garcileccinum viscosum and G. violaceotinctum are new combinations. Boletellus minimatenebris (ITS, nrLSU, and RPB2), Cacaoporus mexicanus (RPB2 and ATP6), Leccinum oaxacanum, Leccinum juarenzense (nrLSU, RPB2, and TEF1), Tylopilus pseudoleucomycelinus (nrLSU and RPB2), and Xerocomus hygrophanus (ITS, nrLSU, and RPB2) are described as new species. Boletus neoregius is reclassified as Pulchroboletus neoregius comb. nov. based on morphological and multigene phylogenetic analysis (ITS and nrLSU), and its geographic distribution is extended to Central Mexico, since the species was only known from Costa Rica. Furthermore, T. leucomycelinus is a new record from Mexico. This study contributes to increasing our knowledge of boletes and expands the diversity found in Mexican forests. Full article
(This article belongs to the Special Issue Polyphasic Identification of Fungi 3.0)
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25 pages, 5331 KiB  
Article
Addition of Five Novel Fungal Flora to the Xylariomycetidae (Sordariomycetes, Ascomycota) in Northern Thailand
by Milan C. Samarakoon, Saisamorn Lumyong, Ishara S. Manawasinghe, Nakarin Suwannarach and Ratchadawan Cheewangkoon
J. Fungi 2023, 9(11), 1065; https://doi.org/10.3390/jof9111065 - 31 Oct 2023
Cited by 2 | Viewed by 1141
Abstract
The deviation of conventional fungal niches is an important factor in the implications of hidden fungal diversity and global fungal numbers. The Xylariomycetidae (Sordariomycetes, Ascomycota), which is also referred to as xylarialean taxa, has a wide range of species that demonstrate a high [...] Read more.
The deviation of conventional fungal niches is an important factor in the implications of hidden fungal diversity and global fungal numbers. The Xylariomycetidae (Sordariomycetes, Ascomycota), which is also referred to as xylarialean taxa, has a wide range of species that demonstrate a high degree of variation in their stromatic characteristics, showing either conspicuous or inconspicuous forms. In this study, samples were collected while focusing on temporal and spatial parameters and substrate characteristics. Based on internal transcribed spacer (ITS), 28S large subunit rDNA (LSU), RNA polymerase II second largest subunit (RPB2), and β-tubulin (TUB2) multigene phylogeny and morphology, five new species are introduced as Muscodor brunneascosporus, M. lamphunensis (Xylariaceae), Nigropunctata hydei, N. saccata (Incertae sedis), and Xenoanthostomella parvispora (Gyrotrichaceae). Plant substrates in the early stages of decay and attached to the host were feasible sample niches, with an emphasis on the collection of inconspicuous, hidden xylarialean species. The appearance of inconspicuous saprobic xylarialean forms during the rainy season may be linked to the change in nutritional mode, from endophytic mode during the dry season to saprobic in the wet. Therefore, it would be fascinating to concentrate future research on how seasonal fluctuations affect nutritional mode shifts, especially in northern Thailand, which would provide the optimal spatial characteristics. In order to establish a comprehensive linkage between endophytic and saprobic modes, it is imperative to have a substantial representation of endophytic isolate sequences resembling inconspicuous xylariaceous fungi within publicly accessible databases. Full article
(This article belongs to the Special Issue Polyphasic Identification of Fungi 3.0)
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22 pages, 6285 KiB  
Article
Five New Species of Aureoboletus and Chalciporus (Boletaceae, Boletales) and Their Ethnomycological Aspects
by Olivia Ayala-Vásquez, Magdalena Martínez-Reyes, Jesús Pérez-Moreno, César Ramiro Martínez-González, Juan Pablo Pinzón, Javier Isaac de la Fuente, Rigoberto Castro-Rivera, Jesús García-Jiménez, Soledad Balbuena-Carrasco, Eliseete Ramírez-Carbajal and Fuqiang Yu
J. Fungi 2023, 9(10), 1041; https://doi.org/10.3390/jof9101041 - 23 Oct 2023
Viewed by 1300
Abstract
Among Boletales, the family Boletaceae has the highest diversity worldwide. Additionally, this fungal group has great ecological relevance because it not only includes mainly ectomycorrhizal but also saprotrophic species. Furthermore, some species are used as food and have sociocultural and economic importance worldwide. [...] Read more.
Among Boletales, the family Boletaceae has the highest diversity worldwide. Additionally, this fungal group has great ecological relevance because it not only includes mainly ectomycorrhizal but also saprotrophic species. Furthermore, some species are used as food and have sociocultural and economic importance worldwide. In Mexico, the Boletaceae family boasts a substantial number of species, yet our understanding of these species remains far from comprehensive. In this work, by using macro- and micromorphological and phylogenetic analyses of DNA sequences from multi-gene analyses based on ITS, nrLSU, rpb1, rpb2, and tef1, we report five new species belonging to the genera Aureoboletus and Chalciporus: A. ayuukii and A. elvirae from a Quercus scytophylla forest, A. readii from a mixed forest, C. perezsilvae from cloud forest, and C. piedracanteadensis from both a mixed coniferous forest and a Quercus-Pinus forest. In Mexico, four species of Aureoboletus are used as a food source, and in this work, we add another one, A. readii, which is traditionally consumed by members of the Tlahuica-Pjiekakjoo culture, who are located in the central part of the country. This work contributes to our knowledge of two genera of Boletaceae in a geographical area that is scarcely studied, and thus, our understanding of its biocultural relevance is enriched. Full article
(This article belongs to the Special Issue Polyphasic Identification of Fungi 3.0)
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30 pages, 7818 KiB  
Article
Exploring the Diversity and Systematics of Phaeosphaeriaceae: Taxonomic Novelties from Ecologically Diverse Habitats and Their Phylogenetic Resolution
by Dhanushka N. Wanasinghe and Sajeewa S. N. Maharachchikumbura
J. Fungi 2023, 9(8), 853; https://doi.org/10.3390/jof9080853 - 15 Aug 2023
Cited by 1 | Viewed by 1338
Abstract
The family Phaeosphaeriaceae is a diverse group of ascomycetous fungi that are commonly found in terrestrial habitats worldwide. In recent years, there has been increasing interest in the biodiversity of Phaeosphaeriaceae in China, particularly in Sichuan Province, which has not been fully explored [...] Read more.
The family Phaeosphaeriaceae is a diverse group of ascomycetous fungi that are commonly found in terrestrial habitats worldwide. In recent years, there has been increasing interest in the biodiversity of Phaeosphaeriaceae in China, particularly in Sichuan Province, which has not been fully explored for its high fungal diversity. In our study, we conducted extensive surveys in Sichuan Province to identify and describe new species of Ascomycota with diverse habitats. Here, we present a taxonomic revision of Phaeosphaeriaceae with taxonomic novelties from terrestrial habitats in Sichuan Province based on a multi-gene phylogenetic approach. Our study focuses on the description of four new species of Phaeosphaeriaceae, representing novel additions to the diversity of this fungal family. Using a combination of morphological and molecular data, we provide detailed descriptions of the new taxa and their placement within the family. Additionally, we discuss the phylogenetic relationships of these new taxa with other members of Phaeosphaeriaceae, providing insights into the correct taxonomic classification of the family. Our taxonomic revision contributes to understanding fungal diversity in China and provides a foundation for future studies investigating the taxonomy and ecological roles of Phaeosphaeriaceae fungi. Furthermore, our multi-gene phylogenetic approach provides increased resolution and accuracy in the delimitation of species boundaries within the family. Our study highlights the importance of continued exploration and taxonomic revision in order to fully understand the diversity and distribution of fungal species in China and beyond. New species: Paraloratospora sichuanensis, Phaeosphaeria chengduensis, P. sichuanensis, and Septoriella shoemakeri. New combinations: Paraloratospora breonadiae, P. fructigena, Septoriella ammophilicola, S. asparagicola, S. festucae, S. luzulae, and S. verrucispora. New names: Septoriella paradactylidis, and S. neomuriformis. Full article
(This article belongs to the Special Issue Polyphasic Identification of Fungi 3.0)
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14 pages, 2900 KiB  
Article
Additions to the Genus Helicosporium (Tubeufiaceae, Tubeufiales) from China with an Identification Key for Helicosporium Taxa
by Xing-Juan Xiao, Jian Ma, Li-Juan Zhang, Ning-Guo Liu, Yuan-Pin Xiao, Xing-Guo Tian, Zong-Long Luo and Yong-Zhong Lu
J. Fungi 2023, 9(7), 775; https://doi.org/10.3390/jof9070775 - 22 Jul 2023
Cited by 1 | Viewed by 980
Abstract
Helicosporous hyphomycetes is a group of filamentous fungi that shows promising application prospects in metabolizing bioactive natural compounds. During a study of helicosporous fungi in China, six new helicosporous taxa were collected and isolated from decaying wood in Guangxi Zhuang Autonomous Region, China. [...] Read more.
Helicosporous hyphomycetes is a group of filamentous fungi that shows promising application prospects in metabolizing bioactive natural compounds. During a study of helicosporous fungi in China, six new helicosporous taxa were collected and isolated from decaying wood in Guangxi Zhuang Autonomous Region, China. Morphological comparisons with multi-gene phylogenetic analyses revealed that these six taxa belong to Helicosporium (Tubeufiaceae, Tubeufiales), and they were recognized as three novel species and were named Helicosporium liuzhouense, H. multidentatum, and H. nanningense. Detailed descriptions and illustrations of the newly discovered taxa and comparisons with similar fungi are provided. In addition, a list and a key to accepted Helicosporium species are provided. Full article
(This article belongs to the Special Issue Polyphasic Identification of Fungi 3.0)
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34 pages, 10180 KiB  
Article
Taxonomic and Phylogenetic Studies of Saprobic Fungi Associated with Mangifera indica in Yunnan, China
by Er-Fu Yang, Dong-Qin Dai, Jayarama D. Bhat, Turki M. Dawoud, Itthayakorn Promputtha, Nimal Adikaram, Steven L. Stephenson, Samantha C. Karunarathna and Saowaluck Tibpromma
J. Fungi 2023, 9(6), 680; https://doi.org/10.3390/jof9060680 - 16 Jun 2023
Cited by 1 | Viewed by 1385
Abstract
Fungi are a large and diverse group of microorganisms, and although the estimated number of species ranges between 2 and 11 million, only around 150,000 species have been described thus far. The investigation of plant-associated fungi is beneficial for estimating global fungal diversity, [...] Read more.
Fungi are a large and diverse group of microorganisms, and although the estimated number of species ranges between 2 and 11 million, only around 150,000 species have been described thus far. The investigation of plant-associated fungi is beneficial for estimating global fungal diversity, for ecosystem conservation, and for the continued development of industry and agriculture. Mango, one of the world’s five most economically important fruit crops, is grown in over 100 countries and has been demonstrated to have a great economical value. During surveys of mango-associated saprobic fungi in Yunnan (China), we discovered three new species (Acremoniisimulans hongheensis, Chaenothecopsis hongheensis and Hilberina hongheensis) and five new records. The phylogenetic analyses of multi-gene sequences (LSU, SSU, ITS, rpb2, tef1-α and tub2) coupled with morphological examinations were used to identify all the taxa. Full article
(This article belongs to the Special Issue Polyphasic Identification of Fungi 3.0)
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21 pages, 4346 KiB  
Article
Morphological and Phylogenetic Characterisations Reveal Four New Species in Leptosphaeriaceae (Pleosporales, Dothideomycetes)
by Ying Gao, Antonio Roberto Gomes de Farias, Hong-Bo Jiang, Samantha C. Karunarathna, Jian-Chu Xu, Saowaluck Tibpromma and Heng Gui
J. Fungi 2023, 9(6), 612; https://doi.org/10.3390/jof9060612 - 26 May 2023
Cited by 1 | Viewed by 1569
Abstract
Leptosphaeriaceae is a widely distributed fungal family with diverse lifestyles. The family includes several genera that can be distinguished by morphology and molecular phylogenetic analysis. During our investigation of saprobic fungi on grasslands in Yunnan Province, China, four fungal taxa belonging to Leptosphaeriaceae [...] Read more.
Leptosphaeriaceae is a widely distributed fungal family with diverse lifestyles. The family includes several genera that can be distinguished by morphology and molecular phylogenetic analysis. During our investigation of saprobic fungi on grasslands in Yunnan Province, China, four fungal taxa belonging to Leptosphaeriaceae associated with grasses were collected. Morphological observations and phylogenetic analyses of the combined SSU, LSU, ITS, tub2, and rpb2 loci based on maximum likelihood and Bayesian inference were used to reveal the taxonomic placement of these fungal taxa. This study introduces four new taxa, viz. Leptosphaeria yunnanensis, L. zhaotongensis, Paraleptosphaeria kunmingensis, and Plenodomus zhaotongensis. Colour photo plates, full descriptions, and a phylogenetic tree to show the placement of the new taxa are provided. Full article
(This article belongs to the Special Issue Polyphasic Identification of Fungi 3.0)
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