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27 pages, 5279 KiB

Open AccessArticle

Genomic Characterization of Parengyodontium torokii sp. nov., a Biofilm-Forming Fungus Isolated from Mars 2020 Assembly Facility

by Ceth W. Parker, Marcus de Melo Teixeira, Nitin K. Singh, Huzefa A. Raja, Kristof B. Cank, Giada Spigolon, Nicholas H. Oberlies, Bridget M. Barker, Jason E. Stajich, Christopher E. Mason and Kasthuri Venkateswaran

J. Fungi 2022, 8(1), 66; https://doi.org/10.3390/jof8010066 - 9 Jan 2022

Cited by 6 | Viewed by 5032

Abstract

A fungal strain (FJII-L10-SW-P1) was isolated from the Mars 2020 spacecraft assembly facility and exhibited biofilm formation on spacecraft-qualified Teflon surfaces. The reconstruction of a six-loci gene tree (ITS, LSU, SSU, RPB1 and RPB2, and TEF1) using multi-locus sequence typing (MLST) [...] Read more.

A fungal strain (FJII-L10-SW-P1) was isolated from the Mars 2020 spacecraft assembly facility and exhibited biofilm formation on spacecraft-qualified Teflon surfaces. The reconstruction of a six-loci gene tree (ITS, LSU, SSU, RPB1 and RPB2, and TEF1) using multi-locus sequence typing (MLST) analyses of the strain FJII-L10-SW-P1 supported a close relationship to other known Parengyodontium album subclade 3 isolates while being phylogenetically distinct from subclade 1 strains. The zig-zag rachides morphology of the conidiogenous cells and spindle-shaped conidia were the distinct morphological characteristics of the P. album subclade 3 strains. The MLST data and morphological analysis supported the conclusion that the P. album subclade 3 strains could be classified as a new species of the genus Parengyodontium and placed in the family Cordycipitaceae. The name Parengyodontium torokii sp. nov. is proposed to accommodate the strain, with FJII-L10-SW-P1 as the holotype. The genome of the FJII-L10-SW-P1 strain was sequenced, annotated, and the secondary metabolite clusters were identified. Genes predicted to be responsible for biofilm formation and adhesion to surfaces were identified. Homology-based assignment of gene ontologies to the predicted proteome of P. torokii revealed the presence of gene clusters responsible for synthesizing several metabolic compounds, including a cytochalasin that was also verified using traditional metabolomic analysis. Full article

(This article belongs to the Special Issue Diversity and Classification of Environmental Fungi)

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19 pages, 45788 KiB

Open AccessArticle

Morphology and Phylogeny Reveal Vamsapriyaceae fam. nov. (Xylariales, Sordariomycetes) with Two Novel Vamsapriya Species

by Ya-Ru Sun, Ning-Guo Liu, Milan C. Samarakoon, Ruvishika S. Jayawardena, Kevin D. Hyde and Yong Wang

J. Fungi 2021, 7(11), 891; https://doi.org/10.3390/jof7110891 - 21 Oct 2021

Cited by 13 | Viewed by 2821

Abstract

Phylogenetic analyses of combined LSU, rpb2, tub2 and ITS sequence data of representative Xylariales taxa indicated that Diabolocovidia, Didymobotryum and Vamsapriya cluster together and form a distinct clade in Xylariales. Morphological comparison also shows their distinctiveness from other families of [...] Read more.

Phylogenetic analyses of combined LSU, rpb2, tub2 and ITS sequence data of representative Xylariales taxa indicated that Diabolocovidia, Didymobotryum and Vamsapriya cluster together and form a distinct clade in Xylariales. Morphological comparison also shows their distinctiveness from other families of Xylariales. Therefore, we introduce it as a novel family, Vamsapriyaceae. Based on morphological characteristics, Podosporium and Tretophragmia, which were previously classified in Ascomycota genera incertae sedis, are now included in the Vamsapriyaceae. In addition, three Vamsapriya species, V. chiangmaiensis sp. nov, V. uniseptata sp. nov, and V. indica are described and illustrated in this paper. Full article

(This article belongs to the Special Issue Diversity and Classification of Environmental Fungi)

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20 pages, 4174 KiB

Open AccessArticle

The Genomic and Transcriptomic Analyses of Floccularia luteovirens, a Rare Edible Fungus in the Qinghai–Tibet Plateau, Provide Insights into the Taxonomy Placement and Fruiting Body Formation

by Zhengjie Liu, Hongyun Lu, Xinglin Zhang and Qihe Chen

J. Fungi 2021, 7(11), 887; https://doi.org/10.3390/jof7110887 - 20 Oct 2021

Cited by 6 | Viewed by 2512

Abstract

Floccularia luteovirens is a famous and precious edible mushroom (Huang Mogu) on the Qinghai–Tibet plateau that has a unique flavor and remarkable medical functions. Herein, we report a reference-grade 27 Mb genome of F. luteovirens containing 7068 protein-coding genes. The genome component and [...] Read more.

Floccularia luteovirens is a famous and precious edible mushroom (Huang Mogu) on the Qinghai–Tibet plateau that has a unique flavor and remarkable medical functions. Herein, we report a reference-grade 27 Mb genome of F. luteovirens containing 7068 protein-coding genes. The genome component and gene functions were predicted. Genome ontology enrichment and pathway analyses indicated the potential production capacity for terpenoids, polyketides and polysaccharides. Moreover, 16 putative gene clusters and 145 genes coding for secondary metabolites were obtained, including guadinomine and melleolides. In addition, phylogenetic and comparative genomic analyses shed light on the precise classification of F. luteovirens suggesting that it belongs to the genus Floccularia instead of Armillaria. RNA-sequencing and comparative transcriptomic analysis revealed differentially expressed genes during four developmental stages of F. luteovirens, that of which helps to identify important genes regulating fruiting body formation for strain modification. This study will provide insight into artificial cultivation and increase the production of useful metabolites. Full article

(This article belongs to the Special Issue Diversity and Classification of Environmental Fungi)

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83 pages, 12995 KiB

Open AccessArticle

Ganoderma (Ganodermataceae, Basidiomycota) Species from the Greater Mekong Subregion

by Thatsanee Luangharn, Samantha C. Karunarathna, Arun Kumar Dutta, Soumitra Paloi, Itthayakorn Promputtha, Kevin D. Hyde, Jianchu Xu and Peter E. Mortimer

J. Fungi 2021, 7(10), 819; https://doi.org/10.3390/jof7100819 - 30 Sep 2021

Cited by 34 | Viewed by 7564

Abstract

The cosmopolitan fungal genus Ganoderma is an important pathogen on arboreal plant hosts, particularly in tropical and temperate regions. It has long been used as a traditional medicine because of its medicinal properties and chemical constituents. In this study, Ganoderma collections were made [...] Read more.

The cosmopolitan fungal genus Ganoderma is an important pathogen on arboreal plant hosts, particularly in tropical and temperate regions. It has long been used as a traditional medicine because of its medicinal properties and chemical constituents. In this study, Ganoderma collections were made in the Greater Mekong Subregion (GMS), encompassing tropical parts of Laos, Myanmar, Thailand, Vietnam, and temperate areas in Yunnan Province, China. The specimens used in this study are described based on micro-macro-characteristics and phylogenetic analysis of combined ITS, LSU, TEF1α, and RPB2 sequence data. In this comprehensive study, we report 22 Ganoderma species from the GMS, namely, G. adspersum, G. applanatum, G. australe, G. calidophilum, G. ellipsoideum, G. flexipes, G. gibbosum, G. heohnelianum, G. hochiminhense, G. leucocontextum, G. lucidum, G. multiplicatum, G. multipileum, G. myanmarense, G. orbiforme, G. philippii, G. resinaceum, G. sichuanense, G. sinense, G. subresinosum, G. williamsianum, and G. tsugae. Some of these species were reported in more than one country within the GMS. Of these 22 species, 12 were collected from Yunnan Province, China; three were collected from Laos; three species, two new records, and one new species were collected from Myanmar; 15 species and four new records were collected from Thailand, and one new species was collected from Vietnam. Comprehensive descriptions, color photographs of macro- and micro-characteristics, the distribution of Ganoderma within the GMS, as well as a phylogenetic tree showing the placement of all reported Ganoderma from the GMS are provided. Full article

(This article belongs to the Special Issue Diversity and Classification of Environmental Fungi)

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14 pages, 2059 KiB

Open AccessArticle

The Response of Airborne Mycobiome to Dust Storms in the Eastern Mediterranean

by Xuefeng Peng, Daniela Gat, Adina Paytan and Yinon Rudich

J. Fungi 2021, 7(10), 802; https://doi.org/10.3390/jof7100802 - 25 Sep 2021

Cited by 9 | Viewed by 2787

Abstract

Airborne microbial communities directly impact the health of humans, animals, plants, and receiving ecosystems. While airborne bacterial and fungal communities have been studied by both cultivation-based methods and metabarcoding surveys targeting specific molecular markers, fewer studies have used shotgun metagenomics to study the [...] Read more.

Airborne microbial communities directly impact the health of humans, animals, plants, and receiving ecosystems. While airborne bacterial and fungal communities have been studied by both cultivation-based methods and metabarcoding surveys targeting specific molecular markers, fewer studies have used shotgun metagenomics to study the airborne mycobiome. We analyzed the diversity and relative abundance of fungi in nine airborne metagenomes collected on clear days (“background”) and during dust storms in the Eastern Mediterranean. The negative correlation between the relative abundance of fungal reads and the concentrations of atmospheric particulate matter having an aerodynamic diameter smaller than 10 μm (PM10) indicate that dust storms lower the proportion of fungi in the airborne microbiome, possibly due to the lower relative abundance of fungi in the dust storm source regions and/or more effective transport of bacteria by the dust. Airborne fungal community composition was altered by the dust storms, particularly those originated from Syria, which was enriched with xerophilic fungi. We reconstructed a high-quality fungal metagenome-assembled genome (MAG) from the order Cladosporiales, which include fungi known to adapt to environmental extremes commonly faced by airborne microbes. The negative correlation between the relative abundance of Cladosporiales MAG and PM10 concentrations indicate that its origin is dominated by local sources and likely includes the indoor environments found in the city. Full article

(This article belongs to the Special Issue Diversity and Classification of Environmental Fungi)

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18 pages, 4656 KiB

Open AccessArticle

Morphology and Phylogeny of Gnomoniopsis (Gnomoniaceae, Diaporthales) from Fagaceae Leaves in China

by Ning Jiang, Hermann Voglmayr, Dan-Ran Bian, Chun-Gen Piao, Sheng-Kun Wang and Yong Li

J. Fungi 2021, 7(10), 792; https://doi.org/10.3390/jof7100792 - 24 Sep 2021

Cited by 28 | Viewed by 3358

Abstract

Gnomoniopsis (Gnomoniaceae, Diaporthales) is a well-classified genus inhabiting leaves, branches and fruits of the hosts in three plant families, namely Fagaceae, Onagraceae and Rosaceae. In the present study, eighteen Gnomoniopsis isolates were obtained from diseased leaves of Fagaceae [...] Read more.

Gnomoniopsis (Gnomoniaceae, Diaporthales) is a well-classified genus inhabiting leaves, branches and fruits of the hosts in three plant families, namely Fagaceae, Onagraceae and Rosaceae. In the present study, eighteen Gnomoniopsis isolates were obtained from diseased leaves of Fagaceae hosts collected from Fujian, Guangdong, Hainan, Henan, Jiangxi and Shaanxi provinces in China. Morphology from the cultures and phylogeny based on the 5.8S nuclear ribosomal DNA gene with the two flanking internally transcribed spacer (ITS) regions, the translation elongation factor 1-alpha (tef1) and the beta-tubulin (tub2) genes were employed to identify these isolates. As a result, seven species were revealed, viz. Gnomoniopsis castanopsidis, G. fagacearum, G. guangdongensis, G. hainanensis, G. rossmaniae and G. silvicola spp. nov, as well as a known species G. daii. In addition, G. daii was firstly reported on the host Quercus aliena. Full article

(This article belongs to the Special Issue Diversity and Classification of Environmental Fungi)

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20 pages, 5569 KiB

Open AccessArticle

Macrofungi Cultivation in Shady Forest Areas Significantly Increases Microbiome Diversity, Abundance and Functional Capacity in Soil Furrows

by Dong Liu, Yanliang Wang, Peng Zhang, Fuqiang Yu and Jesús Perez-Moreno

J. Fungi 2021, 7(9), 775; https://doi.org/10.3390/jof7090775 - 18 Sep 2021

Cited by 9 | Viewed by 5047

Abstract

Cultivating macrofungi is an important management measure to develop economy in shady forest areas; however, its effect on soil ecology, especially microbial abundance and structure, remains insufficiently studied. Herein, in a subtropical forestland, soil chemical and enzyme analyses, metagenomic sequencing and quantitative real-time [...] Read more.

Cultivating macrofungi is an important management measure to develop economy in shady forest areas; however, its effect on soil ecology, especially microbial abundance and structure, remains insufficiently studied. Herein, in a subtropical forestland, soil chemical and enzyme analyses, metagenomic sequencing and quantitative real-time PCR were employed to evaluate the impact of Stropharia rugosoannulata cultivation on soil microbiomes in three niches: soil below fungal beds, soil from furrows, and control forest soil with no influence from mushroom cultivation. Nutrients were accumulated in the soil below fungal beds with a significant increase (p < 0.05) in SOC, total C, total N, available P, and the activities of glucosidase and cellobiosidase. Non-metric multidimensional scaling and PERMANOVA results indicated that the structure of the microbiomes had been significantly (p < 0.05) shaped among the different niches. Soil furrows were microbial hotspots characterized by the higher microbial diversity and richness. Moreover, the increased microbiome abundance (assessed through qPCR) and the high number of significant stimulated functional types (based on MetaCyc genome database) indicated an enhanced functional capacity in furrows. Together, these results provide a comprehensive understanding of the microbial assemblies and the differently influenced soil properties in mushroom cultivation areas. Full article

(This article belongs to the Special Issue Diversity and Classification of Environmental Fungi)

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18 pages, 36413 KiB

Open AccessArticle

Discovery and Extrolite Production of Three New Species of Talaromyces Belonging to Sections Helici and Purpurei from Freshwater in Korea

by Thuong T. T. Nguyen, Jens Christian Frisvad, Paul M. Kirk, Hyo Jin Lim and Hyang Burm Lee

J. Fungi 2021, 7(9), 722; https://doi.org/10.3390/jof7090722 - 3 Sep 2021

Cited by 13 | Viewed by 3668

Abstract

Three novel fungal species, Talaromyces gwangjuensis, T. koreana, and T. teleomorpha were found in Korea during an investigation of fungi in freshwater. The new species are described here using morphological characters, a multi-gene phylogenetic analysis of the ITS, BenA, [...] Read more.

Three novel fungal species, Talaromyces gwangjuensis, T. koreana, and T. teleomorpha were found in Korea during an investigation of fungi in freshwater. The new species are described here using morphological characters, a multi-gene phylogenetic analysis of the ITS, BenA, CaM, RPB2 regions, and extrolite data. Talaromyces gwangjuensis is characterized by restricted growth on CYA, YES, monoverticillate and biverticillate conidiophores, and globose smooth-walled conidia. Talaromyces koreana is characterized by fast growth on MEA, biverticillate conidiophores, or sometimes with additional branches and the production of acid on CREA. Talaromyces teleomorpha is characterized by producing creamish-white or yellow ascomata on OA and MEA, restricted growth on CREA, and no asexual morph observed in the culture. A phylogenetic analysis of the ITS, BenA, CaM, and RPB2 sequences showed that the three new taxa form distinct monophyletic clades. Detailed descriptions, illustrations, and phylogenetic trees are provided. Full article

(This article belongs to the Special Issue Diversity and Classification of Environmental Fungi)

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13 pages, 1565 KiB

Open AccessArticle

Genetic Analyses of Saprolegnia Strains Isolated from Salmonid Fish of Different Geographic Origin Document the Connection between Pathogenicity and Molecular Diversity

by Abdelhameed Elameen, Svein Stueland, Ralf Kristensen, Rosa F. Fristad, Trude Vrålstad and Ida Skaar

J. Fungi 2021, 7(9), 713; https://doi.org/10.3390/jof7090713 - 30 Aug 2021

Cited by 10 | Viewed by 3209

Abstract

Saprolegnia parasitica is recognized as one of the most important oomycetes pests of salmon and trout species. The amplified fragment length polymorphism (AFLP) and method sequence data of the internal transcribed spacer (ITS) were used to study the genetic diversity and relationships of [...] Read more.

Saprolegnia parasitica is recognized as one of the most important oomycetes pests of salmon and trout species. The amplified fragment length polymorphism (AFLP) and method sequence data of the internal transcribed spacer (ITS) were used to study the genetic diversity and relationships of Saprolegnia spp. collected from Canada, Chile, Japan, Norway and Scotland. AFLP analysis of 37 Saprolegnia spp. isolates using six primer combinations gave a total of 163 clear polymorphic bands. Bayesian cluster analysis using genetic similarity divided the isolates into three main groups, suggesting that there are genetic relationships among the isolates. The unweighted pair group method with arithmetic mean (UPGMA) and principal coordinate analysis (PCO) confirmed the pattern of the cluster analyses. ITS analyses of 48 Saprolegnia sequences resulted in five well-defined clades. Analysis of molecular variance (AMOVA) revealed greater variation within countries (91.01%) than among countries (8.99%). We were able to distinguish the Saprolegnia isolates according to their species, ability to produce oogonia with and without long spines on the cysts and their ability to or not to cause mortality in salmonids. AFLP markers and ITS sequencing data obtained in the study, were found to be an efficient tool to characterize the genetic diversity and relationships of Saprolegnia spp. The comparison of AFLP analysis and ITS sequence data using the Mantel test showed a very high and significant correlation (r² = 0.8317). Full article

(This article belongs to the Special Issue Diversity and Classification of Environmental Fungi)

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24 pages, 3266 KiB

Open AccessArticle

Five Novel Taxa from Freshwater Habitats and New Taxonomic Insights of Pleurotheciales and Savoryellomycetidae

by Wei Dong, Rajesh Jeewon, Kevin D. Hyde, Er-Fu Yang, Huang Zhang, Xiandong Yu, Gennuo Wang, Nakarin Suwannarach, Mingkwan Doilom and Zhangyong Dong

J. Fungi 2021, 7(9), 711; https://doi.org/10.3390/jof7090711 - 30 Aug 2021

Cited by 14 | Viewed by 3037

Abstract

Pleurotheciales is the largest order in Savoryellomycetidae with a large proportion of species known from freshwater habitats. In order to investigate the phylogenetic relationships of taxa within Pleurotheciales and contribute to their diversity, submerged wood was collected from freshwater habitats in China (Yunnan [...] Read more.

Pleurotheciales is the largest order in Savoryellomycetidae with a large proportion of species known from freshwater habitats. In order to investigate the phylogenetic relationships of taxa within Pleurotheciales and contribute to their diversity, submerged wood was collected from freshwater habitats in China (Yunnan Province) and Thailand. Two dematiaceous, sporodochial hyphomycetes and one annulatascales-like ascomycete with unusual morphology as compared to extant ones were discovered. They were subjected to DNA-based phylogenetic analyses and the results revealed three distinct lineages in Savoryellomycetidae. This morpho-phylo taxonomic study supports the establishment of five novel taxa including two novel genera, Obliquifusoideum and Saprodesmium, and three novel species, Coleodictyospora muriformis, Obliquifusoideum guttulatum and Saprodesmium dematiosporum. Coleodictyospora muriformis and S. dematiosporum are placed in Pleurotheciales, while O. guttulatum is referred to Savoryellomycetidae genera incertae sedis. The phylogenetic relationships are also presented for Coleodictyospora and Pseudocoleodictyospora, which raises an intriguing taxonomic issue. These two genera are positioned in two different classes, viz Sordariomycetes and Dothideomycetes, although they are quite similar except for the presence of a conidial sheath. This study expands our knowledge of the fungal diversity of freshwater fungi, and also indicates that Pleurotheciales species are mostly found in freshwater habitats. Full article

(This article belongs to the Special Issue Diversity and Classification of Environmental Fungi)

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16 pages, 7686 KiB

Open AccessArticle

Complete Genomic Characterization and Identification of Saccharomycopsisphalluae sp. nov., a Novel Pathogen Causes Yellow Rot Disease on Phallus rubrovolvatus

by Xiaoxiao Yuan, Keqin Peng, Changtian Li, Zhibo Zhao, Xiangyu Zeng, Fenghua Tian and Yu Li

J. Fungi 2021, 7(9), 707; https://doi.org/10.3390/jof7090707 - 28 Aug 2021

Cited by 14 | Viewed by 3195

Abstract

“Hongtuozhusun” (Phallus rubrovolvatus) is an important edible and medicinal mushroom endemic to Southwest China. However, yellow rot disease is a severe disease of P. rubrovolvatus that occurs extensively in Guizhou Province. It has caused major economic losses and hinders the [...] Read more.

“Hongtuozhusun” (Phallus rubrovolvatus) is an important edible and medicinal mushroom endemic to Southwest China. However, yellow rot disease is a severe disease of P. rubrovolvatus that occurs extensively in Guizhou Province. It has caused major economic losses and hinders the development of the P. rubrovolvatus industry. In this study, 28 microorganism strains were isolated from diseased fruiting bodies of P. rubrovolvatus at various stages, two of which were confirmed to be pathogenic based on Koch’s postulates. These two strains are introduced herein as Saccharomycopsisphalluae sp. nov. based on morphological, physiological, and molecular analysis. We reported a high-quality de novo sequencing and assembly of the S. phalluae genome using single-molecule real-time sequencing technology. The whole genome was approximately 14.148 Mb with a G+C content of 43.55%. Genome assembly generated 8 contigs with an N50 length of 1,822,654 bp. The genome comprised 5966 annotated protein-coding genes. This is the first report of mushroom disease caused by Saccharomycopsis species. We expect that the information on genome properties, particularly in pathogenicity-related genes, assist in developing effective control measures in order to prevent severe losses and make amendments in management strategies. Full article

(This article belongs to the Special Issue Diversity and Classification of Environmental Fungi)

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20 pages, 7736 KiB

Open AccessArticle

First Characterization and Description of Aspergillus Series Versicolores in French Bioaerosols

by Antoine Géry, Jean-Philippe Rioult, Natacha Heutte, Virginie Séguin, Julie Bonhomme and David Garon

J. Fungi 2021, 7(8), 676; https://doi.org/10.3390/jof7080676 - 21 Aug 2021

Cited by 9 | Viewed by 5449

Abstract

Air quality can be altered by fungal contaminants suspended in the air, forming bioaerosols. Aspergilli section Nidulantes series Versicolores are recurrent in bioaerosols and are mainly responsible for allergies and asthma aggravation. Phylogenetic studies recently identified 12 new species within this series. This [...] Read more.

Air quality can be altered by fungal contaminants suspended in the air, forming bioaerosols. Aspergilli section Nidulantes series Versicolores are recurrent in bioaerosols and are mainly responsible for allergies and asthma aggravation. Phylogenetic studies recently identified 12 new species within this series. This study is the first to identify species of Aspergillus series Versicolores in French bioaerosols and to characterize them macroscopically, microscopically and molecularly. Bioaerosols were collected in a cancer treatment center, in contaminated homes and in agricultural environments. A total of 93 isolates were cultured on selective media, observed by optical microscopy and identified by benA amplification before sequencing. The field data (temperature and relative humidity) were statistically tested to explore the ecology of these species. Eight species were identified from bioaerosols: Aspergillus creber and A. jensenii, which represent more than 80% of the isolates, and A. protuberus, A. puulaauensis, A. sydowii, A. tabacinus, A. amoenus and A. fructus. Aspergilli series Versicolores are distributed differently depending on the sampling site and climatic determinants. Aspergillus protuberus was found in bioaerosols collected under significantly lower relative humidity (p = 3.899 × 10⁻⁴). Characterization and repartition of these isolates belonging to the Versicolores series constitute an important step to better assess exposure to fungal bioaerosols. Full article

(This article belongs to the Special Issue Diversity and Classification of Environmental Fungi)

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46 pages, 24582 KiB

Open AccessArticle

Biodiversity of Lignicolous Freshwater Hyphomycetes from China and Thailand and Description of Sixteen Species

by Dan-Feng Bao, Kevin D. Hyde, Eric H. C. McKenzie, Rajesh Jeewon, Hong-Yan Su, Sarunya Nalumpang and Zong-Long Luo

J. Fungi 2021, 7(8), 669; https://doi.org/10.3390/jof7080669 - 18 Aug 2021

Cited by 32 | Viewed by 4850

Abstract

Freshwater hyphomycetes are a highly diverse group of fungi with a worldwide distribution and have been mostly reported from tropical and subtropical regions. During investigations of freshwater fungi from the Greater Mekong subregion in China and Thailand, sixteen freshwater hyphomycetes (three of them [...] Read more.

Freshwater hyphomycetes are a highly diverse group of fungi with a worldwide distribution and have been mostly reported from tropical and subtropical regions. During investigations of freshwater fungi from the Greater Mekong subregion in China and Thailand, sixteen freshwater hyphomycetes (three of them belong to the class Dothideomycetes while thirteen belong to the class Sordariomycetes) were collected. Based on morphology and multi-gene phylogenetic analyses, Neospadicoides thailandica, Pseudodactylaria aquatica, Sporidesmium nujiangense, Tetraploa thailandica, Vamsapriyaaquatica and Wongia fusiformis are described as new species; Aquapteridospora bambusinum is proposed as a new combination; Acrodictys liputii, Chloridium gonytrichii, Pseudoberkleasmium chiangmaiense, Pleomonodictys capensis, Sporidesmium aturbinatum and Vamsapriya indica are reported as new country records; and Sporidesmium tropicale, Sporoschisma chiangraiense and Sporoschisma longicatenatum are introduced as three new collections. In addition, a checklist of freshwater fungi from China over the last five years is also provided. Full article

(This article belongs to the Special Issue Diversity and Classification of Environmental Fungi)

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21 pages, 3860 KiB

Open AccessArticle

Insight into the Systematics of Novel Entomopathogenic Fungi Associated with Armored Scale Insect, Kuwanaspis howardi (Hemiptera: Diaspididae) in China

by Xiu-Lan Xu, Qian Zeng, Yi-Cong Lv, Rajesh Jeewon, Sajeewa S. N. Maharachchikumbura, Dhanushka N. Wanasinghe, Kevin D. Hyde, Qian-Gang Xiao, Ying-Gao Liu and Chun-Lin Yang

J. Fungi 2021, 7(8), 628; https://doi.org/10.3390/jof7080628 - 2 Aug 2021

Cited by 7 | Viewed by 3710

Abstract

This study led to the discovery of three entomopathogenic fungi associated with Kuwanaspis howardi, a scale insect on Phyllostachys heteroclada (fishscale bamboo) and Pleioblastus amarus (bitter bamboo) in China. Two of these species belong to Podonectria: P. kuwanaspidis X.L. Xu & [...] Read more.

This study led to the discovery of three entomopathogenic fungi associated with Kuwanaspis howardi, a scale insect on Phyllostachys heteroclada (fishscale bamboo) and Pleioblastus amarus (bitter bamboo) in China. Two of these species belong to Podonectria: P. kuwanaspidis X.L. Xu & C.L. Yang sp. nov. and P. novae-zelandiae Dingley. The new species P. kuwanaspidis has wider and thicker setae, longer and wider asci, longer ascospores, and more septa as compared with similar Podonectria species. The morphs of extant species P. novae-zelandiae is confirmed based on sexual and asexual morphologies. Maximum likelihood and Bayesian inference analyses of ITS, LSU, SSU, tef1-α, and rpb2 sequence data provide further evidence for the validity of the two species and their placement in Podonectriaceae (Pleosporales). The second new species, Microcera kuwanaspidis X.L. Xu & C.L. Yang sp. nov., is established based on DNA sequence data from ITS, LSU, SSU, tef1-α, rpb1, rpb2, acl1, act, cmdA, and his3 gene regions, and it is characterized by morphological differences in septum numbers and single conidial mass. Full article

(This article belongs to the Special Issue Diversity and Classification of Environmental Fungi)

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15 pages, 2087 KiB

Open AccessArticle

Distinct Compartmentalization of Microbial Community and Potential Metabolic Function in the Fruiting Body of Tricholoma matsutake

by Dong Liu, Jesús Perez-Moreno, Peng Zhang, Ran Wang, Caspar C. C. Chater and Fuqiang Yu

J. Fungi 2021, 7(8), 586; https://doi.org/10.3390/jof7080586 - 22 Jul 2021

Cited by 7 | Viewed by 4483

Abstract

The uniquely compartmentalized fruiting body structure of the ectomycorrhizal fungus (EMF) Tricholoma matsutake, is a hotspot of microbial habitation and interaction. However, microbial diversity within this microniche structure of the EMF is rarely investigated. Furthermore, there is limited information concerning microbiomes associated [...] Read more.

The uniquely compartmentalized fruiting body structure of the ectomycorrhizal fungus (EMF) Tricholoma matsutake, is a hotspot of microbial habitation and interaction. However, microbial diversity within this microniche structure of the EMF is rarely investigated. Furthermore, there is limited information concerning microbiomes associated with sporomes belonging to the ubiquitous fungal phylum Basidiomycota, particularly with respect to fungus-EMF interactions. In this study, we conducted high throughput sequencing, using ITS (fungal) and 16S rRNA (bacterial) marker genes to characterize and compare fruiting body microbiomes in the outer (pileipellis and stipitipellis) and inner layers (pileum context, stipe context, and lamellae) of the fruiting body of T. matsutake. Our results show the number of unique bacterial operational taxonomic units (OTUs) among the different compartments ranged from 410 to 499 and was more than double that of the shared/common OTUs (235). Micrococcales, Bacillales, Caulobacter, and Sphingomonas were the primary significant bacterial taxa within the different compartments of the dissected T. matsutake fruiting body. Non-parametric multivariate analysis of variance showed significant compartmental differences for both the bacterial and the fungal community structure within the T. matsutake fruiting body. The metabolic profiling revealed putative metabolisms (of amino acids, carbohydrates, and nucleotides) and the biosynthesis of secondary metabolites to be highly enriched in outer layers; in the inner parts, the metabolisms of energy, cofactors, vitamins, and lipids were significantly higher. This study demonstrates for the first time the distinct compartmentalization of microbial communities and potential metabolic function profiles in the fruiting body of an economically important EMF T. matsutake. Full article

(This article belongs to the Special Issue Diversity and Classification of Environmental Fungi)

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25 pages, 3941 KiB

Open AccessArticle

Diversity, Phylogeny and Antagonistic Activity of Fungal Endophytes Associated with Endemic Species of Cycas (Cycadales) in China

by Melissa H. Pecundo, Thomas Edison E. dela Cruz, Tao Chen, Kin Israel Notarte, Hai Ren and Nan Li

J. Fungi 2021, 7(7), 572; https://doi.org/10.3390/jof7070572 - 18 Jul 2021

Cited by 22 | Viewed by 5120

Abstract

The culture-based approach was used to characterize the fungal endophytes associated with the coralloid roots of the endemic Cycas debaoensis and Cycas fairylakea from various population sites in China. We aim to determine if the assemblages of fungal endophytes inside these endemic plant [...] Read more.

The culture-based approach was used to characterize the fungal endophytes associated with the coralloid roots of the endemic Cycas debaoensis and Cycas fairylakea from various population sites in China. We aim to determine if the assemblages of fungal endophytes inside these endemic plant hosts are distinct and could be explored for bioprospecting. The isolation method yielded a total of 284 culturable fungal strains. Identification based on the analysis of the internal transcribed spacer (ITS) rDNA showed that they belonged to two phyla, five classes, eight orders and 22 families. At least 33 known genera and 62 different species were confirmed based on >97% ITS sequence similarity. The most frequent and observed core taxa in the two host species regardless of their population origin were Talaromyces, Penicillium, Fusarium, Pochonia and Gliocladiopsis. Seventy percent was a rare component of the fungal communities with only one or two recorded isolates. Contrary to common notions, diversity and fungal richness were significantly higher in C. debaoensis and C. fairylakea collected from a botanical garden, while the lowest was observed in C. debaoensis from a natural habitat; this provides evidence that garden management, and to a minor extent, ex-situ conservation practice, could influence fungal endophyte communities. We further selected nineteen fungal isolates and screened for their antagonistic activities via a co-cultivation approach against the phytopathogens, Diaporthe sp. and Colletotrichum sp. Among these, five isolates with high ITS similarity matches with Hypoxylon vinosupulvinatum (GD019, 99.61%), Penicillium sp. (BD022, 100%), Penicillifer diparietisporus (GD008, 99.46%), Clonostachys rogersoniana (BF024, 99.46%) and C. rosea (BF011, 99.1%), which showed exceptional antagonistic activities against the phytopathogenic fungi with a significant inhibition rate of 70–80%. Taken together, our data presented the first and most comprehensive molecular work on culturable fungal endophytes associated with the coralloid roots of cycads. Our study also demonstrated that about 5% of fungal endophytes were not detected by the high-throughput sequencing approach, implying the equal importance of a culture-dependent approach to study fungal communities of cycads. We further highlighted the potential role of endemic and rare plants to discover and isolate unique plant-associated fungal taxa with excellent biocontrol properties. Full article

(This article belongs to the Special Issue Diversity and Classification of Environmental Fungi)

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15 pages, 15005 KiB

Open AccessArticle

Discovery of Novel Backusella (Backusellaceae, Mucorales) Isolated from Invertebrates and Toads in Cheongyang, Korea

by Thuong T.T. Nguyen, Kerstin Voigt, André Luiz Cabral Monteiro de Azevedo Santiago, Paul M. Kirk and Hyang Burm Lee

J. Fungi 2021, 7(7), 513; https://doi.org/10.3390/jof7070513 - 27 Jun 2021

Cited by 16 | Viewed by 3964

Abstract

Three novel fungal species, Backusella chlamydospora sp. nov., B. koreana sp. nov., and B. thermophila sp. nov., as well as two new records, B. oblongielliptica and B. oblongispora, were found in Cheongyang, Korea, during an investigation of fungal [...] Read more.

Three novel fungal species, Backusella chlamydospora sp. nov., B. koreana sp. nov., and B. thermophila sp. nov., as well as two new records, B. oblongielliptica and B. oblongispora, were found in Cheongyang, Korea, during an investigation of fungal species from invertebrates and toads. All species are described here using morphological characters and sequence data from internal transcribed spacer sequences of ribosomal DNA and large subunit of the ribosomal DNA. Backusella chlamydospora is different from other Backusella species by producing chlamydospores. Backusella koreana can be distinguished from other Backusella species by producing abundant yeast-like cells. Backusella thermophila is characterized by a variable (subglobose to oblong, applanate to oval, conical and ellipsoidal to pyriform) columellae and grows well at 37 °C. Multigene phylogenetic analyses of the combined ITS and LSU rDNA sequences data generated from maximum likelihood and MrBayes analyses indicate that B. chlamydospora, B. koreana, and B. thermophila form distinct lineages in the family Backusellaceae. Detailed descriptions, illustrations, phylogenetic tree, and taxonomic key to the Backusella species present in Korea are provided. Full article

(This article belongs to the Special Issue Diversity and Classification of Environmental Fungi)

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76 pages, 37877 KiB

Open AccessArticle

Towards a Natural Classification of Hyphodontia Sensu Lato and the Trait Evolution of Basidiocarps within Hymenochaetales (Basidiomycota)

by Xue-Wei Wang, Tom W. May, Shi-Liang Liu and Li-Wei Zhou

J. Fungi 2021, 7(6), 478; https://doi.org/10.3390/jof7060478 - 12 Jun 2021

Cited by 41 | Viewed by 4720

Abstract

Hyphodontia sensu lato, belonging to Hymenochaetales, accommodates corticioid wood-inhabiting basidiomycetous fungi with resupinate basidiocarps and diverse hymenophoral characters. Species diversity of Hyphodontia sensu lato has been extensively explored worldwide, but in previous studies the six accepted genera in Hyphodontia sensu lato, viz. [...] Read more.

Hyphodontia sensu lato, belonging to Hymenochaetales, accommodates corticioid wood-inhabiting basidiomycetous fungi with resupinate basidiocarps and diverse hymenophoral characters. Species diversity of Hyphodontia sensu lato has been extensively explored worldwide, but in previous studies the six accepted genera in Hyphodontia sensu lato, viz. Fasciodontia, Hastodontia, Hyphodontia, Kneiffiella, Lyomyces and Xylodon were not all strongly supported from a phylogenetic perspective. Moreover, the relationships among these six genera in Hyphodontia sensu lato and other lineages within Hymenochaetales are not clear. In this study, we performed comprehensive phylogenetic analyses on the basis of multiple loci. For the first time, the independence of each of the six genera receives strong phylogenetic support. The six genera are separated in four clades within Hymenochaetales: Fasciodontia, Lyomyces and Xylodon are accepted as members of a previously known family Schizoporaceae, Kneiffiella and Hyphodontia are, respectively, placed in two monotypic families, viz. a previous name Chaetoporellaceae and a newly introduced name Hyphodontiaceae, and Hastodontia is considered to be a genus with an uncertain taxonomic position at the family rank within Hymenochaetales. The three families emerged between 61.51 and 195.87 million years ago. Compared to other families in the Hymenochaetales, these ages are more or less similar to those of Coltriciaceae, Hymenochaetaceae and Oxyporaceae, but much older than those of the two families Neoantrodiellaceae and Nigrofomitaceae. In regard to species, two, one, three and 10 species are newly described from Hyphodontia, Kneiffiella, Lyomyces and Xylodon, respectively. The taxonomic status of additional 30 species names from these four genera is briefly discussed; an epitype is designated for X. australis. The resupinate habit and poroid hymenophoral configuration were evaluated as the ancestral state of basidiocarps within Hymenochaetales. The resupinate habit mainly remains, while the hymenophoral configuration mainly evolves to the grandinioid-odontioid state and also back to the poroid state at the family level. Generally, a taxonomic framework for Hymenochaetales with an emphasis on members belonging to Hyphodontia sensu lato is constructed, and trait evolution of basidiocarps within Hymenochaetales is revealed accordingly. Full article

(This article belongs to the Special Issue Diversity and Classification of Environmental Fungi)

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16 pages, 5104 KiB

Open AccessFeature PaperArticle

Taxonomy and Phylogeny of the Wood-Inhabiting Fungal Genus Hyphoderma with Descriptions of Three New Species from East Asia

by Qian-Xin Guan and Chang-Lin Zhao

J. Fungi 2021, 7(4), 308; https://doi.org/10.3390/jof7040308 - 16 Apr 2021

Cited by 12 | Viewed by 3698

Abstract

Three new wood-inhabiting fungi, Hyphoderma crystallinum, H. membranaceum, and H. microporoides spp. nov., are proposed based on a combination of morphological features and molecular evidence. Hyphoderma crystallinum is characterized by the resupinate basidiomata with smooth hymenial surface scattering scattered nubby crystals, a [...] Read more.

Three new wood-inhabiting fungi, Hyphoderma crystallinum, H. membranaceum, and H. microporoides spp. nov., are proposed based on a combination of morphological features and molecular evidence. Hyphoderma crystallinum is characterized by the resupinate basidiomata with smooth hymenial surface scattering scattered nubby crystals, a monomitic hyphal system with clamped generative hyphae, and numerous encrusted cystidia present. Hyphoderma membranaceum is characterized by the resupinate basidiomata with tuberculate hymenial surface, presence of the moniliform cystidia, and ellipsoid to cylindrical basidiospores. Hyphoderma microporoides is characterized by the resupinate, cottony basidiomata distributing the scattered pinholes visible using hand lens on the hymenial surface, presence of halocystidia, and cylindrical to allantoid basidiospores. Sequences of ITS+nLSU rRNA gene regions of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony, and Bayesian inference methods. These phylogenetic analyses showed that three new species clustered into Hyphoderma, in which H. crystallinum was sister to H. variolosum, H. membranaceum was retrieved as a sister species of H. sinense, and H. microporoides was closely grouped with H. nemorale. In addition to new species, map to show global distribution of Hyphoderma species treated in the phylogenetic tree and an identification key to Chinese Hyphoderma are provided. Full article

(This article belongs to the Special Issue Diversity and Classification of Environmental Fungi)

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16 pages, 27354 KiB

Open AccessArticle

Soil Metabarcoding Offers a New Tool for the Investigation and Hunting of Truffles in Northern Thailand

by Nakarin Suwannarach, Jaturong Kumla, Ammarin In-on and Saisamorn Lumyong

J. Fungi 2021, 7(4), 293; https://doi.org/10.3390/jof7040293 - 13 Apr 2021

Cited by 3 | Viewed by 3262

Abstract

Truffles (Tuber spp.) are well-known as edible ectomycorrhizal mushrooms, and some species are one of the most expensive foods in the world. During the fruiting process, truffles produce hypogeous ascocarps; a trained pig or dog is needed to locate the ascocarps under [...] Read more.

Truffles (Tuber spp.) are well-known as edible ectomycorrhizal mushrooms, and some species are one of the most expensive foods in the world. During the fruiting process, truffles produce hypogeous ascocarps; a trained pig or dog is needed to locate the ascocarps under the ground. Truffles in northern Thailand have been recorded in association with Betulaalnoides and Carpinus poilanei. In this study, we investigated the soil mycobiota diversity of soil samples from both of these truffle host plants in native forests using environmental DNA metabarcoding to target the internal transcribed spacer 1 (ITS1) region of the rDNA gene for the purposes of investigation of truffle diversity and locating truffles during the non-fruiting phase. In this study, a total of 38 soil samples were collected from different locations. Of these, truffles had been found at three of these locations. Subsequently, a total of 1341 putative taxonomic units (OTUs) were obtained. The overall fungal community was dominated by phylum-level sequences assigned to Ascomycota (57.63%), Basidiomycota (37.26%), Blastocladiomycota (0.007%), Chytridiomycota (0.21%), Glomeromycota (0.01%), Kickxellomycota (0.01%), Mortierellomycota (2.08%), Mucoromycota (0.24%), Rozellomycota (0.01%), Zoopagomycota (0.003%), and unidentified (2.54%). The results revealed that six OTUs were determined to be representative and belonged to the genus Tuber. OTU162, OTU187, OTU447, and OTU530 belonged to T. thailandicum, T. lannaense, T. bomiense, and T. magnatum, whereas OTU105 and OTU720 were acknowledged as unrecognized Tuber species. From 38 locations, OTUs of truffles were found in 33 locations (including three previously known truffle locations). Thus, 30 collection sites were considered new locations for T. thailandicum, T. bomiense, and other unrecognized Tuber species. Interestingly, at 16 new locations, mature ascocarps of truffles that were undergoing the fruiting phase were located underground. All 16 truffle samples were identified as T. thailandicum based on morphological characteristics and molecular phylogenetic analysis. However, ascocarps of other truffle species were not found at the new OTUs representative locations. The knowledge gained from this study can be used to lead researchers to a better understanding of the occurrence of truffles using soil mycobiota diversity investigation. The outcomes of this study will be particularly beneficial with respect to the search and hunt for truffles without the need for trained animals. In addition, the findings of this study will be useful for the management and conservation of truffle habitats in northern Thailand. Full article

(This article belongs to the Special Issue Diversity and Classification of Environmental Fungi)

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Review

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21 pages, 783 KiB

Open AccessReview

Current Insight into Culture-Dependent and Culture-Independent Methods in Discovering Ascomycetous Taxa

by Nalin N. Wijayawardene, Mohammad Bahram, Iván Sánchez-Castro, Dong-Qin Dai, Kahandawa G. S. U. Ariyawansa, Udeni Jayalal, Nakarin Suwannarach and Leho Tedersoo

J. Fungi 2021, 7(9), 703; https://doi.org/10.3390/jof7090703 - 28 Aug 2021

Cited by 28 | Viewed by 6637

Abstract

Culture techniques are vital in both traditional and modern fungal taxonomy. Establishing sexual–asexual links and synanamorphs, extracting DNA and secondary metabolites are mainly based on cultures. However, it is widely accepted that a large number of species are not sporulating in nature while [...] Read more.

Culture techniques are vital in both traditional and modern fungal taxonomy. Establishing sexual–asexual links and synanamorphs, extracting DNA and secondary metabolites are mainly based on cultures. However, it is widely accepted that a large number of species are not sporulating in nature while others cannot be cultured. Recent ecological studies based on culture-independent methods revealed these unculturable taxa, i.e., dark taxa. Recent fungal diversity estimation studies suggested that environmental sequencing plays a vital role in discovering missing species. However, Sanger sequencing is still the main approach in determining DNA sequences in culturable species. In this paper, we summarize culture-based and culture-independent methods in the study of ascomycetous taxa. High-throughput sequencing of leaf endophytes, leaf litter fungi and fungi in aquatic environments is important to determine dark taxa. Nevertheless, currently, naming dark taxa is not recognized by the ICN, thus provisional naming of them is essential as suggested by several studies. Full article

(This article belongs to the Special Issue Diversity and Classification of Environmental Fungi)

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