One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes

Protocol for rapid and cost-effective extraction of genomic DNA from a wide range of wild yeast species for use in PCR-based applications

Isolation of amplifiable genomic DNA is a prerequisite for the implementation of PCR-based techniques. Here we present a protocol for isolating the genomic DNA from a variety of wild yeast species. This can be completed in approximately 1 h and does not require sophisticated laboratory equipment. We describe steps for growing yeast cells, genomic data extraction, and downstream assay for amplification of specific sequences from the genomic DNA. We then detail procedures for gel electrophoresis and analysis of the results. For complete details on the use and execution of this protocol, please refer to Kristjuhan et al.1.

Three new species of Laccaria (Agaricales, Basidiomycota) from Southwest China (Yunnan) based on morphological and multi-gene sequence data

Introduction

The genus Laccaria has been reported from temperate and tropical areas and is an important constituent in forest ecosystems. However, the species diversity of Laccaria in Southwest China (Yunnan) has been underestimated.

Methods

In this paper, descriptions based on morphological and multi-gene sequence data from internal transcribed spacer (ITS) region, large subunit ribosomal RNA gene (nrLSU), translation elongation factor 1-α (TEF1α) and the polymerase II second largest subunit (RPB2) of three new Laccaria species from Southwest China (Yunnan) are reported.

Results

Two of these were characterized by orange pileus and globose to subglobose basidiospores: L. cinnabarina and L. spinulosa. While L. cinnabarina has orange red colored basidiocarps with conspicuously pellucid-striate pattern, and a fibrillose stipe with longitudinally striations, L. spinulosa has a brownish orange to brown fruiting body with light white pruinae and 2-spored basidia. Laccaria longistriata is characterized by brown to flesh-colored basidioma, prominently striate to sulcate pileus and globose to subglobose basidiospores.

Discussion

The three new species were described, illustrated and compared with closely related species in morphology and phylogeny.

Inopinatus corneliae sp. nov. gen. nov. isolated from human skin: A newly discovered keratinophilic hyphomycete, order Onygenales

BACKGROUND

Fungi clinically relevant to human skin comprise prevalent commensals and well-known pathogens. Only rarely human skin harbours fungi that evade identification.

OBJECTIVE

To characterise an enigmatic specimen isolated from a skin lesion.

METHODS

A comprehensive clinical and mycological workup including conventional methods for phenotypic characterisation and sequencing based on internal transcribed spacer (ITS) and large subunit (LSU) regions to infer a phylogenetic tree.

RESULTS

Cultures on common solid media were macroscopically inconspicuous initially until mycelial tufts developed on the surface, notably on potato dextrose agar. Polymorphous chlamydospores were detected but no aleurospores and ascomata. At 26°C, the isolate grew on standard agars, plant materials and garden soil and utilised peptone, keratins, lipids, inulin, erythrocytes and cellulose. It also grew at 5°C and at 37°C. Nucleotide sequences of its ITS region showed 93% similarity to sequences of different Malbranchea species. The closest matches among LSU rRNA sequences were obtained with the genera Amauroascus, Arthroderma, Auxarthronopsis and Malbranchea (93%-95%). A combined phylogenetic analysis placed the fungus in a sister clade to Neogymnomycetaceae, classified as incertae sedis in Onygenales, on a large distance to either Diploospora rosea or 'Amauroascus' aureus.

CONCLUSIONS

The genus Inopinatus gen. nov. (MB854685) with the species Inopinatus corneliae sp. nov. (MB854687) is introduced to accommodate our isolate (holotype: DSM 116806; isotypes: CBS 151104, IHEM 29063). Probably Inopinatus corneliae is a geophilic species that, although potentially harmful, was no relevant pathogen in our case. Its ecology, epidemiology and pathogenicity need to be further clarified.

Fusarium amaranthi sp. nov. from Amaranth Is an Emergent Species Closely Related to F. circinatum

Amaranth (Amaranthus spp. L) is not native to South Korea but is cultivated in small scales for ornamental purposes as well as leafy vegetables and pseudo cereals. In this study, a new species within the genus Fusarium was isolated from amaranth, showing stem rot symptoms from a farmer field in Hwaseong, South Korea. The disease is characterized by dark-brown spots with black borders, leading to withering. Phylogenetic analysis-based concatenated sequences of translation elongation factor 1-alpha (TEF1), beta-tubulin (tub2), calmodulin (cmdA), RNA polymerase largest subunit (RPB1), and RNA polymerase II second largest subunit (RPB2) genes revealed that the obtained isolates formed a distinct clad within the Fusarium fujikuroi species complex and is closely related to F. circinatum. Cultural and morphological characteristics and pathogenicity on healthy amaranth plants (stem and leaves) were examined. The isolates readily differentiated from F. circinatum based on one- to five-septate macroconidia and the absence of sterile hyphae. Based on molecular and morphological characteristics, this fungus is demonstrated to be a new species and is described here as F. amaranthi, the causal agent of stem rot of amaranth in South Korea.

Alternaria alternata Pathogen from Cuscuta japonica Could Serve as a Potential Bioherbicide

Dodder (Cuscuta spp.) is a dangerous parasitic plant that causes serious damage to crop production and is challenging to eliminate. Herbicide application is a common strategy to control dodder in the field, but it is costly, ineffective, and further results in hazardous outcomes. Therefore, our study aims to identify the potential pathogens in naturally occurring dodder infections which may provide efficient biocontrol options. In this regard, the pathogens were isolated from the infected plants, their pathogenicity was validated through inoculation, and the optimal culture conditions for their growth were identified by determining the pathogenicity difference. The pathogenicity range was determined in vitro using the leaves of common horticultural plants and crops. Furthermore, a small range of horticultural plants parasitized by Cuscuta reflexa in the field were inoculated with the pathogen to determine their biosafety and biocontrol potential, and the pathogens were identified by morphological and molecular characterization. We found 7 strains that were isolated after pathogen enrichment culture. Among them, Cbp6 and Cbp7 showed the highest pathogenicity against C. reflexa. After testing the inoculation of more than 50 species of plants, only 9 species showed varying degrees of lesions on leaves, which proved the high biosafety for common plants. Field spraying of these pathogens showed a good control effect on C. reflexa after 21 days; the disease severityreached 66.0%, while its host plant did not display obvious symptoms. In conclusion, the pathogens Cbp6 and Cbp7 were identified as Alternaria alternata, and the results of this study provide a theoretical basis for the biological control of dodder.

Lecanicillium psalliotae (Hypocreales: Cordycipitaceae) Exerts Ovicidal and Larvicidal Effects against the Sheep Blood-Feeding Nematode Haemonchus contortus through Its Liquid Culture Filtrates

Nematophagous fungi (NF) form part of the soil microbiota and are natural enemies of nematodes, helping to regulate nematode populations. A verticillate NF isolated from soil from Tepalcingo, Mexico, was morphologically and molecularly characterised. This fungus was cultured in two different liquid media-Czapek-Dox broth (CzDoxB) and sweet potato dextrose broth (SPDB)-for 21 days. The ovicidal (OA) and larvicidal (LA) activities of fungal liquid culture filtrates (LCFs) were assessed in 96-well microtitre plates at different concentrations against Haemonchus contortus after 48 h. The morphological and molecular identification revealed the presence of Lecanicillium psalliotae. Additionally, the groups of compounds associated with nematocidal activity were determined from a qualitative chemical profile (QCP) using different reagents. The highest OA of the LCFs was obtained at 25 mg/mL from SPDB and CzDoxB and amounted to 97.2 and 99.06%, respectively. Meanwhile, the highest LA recorded with these LCFs at 100 mg/mL was 54.27% and 96.8%, respectively. The QCP revealed the presence of alkaloids and tannins in both LCFs that have previously been associated with nematocidal activity. Lecanicillium psalliotae exerted an important effect on H. contortus and could be of significance in future studies focused on the control and prevention of haemonchosis in small ruminants.

Epidemiology of Candidemia in Mashhad, Northeast Iran: A Prospective Multicenter Study (2019-2021)

Candidemia is a major cause of morbidity and mortality in health care settings, and its epidemiology is changing. In the last two decades, the proportion of non-albicans Candida (NAC) yeasts in candidemia has increased. These yeasts more often display resistance to common antifungals. In many western countries, candidemia is mainly caused by susceptible C. albicans, while in resource-limited countries, including Iran, the candidemia species distribution is studied less often. Here, we investigated the species distribution, resistance levels, and characteristics of patients with candidemia in five hospitals in Mashhad (northeast Iran) for two years (2019-2021). Yeast isolates from blood were identified with MALDI-TOF MS and subjected to antifungal susceptibility testing (AFST) using the broth microdilution method, while molecular genotyping was applied to Candida parapsilosis isolates. In total, 160 yeast isolates were recovered from 160 patients, of which the majority were adults (60%). Candidemia was almost equally detected in men (48%) and women (52%). Almost half of patients (n = 67, 49%) were from intensive care units (ICUs). C. parapsilosis (n = 58, 36%) was the most common causative agent, surpassing C. albicans (n = 52, 33%). The all-cause mortality rate was 53%, with C. albicans candidemia displaying the lowest mortality with 39%, in contrast to a mortality rate of 59% for NAC candidemia. With microbroth AFST, nearly all tested isolates were found to be susceptible, except for one C. albicans isolate that was resistant to anidulafungin. By applying short tandem repeat (STR) genotyping to C. parapsilosis, multiple clusters were found. To summarize, candidemia in Mashhad, Iran, from 2019 to 2021, is characterized by common yeast species, in particular C. parapsilosis, for which STR typing indicates potential nosocomial transmission. The overall mortality is high, while resistance rates were found to be low, suggesting that the high mortality is linked to limited diagnostic options and insufficient medical care, including the restricted use of echinocandins as the first treatment option.

New insights into the DNA extraction and PCR amplification of minute ascomycetes in the genus Laboulbenia (Pezizomycotina, Laboulbeniales)

Molecular studies of fungi within the order Laboulbeniales (Ascomycota, Pezizomycotina) have been hampered for years because of their minute size, inability to grow in axenic culture, and lack of reliable and cost-efficient DNA extraction protocols. In particular, the genus Laboulbenia is notorious for low success with DNA extraction and polymerase chain reaction (PCR) amplification. This is attributed to the presence of melanin, a molecule known to inhibit PCR, in the cells. We evaluated the efficacy of a standard single cell-based DNA extraction protocol by halving the recommended amount of reagents to reduce the cost per extraction and adding bovine serum albumin (BSA) during the multiple displacement amplification step to reverse the effect of melanin. A total of 196 extractions were made, 111 of which were successful. We found that halving the reagents used in the single cell-based extraction kit did not significantly affect the probability of successful DNA extraction. Using the halved protocol reduces cost and resource consumption. Moreover, there was no significant difference in the probability of successfully extracting DNA based on whether BSA was added or not, suggesting that the amount of melanin present in cells of the thallus has no major inhibitory effect on PCR. We generated 277 sequences from five loci, but amplification of the internal transcribed spacer region, the mitochondrial small subunit rDNA, and protein-coding genes remains challenging. The probability of successfully extracting DNA from Laboulbeniales was also impacted by specimen storage methods, with material preserved in > 95% ethanol yielding higher success rates compared to material stored in 70% ethanol and dried material. We emphasize the importance of proper preservation of material and propose the design of Laboulbeniales-specific primers to overcome the problems of primer mismatches and contaminants. Our new insights apply not only to the genus Laboulbenia; Laboulbeniales generally are understudied, and the vast majority of species remain unsequenced. New and approachable molecular developments will benefit the study of Laboulbeniales, helping to elucidate the true diversity and evolutionary relationships of these peculiar microfungi.

Combined Use of Phenotype-Based and Genome-Informed Approaches Identified a Unique Fusarium oxysporum f. sp. cubense Isolate in Hawaii

Fusarium wilt of banana, caused by Fusarium oxysporum f. sp. cubense (Foc), is a serious disease that threatens banana production worldwide. It is a long-standing problem in Hawaii, but previously, there was little knowledge of the causal pathogen. We isolated a strain of Foc, named Foc-UH, from a field experiencing the disease epidemic in Hawaii. Infection assays of a diverse panel of 26 banana clones, including varieties used for differentiating pathogen races and fruit production, revealed that Foc-UH has a race 1 pathogenic phenotype with an intermediate race 2 virulence and revealed the differential resistance of varieties to infection. Separate phylogenetic analyses using the barcoding regions of three nuclear genes, seven complete nuclear genes, and single-nucleotide polymorphisms within conserved whole-genome protein coding sequences placed Foc-UH into recently proposed taxonomic frameworks relevant to Foc and the F. oxysporum species complex. Screening of the 99.7% complete draft genome identified five secreted in xylem (SIX) gene homologs: SIX1d, SIX1f, SIX9a, SIX9b, and SIX13a. This profile is similar to that of several race 1 isolates except for the absence of SIX4 and SIX6. Foc-UH was morphologically dissimilar to the nearest related isolates. Altogether, this study identified a unique isolate that causes banana Fusarium wilt, which represents the first characterization of the causal pathogen in Hawaii. The findings and genomic resources generated in this study are expected to guide banana breeding and cultivar deployment in Hawaii and beyond and contribute to further understanding of the pathogenicity and evolutionary systematics of Foc.

Revisiting the phylogeny and taxonomy of the genus Sidera (Hymenochaetales, Basidiomycota) with particular emphasis on S.vulgaris

The genus Sidera (Hymenochaetales, Basidiomycota) comprises white-rot, mono- or dimitic fungi with poroid or hydnoid hymenophore. It has a worldwide distribution albeit with fewer species present in the Southern Hemisphere. Although recent studies revealed the existence of several new Sidera species, there are still taxonomic inconsistencies and obscure phylogenetic relationships amongst certain taxa of the genus. In this work, a large number of Sidera collections were used to obtain an updated phylogeny, based on ITS and 28S rDNA sequences by including new material from Mediterranean Europe. The monophyly of the genus was strongly supported and all species with poroid hymenophore formed a highly-supported lineage with two major subclades. In total, 23 putative species were recognised. Amongst those, five are considered to possibly represent entities new to science, but further work is required since they are represented by single specimens or environmental sequences. Examined collections originally named S.lenis from southern Europe were grouped within S.vulgaris. Similarly, several collections under various names were hereby identified as S.vulgaris, including those of the recently described species S.tibetica. Furthermore, a critical discussion (based on morphoanatomical findings) is made on the key features that could be used to distinguish S.lenis from S.vulgaris.

Ascomycetes yeasts: The hidden part of human microbiome

The fungal component of the microbiota, the mycobiota, has been neglected for a long time due to its poor richness compared to bacteria. Limitations in fungal detection and taxonomic identification arise from using metagenomic approaches, often borrowed from bacteriome analyses. However, the relatively recent discoveries of the ability of fungi to modulate the host immune response and their involvement in human diseases have made mycobiota a fundamental component of the microbial communities inhabiting the human host, deserving some consideration in host-microbe interaction studies and in metagenomics. Here, we reviewed recent data on the identification of yeasts of the Ascomycota phylum across human body districts, focusing on the most representative genera, that is, Saccharomyces and Candida. Then, we explored the key factors involved in shaping the human mycobiota across the lifespan, ranging from host genetics to environment, diet, and lifestyle habits. Finally, we discussed the strengths and weaknesses of culture-dependent and independent methods for mycobiota characterization. Overall, there is still room for some improvements, especially regarding fungal-specific methodological approaches and bioinformatics challenges, which are still critical steps in mycobiota analysis, and to advance our knowledge on the role of the gut mycobiota in human health and disease. This article is categorized under: Immune System Diseases > Genetics/Genomics/Epigenetics Immune System Diseases > Environmental Factors Infectious Diseases > Environmental Factors.

Genome assembly of the edible jelly fungus Dacryopinax spathularia (Dacrymycetaceae)

The edible jelly fungus Dacryopinax spathularia (Dacrymycetaceae) is wood-decaying and can be commonly found worldwide. It has found application in food additives, given its ability to synthesize long-chain glycolipids, among other uses. In this study, we present the genome assembly of D. spathularia using a combination of PacBio HiFi reads and Omni-C data. The genome size is 29.2 Mb. It has high sequence contiguity and completeness, with a scaffold N50 of 1.925 Mb and a 92.0% BUSCO score. A total of 11,510 protein-coding genes and 474.7 kb repeats (accounting for 1.62% of the genome) were predicted. The D. spathularia genome assembly generated in this study provides a valuable resource for understanding their ecology, such as their wood-decaying capability, their evolutionary relationships with other fungi, and their unique biology and applications in the food industry.

Sunken Riches: Ascomycete Diversity in the Western Mediterranean Coast through Direct Plating and Flocculation, and Description of Four New Taxa

The Mediterranean Sea stands out as a hotspot of biodiversity, whose fungal composition remains underexplored. Marine sediments represent the most diverse substrate; however, the challenge of recovering fungi in culture hinders the precise identification of this diversity. Concentration techniques like skimmed milk flocculation (SMF) could represent a suitable solution. Here, we compare the effectiveness in recovering filamentous ascomycetes of direct plating and SMF in combination with three culture media and two incubation temperatures, and we describe the fungal diversity detected in marine sediments. Sediments were collected at different depths on two beaches (Miracle and Arrabassada) on the Spanish western Mediterranean coast between 2021 and 2022. We recovered 362 strains, and after a morphological selection, 188 were identified primarily with the LSU and ITS barcodes, representing 54 genera and 94 species. Aspergillus, Penicillium, and Scedosporium were the most common genera, with different percentages of abundance between both beaches. Arrabassada Beach was more heterogeneous, with 42 genera representing 60 species (Miracle Beach, 28 genera and 54 species). Although most species were recovered with direct plating (70 species), 20 species were exclusively obtained using SMF as a sample pre-treatment, improving our ability to detect fungi in culture. In addition, we propose three new species in the genera Exophiala, Nigrocephalum, and Queenslandipenidiella, and a fourth representing the novel genus Schizochlamydosporiella. We concluded that SMF is a useful technique that, in combination with direct plating, including different culture media and incubation temperatures, improves the chance of recovering marine fungal communities in culture-dependent studies.

Analysis of Whole-Genome facilitates rapid and precise identification of fungal species

Fungal identification is a cornerstone of fungal research, yet traditional molecular methods struggle with rapid and accurate onsite identification, especially for closely related species. To tackle this challenge, we introduce a universal identification method called Analysis of whole GEnome (AGE). AGE includes two key steps: bioinformatics analysis and experimental practice. Bioinformatics analysis screens candidate target sequences named Targets within the genome of the fungal species and determines specific Targets by comparing them with the genomes of other species. Then, experimental practice using sequencing or non-sequencing technologies would confirm the results of bioinformatics analysis. Accordingly, AGE obtained more than 1,000,000 qualified Targets for each of the 13 fungal species within the phyla Ascomycota and Basidiomycota. Next, the sequencing and genome editing system validated the ultra-specific performance of the specific Targets; especially noteworthy is the first-time demonstration of the identification potential of sequences from unannotated genomic regions. Furthermore, by combining rapid isothermal amplification and phosphorothioate-modified primers with the option of an instrument-free visual fluorescence method, AGE can achieve qualitative species identification within 30 min using a single-tube test. More importantly, AGE holds significant potential for identifying closely related species and differentiating traditional Chinese medicines from their adulterants, especially in the precise detection of contaminants. In summary, AGE opens the door for the development of whole-genome-based fungal species identification while also providing guidance for its application in plant and animal kingdoms.

Three new species in Russula subsection Xerampelinae supported by genealogical and phenotypic coherence

Xerampelinae is a subsection composed of species of ectomycorrhizal fungi belonging to the hyperdiverse and cosmopolitan genus Russula (Russulales). Species of Xerampelinae are recognized by their fishy or shrimp odor, browning context, and a green reaction to iron sulfate. However, species delimitation has traditionally relied on morphology and analysis of limited molecular data. Prior taxonomic work in Xerampelinae has led to the description of as many as 59 taxa in Europe and 19 in North America. Here we provide the first multilocus phylogeny of European and North American members based on two nrDNA loci and two protein-coding genes. The resulting phylogeny supports the recognition of 17 species-rank Xerampelinae clades; however, higher species richness (~23) is suggested by a more inclusive nuclear rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode) analysis. Phylogenetic and morphological analyses support three new species with restricted geographic distributions: R. lapponica, R. neopascua, and R. olympiana. We confirm that the European species R. subrubens is present in North America and the North American species R. serissima (previously known as R. favrei) is present in Europe. Most other Xerampelinae appear restricted to either North America or Eurasia, which indicates a high degree of regional endemism; this includes R. xerampelina, a name widely applied to North American taxa, but a species restricted to Eurasia.

Development of a novel mycobiome diagnostic for fungal infection

BACKGROUND

Amplicon-based mycobiome analysis has the potential to identify all fungal species within a sample and hence could provide a valuable diagnostic assay for use in clinical mycology settings. In the last decade, the mycobiome has been increasingly characterised by targeting the internal transcribed spacer (ITS) regions. Although ITS targets give broad coverage and high sensitivity, they fail to provide accurate quantitation as the copy number of ITS regions in fungal genomes is highly variable even within species. To address these issues, this study aimed to develop a novel NGS fungal diagnostic assay using an alternative amplicon target.

METHODS

Novel universal primers were designed to amplify a highly diverse single copy and uniformly sized DNA target (Tef1) to enable mycobiome analysis on the Illumina iSeq100 which is a low cost, small footprint and simple to use next-generation sequencing platform. To enable automated analysis and rapid results, a streamlined bioinformatics workflow and sequence database were also developed. Sequencing of mock fungal communities was performed to compare the Tef1 assay and established ITS1-based method. The assay was further evaluated using clinical respiratory samples and the feasibility of using internal spike-in quantitative controls was assessed.

RESULTS

The Tef1 assay successfully identified and quantified Aspergillus, Penicillium, Candida, Cryptococcus, Rhizopus, Fusarium and Lomentospora species from mock communities. The Tef1 assay was also capable of differentiating closely related species such as A. fumigatus and A. fischeri. In addition, it outperformed ITS1 at identifying A. fumigatus and other filamentous pathogens in mixed fungal communities (in the presence or absence of background human DNA). The assay could detect as few as 2 haploid genome equivalents of A. fumigatus from clinical respiratory samples. Lastly, spike-in controls were demonstrated to enable semi-quantitation of A. fumigatus load in clinical respiratory samples using sequencing data.

CONCLUSIONS

This study has developed and tested a novel metabarcoding target and found the assay outperforms ITS1 at identifying clinically relevant filamentous fungi. The assay is a promising diagnostic candidate that could provide affordable NGS analysis to clinical mycology laboratories.

Bibliometric, taxonomic, and medicinal perspectives of Ganoderma neo-japonicum Imazeki: A mini review

Ganoderma, a traditional medicine in Asian countries, has been used to prevent and treat various ailments for centuries. Ganoderma neo-japonicum (synonym Ganoderma bambusicola), also known as purple Lingzhi, is a species that is currently underutilised when compared to Ganoderma lucidum (Lingzhi). However, in recent decades, this mushroom has garnered significant attention due to its ethnomedicinal uses, especially in Southeast Asia regions like Malaysia. The taxonomy and nomenclature of this mushroom have been extensively studied. Numerous publications have reported that G. neo-japonicum displays a variety of medicinal properties, including antioxidation, anticancer, anti-hyperglycaemic, genoprotective, hepatoprotective, neuritogenic, and antidiabetic effects, both in vitro and in vivo. With the surge of research findings on this mushroom, this review aims to provide a systematic bibliometric analysis of G. neo-japonicum, published between 1991 to 2021. Additionally, the taxonomic description of this mushroom is discussed in detail. Our review reveals that G. neo-japonicum contains polysaccharides (α/β-D-glucans), triterpenoids, and sterols/ergosterol. However, the existing literature suggests that these active compounds have not yet been explored to their full potential as drug candidates. Moreover, most of the studies are preclinical and have several drawbacks. In conclusion, G. neo-japonicum possesses valuable pharmacological activities that merit further exploration.

First Record of Flavocillium subprimulinum (Cordycipitaceae, Hypocreales) in Mexico: Morphological and Molecular Characterisation, Nematocidal Activity of Its Liquid Culture Filtrates against Haemonchus contortus and Protease Activity

This is the first record of the fungus Flavocillium subprimulinum in Mexico. The isolate was taxonomically characterised and cultured in potato dextrose broth (PDB), Czapek-Dox broth (CzDoxB), and sweet potato dextrose broth (SPDB) to obtain its filtrates (FLCF). The nematocidal activity (NA) of three FLCF concentrations was assessed against Haemonchus contortus L3. Protease activity (PA) was assessed with SDS-PAGE, followed by a zymogram. The NA of the FLCF reached 94.43% in PDB and 95.82% in CzDoxB, respectively, at 100 mg/mL. Lower mortality (64%) was found in SPDB at 100 mg/mL. SDS-PAGE showed bands (in PBS) of ~25, ~40, and ~55 kDa. The zymogram showed protein bands (PBs) with PA in the media, including PBs of ~14, ~40, and ~55 kDa. This study establishes the basis for exploring the potential use of this fungus against H. contortus, which is considered the most pathogenic parasite affecting lambs.

Characterization of the Cassava Mycobiome in Symptomatic Leaf Tissues Displaying Cassava Superelongation Disease

Superelongation disease (SED) is a fungal disease that affects cassava in the Caribbean. The symptoms include the appearance of dry necrotic spots and lesions on the leaves, which may severely affect the plant yield. However, the primary causal pathogen is difficult to culture and isolate in the lab because of its slow growth and potential contamination from faster-growing organisms. In addition, the leaf symptoms can be confused with those caused by other pathogens that produce similar necrotic spots and scab-like lesions. There is also little or no information on the contribution of endophytes, if any, to disease symptoms in cassava, a plant where the disease is prevalent. Therefore, this study aimed to characterize the fungal communities in cassava associated with SED symptoms by analyzing gross fungal morphology and performing metagenomics profiling. First, several individual pathogenic fungi were isolated and cultured from diseased cassava leaf tissues from seven locations in Barbados (BB). Both culture isolation and molecular community analyses showed the presence of several other fungi in the disease microenvironment of symptomatic cassava leaves. These included Fusarium, Colletotrichum, and Alternaria species and the suspected species Elsinoë brasiliensis synonym Sphaceloma manihoticola. Additionally, a community analysis using ITS2 amplicon sequencing of 21 symptomatic leaf tissues from BB, St. Vincent and the Grenadines (SVG), Trinidad and Tobago (TT), and Jamaica (JA) revealed that the disease symptoms of superelongation may also result from the interactions of fungal communities in the mycobiome, including Elsinoë species and other fungi such as Colletotrichum, Cercospora, Alternaria, and Fusarium. Therefore, we suggest that examining the pathobiome concept in SED in the future is necessary.

Insights into Some Onygenalean Fungi from Freshwater Sediments in Spain and Description of Novel Taxa

During the course of a project investigating culturable Ascomycota diversity from freshwater sediments in Spain, we isolated 63 strains of cycloheximide-resistant fungi belonging to the order Onygenales. These well-known ascomycetes, able to infect both humans and animals, are commonly found in terrestrial habitats, colonizing keratin-rich soils or dung. Little is known about their diversity in aquatic environments. Combining morphological features and sequence analyses of the ITS and LSU regions of the nrDNA, we identified 14 species distributed in the genera Aphanoascus, Arachniotus, Arthroderma, Arthropsis, Emmonsiellopsis, Gymnoascoideus, Leucothecium, Malbranchea, and Myriodontium. Furthermore, three novel species for the genus Malbranchea are proposed as M. echinulata sp. nov., M. irregularis sp. nov., and M. sinuata sp. nov. The new genera Albidomyces and Neoarthropsis are introduced based on Arachniotus albicans and Arthropsis hispanica, respectively. Neoarthropsis sexualis sp. nov. is characterized and differentiated morphologically from its counterpart by the production of a sexual morph. The novel family Neoarthropsidaceae is proposed for the genera Albidomyes, Apinisia, Arachnotheca, Myriodontium, and Neoarthropsis, based on their phylogenetic relationships and phenotypic and ecological traits. Pseudoamaurascopsis gen. nov. is introduced to accommodate P. spiralis sp. nov., a fungus with unclear taxonomy related to Amaurascopsis and Polytolypa. We traced the ecology and global distribution of the novel fungi through ITS environmental sequences deposited in the GlobalFungi database. Studying the fungal diversity from freshwater sediments not only contributes to filling gaps in the relationships and taxonomy of the Ascomycota but also gives us insights into the fungal community that might represent a putative risk to the health of animals and humans inhabiting or transient in aquatic environments.

SM, Lee F, Lockhart SR, Luethy P, Martin I, Kwon-Chung KJ, Meyer W, Nguyen MH, Ostrosky-Zeichner L, Palavecino E, Pancholi P, Pappas PG, Procop GW, Redhead SA, Rhoads DD, Riedel S, Stevens B, Sullivan KO, Vergidis P, Roilides E, Seyedmousavi A, Tao L, Vicente VA, Vitale RG, Wang QM, Wengenack NL, Westblade L, Wiederhold N, White L, Wojewoda CM, Zhang SX. A conceptual framework for nomenclatural stability and validity of medically important fungi: a proposed global consensus guideline for fungal name changes supported by ABP, ASM, CLSI, ECMM, ESCMID-EFISG, EUCAST-AFST, FDLC, IDSA, ISHAM, MMSA, and MSGERC

The rapid pace of name changes of medically important fungi is creating challenges for clinical laboratories and clinicians involved in patient care. We describe two sources of name change which have different drivers, at the species versus the genus level. Some suggestions are made here to reduce the number of name changes. We urge taxonomists to provide diagnostic markers of taxonomic novelties. Given the instability of phylogenetic trees due to variable taxon sampling, we advocate to maintain genera at the largest possible size. Reporting of identified species in complexes or series should where possible comprise both the name of the overarching species and that of the molecular sibling, often cryptic species. Because the use of different names for the same species will be unavoidable for many years to come, an open access online database of the names of all medically important fungi, with proper nomenclatural designation and synonymy, is essential. We further recommend that while taxonomic discovery continues, the adaptation of new name changes by clinical laboratories and clinicians be reviewed routinely by a standing committee for validation and stability over time, with reference to an open access database, wherein reasons for changes are listed in a transparent way.

New genera and species with chloridium-like morphotype in the Chaetosphaeriales and Vermiculariopsiellales

In this study, we investigated the morphological and genetic variability of selected species belonging to the genus Chloridium sensu lato, some also referred to as chloridium-like asexual morphs and other undescribed morphologically similar fungi. These species do not conform to the revised generic concept and thus necessitate a re-evaluation in terms of taxonomy and phylogeny. The family Chaetosphaeriaceae (Chaetosphaeriales) encompasses a wide range of asexual morphotypes, and among them, the simplest form is represented by Chloridium sect. Chloridium. The morphological simplicity of the Chloridium morphotype has historically led to the amalgamation of numerous unrelated species, thereby creating a heterogeneous genus. By conducting phylogenetic reconstruction of four DNA loci and examining a set of 71 strains, including all available ex-type and other non-type strains as well as holotypes and other herbarium material, we were able to gain new insights into the relationships between these taxa. Phylogenetic analyses revealed that the studied species are distantly related to Chloridium sensu stricto and can be grouped into two orders in the Sordariomycetes. Within the Chaetosphaeriales, they formed nine well-separated genera in four clades, such as Cacumisporium, Caliciastrum gen. nov., Caligospora gen. nov., Capillisphaeria gen. nov., Curvichaeta, Fusichloridium, Geniculoseta gen. nov., Papillospora gen. nov., and Spicatispora gen. nov. We also established Chloridiopsiella gen. nov. and Chloridiopsis gen. nov. in Vermiculariopsiellales. Four new species and eight new combinations are proposed in these genera. Our study provides a clearer understanding of the genus Chloridium, its relationship to other morphologically similar fungi, and a new taxonomic treatment and molecular phylogeny to facilitate their accurate identification and classification in future research. Taxonomic novelties: New genera: Caliciastrum Réblová, Caligospora Réblová, Capillisphaeria Réblová, Chloridiopsiella Réblová, Chloridiopsis Réblová, Geniculoseta Réblová, Papillospora Réblová, Spicatispora Réblová; New species: Caliciastrum bicolor Réblová, Caligospora pannosa Réblová, Chloridiopsis syzygii Réblová, Gongromerizella silvana Réblová; New combinations: Caligospora dilabens (Réblová & W. Gams) Réblová, Capillisphaeria crustacea (Sacc.) Réblová, Chloridiopsiella preussii (W. Gams & Hol.-Jech.) Réblová, Chloridiopsis constrictospora (Crous et al.) Réblová, Geniculoseta preussii (W. Gams & Hol.-Jech.) Réblová, Papillospora hebetiseta (Réblová & W. Gams) Réblová, Spicatispora carpatica (Hol.-Jech. & Révay) Réblová, Spicatispora fennica (P. Karst.) Réblová; Epitypifications (basionyms): Chaetosphaeria dilabens Réblová & W. Gams, Chloridium cylindrosporum W. Gams & Hol.-Jech. Citation: Réblová M, Nekvindová J (2023). New genera and species with chloridium-like morphotype in the Chaetosphaeriales and Vermiculariopsiellales. Studies in Mycology 106: 199-258. doi: 10.3114/sim.2023.106.04.

Yeast metagenomics: analytical challenges in the analysis of the eukaryotic microbiome

Even if their impact is often underestimated, yeasts and yeast-like fungi represent the most prevalent eukaryotic members of microbial communities on Earth. They play numerous roles in natural ecosystems and in association with their hosts. They are involved in the food industry and pharmaceutical production, but they can also cause diseases in other organisms, making the understanding of their biology mandatory. The ongoing loss of biodiversity due to overexploitation of environmental resources is a growing concern in many countries. Therefore, it becomes crucial to understand the ecology and evolutionary history of these organisms to systematically classify them. To achieve this, it is essential that our knowledge of the mycobiota reaches a level similar to that of the bacterial communities. To overcome the existing challenges in the study of fungal communities, the first step should be the establishment of standardized techniques for the correct identification of species, even from complex matrices, both in wet lab practices and in bioinformatic tools.

Plant growth promotion under phosphate deficiency and improved phosphate acquisition by new fungal strain, Penicillium olsonii TLL1

Microbiomes in soil ecosystems play a significant role in solubilizing insoluble inorganic and organic phosphate sources with low availability and mobility in the soil. They transfer the phosphate ion to plants, thereby promoting plant growth. In this study, we isolated an unidentified fungal strain, POT1 (Penicillium olsonii TLL1) from indoor dust samples, and confirmed its ability to promote root growth, especially under phosphate deficiency, as well as solubilizing activity for insoluble phosphates such as AlPO4, FePO4·4H2O, Ca3(PO4)2, and hydroxyapatite. Indeed, in vermiculite containing low and insoluble phosphate, the shoot fresh weight of Arabidopsis and leafy vegetables increased by 2-fold and 3-fold, respectively, with POT1 inoculation. We also conducted tests on crops in Singapore's local soil, which contains highly insoluble phosphate. We confirmed that with POT1, Bok Choy showed a 2-fold increase in shoot fresh weight, and Rice displayed a 2-fold increase in grain yield. Furthermore, we demonstrated that plant growth promotion and phosphate solubilizing activity of POT1 were more effective than those of four different Penicillium strains such as Penicillium bilaiae, Penicillium chrysogenum, Penicillium janthinellum, and Penicillium simplicissimum under phosphate-limiting conditions. Our findings uncover a new fungal strain, provide a better understanding of symbiotic plant-fungal interactions, and suggest the potential use of POT1 as a biofertilizer to improve phosphate uptake and use efficiency in phosphate-limiting conditions.

Next-generation fungal identification using target enrichment and Nanopore sequencing

BACKGROUND

Rapid and accurate pathogen identification is required for disease management. Compared to sequencing entire genomes, targeted sequencing may be used to direct sequencing resources to genes of interest for microbe identification and mitigate the low resolution that single-locus molecular identification provides. This work describes a broad-spectrum fungal identification tool developed to focus high-throughput Nanopore sequencing on genes commonly employed for disease diagnostics and phylogenetic inference.

RESULTS

Orthologs of targeted genes were extracted from 386 reference genomes of fungal species spanning six phyla to identify homologous regions that were used to design the baits used for enrichment. To reduce the cost of producing probes without diminishing the phylogenetic power, DNA sequences were first clustered, and then consensus sequences within each cluster were identified to produce 26,000 probes that targeted 114 genes. To test the efficacy of our probes, we applied the technique to three species representing Ascomycota and Basidiomycota fungi. The efficiency of enrichment, quantified as mean target coverage over the mean genome-wide coverage, ranged from 200 to 300. Furthermore, enrichment of long reads increased the depth of coverage across the targeted genes and into non-coding flanking sequence. The assemblies generated from enriched samples provided well-resolved phylogenetic trees for taxonomic assignment and molecular identification.

CONCLUSIONS

Our work provides data to support the utility of targeted Nanopore sequencing for fungal identification and provides a platform that may be extended for use with other phytopathogens.

Targeted sequencing analysis pipeline for species identification of human pathogenic fungi using long-read nanopore sequencing

Among molecular-based techniques for fungal identification, Sanger sequencing of the primary universal fungal DNA barcode, the internal transcribed spacer (ITS) region (ITS1, 5.8S, ITS2), is commonly used in clinical routine laboratories due to its simplicity, universality, efficacy, and affordability for fungal species identification. However, Sanger sequencing fails to identify mixed ITS sequences in the case of mixed infections. To overcome this limitation, different high-throughput sequencing technologies have been explored. The nanopore-based technology is now one of the most promising long-read sequencing technologies on the market as it has the potential to sequence the full-length ITS region in a single read. In this study, we established a workflow for species identification using the sequences of the entire ITS region generated by nanopore sequencing of both pure yeast isolates and mocked mixed species reads generated with different scenarios. The species used in this study included Candida albicans (n = 2), Candida tropicalis (n = 1), Nakaseomyces glabratus (formerly Candida glabrata) (n = 1), Trichosporon asahii (n = 2), Pichia kudriavzevii (formerly Candida krusei) (n = 1), and Cryptococcus neoformans (n = 1). Comparing various methods to generate the consensus sequence for fungal species identification, the results from this study indicate that read clustering using a modified version of the NanoCLUST pipeline is more sensitive than Canu or VSEARCH, as it classified species accurately with a lower abundance cluster of reads (3% abundance compared to 10% with VSEARCH). The modified NanoCLUST also reduced the number of classified clusters compared to VSEARCH, making the subsequent BLAST+ analysis faster. Subsampling of the datasets, which reduces the size of the datasets by approximately tenfold, did not significantly affect the identification results in terms of the identified species name, percent identity, query coverage, percentage of reads in the classified cluster, and the number of clusters. The ability of the method to distinguish mixed species within sub-populations of large datasets has the potential to aid computer analysis by reducing the required processing power. The herein presented new sequence analysis pipeline will facilitate better interpretation of fungal sequence data for species identification.

Five new species of Gloeandromyces (Fungi, Laboulbeniales) from tropical American bat flies (Diptera, Streblidae), revealed by morphology and phylogenetic reconstruction

This paper describes and illustrates five new species of Gloeandromyces (Ascomycota, Laboulbeniales) associated with tropical American bat flies (Diptera, Streblidae). These are Gloeandromyces cusucoensis sp. nov. from Trichobius uniformis in Costa Rica and Honduras, G. diversiformis sp. nov. from Strebla wiedemanni in Costa Rica, G. plesiosaurus sp. nov. from Trichobius yunkeri in Panama, G. pseudodickii sp. nov. from Trichobius longipes in Ecuador and Panama, and G. verbekeniae sp. nov. from Strebla galindoi in Ecuador and Panama. The description of these five species doubles the number of known species in the genus. Morphological characteristics, host association, and a three-locus (18S nuc rDNA, 28S nuc rDNA, TEF1) phylogenetic reconstruction support placement of these taxa in the genus Gloeandromyces. Three of the new species are polymorphic; they have multiple morphotypes that grow in specific positions on the host integument: G. diversiformis f. diversiformis, f. musiformis, and f. vanillicarpiformis; G. plesiosaurus f. asymmetricus and f. plesiosaurus; and G. verbekeniae f. verbekeniae and f. inflexus. Finally, a dichotomous key to all species and morphotypes is presented.

Fungal taxonomy: A puzzle with many missing pieces

Fungi are multifaceted organisms found in almost all ecosystems on Earth, where they establish various types of symbiosis with other living beings. Despite being recognized by humans since ancient times, and the high number of works delving into their biology and ecology, much is still unknown about these organisms. Some criteria classically used for their study are nowadays limited, generating confusion in categorizing them, and even more, when trying to understand their genealogical relationships. To identify species within Fungi, phenotypic characters to date are not sufficient, and to construct a broad phylogeny or a phylogeny of a particular group, there are still gaps affecting the generated trees, making them unstable and easily debated. For health professionals, fungal identification at lower levels such as genus and species, is enough to select the most appropriate therapy for their control, understand the epidemiology of clinical pictures associated, and recognize outbreaks and antimicrobial resistance. However, the taxonomic location within the kingdom, information with apparently little relevance, can allow phylogenetic relationships to be established between fungal taxa, facilitating the understanding of their biology, distribution in nature, and pathogenic potential evolution. Advances in molecular biology and computer science techniques from the last 30 years have led to crucial changes aiming to establish the criteria to define a fungal species, allowing us to reach a kind of stable phylogenetic construction. However, there is still a long way to go, and it requires the joint work of the scientific community at a global level and support for basic research.

Effects of the multi-stress-resistant strain Zygosaccharomyces parabailii MC-5K3 bioaugmentation on microbial communities and metabolomics in tobacco waste extract

Industrial tobacco waste was mainly treated via a reconstituted tobacco process using the paper-making method, which involves aqueous concentrated tobacco waste extract (cTWE) fermentation (aging). The fermentation was done to improve the quality of reconstituted tobacco. However, cTWE is a multi-stress environment that is characterized by low pH (about 4), as well as high sugar (above 150 g/L) and nicotine (above 15 g/L) content. In this study, a specific selection strategy was used to successfully isolate multi-stress-resistant bacterial or fungal strains, that exhibited positive effects on cTWE fermentation, thereby improving the quality of final products. A potential strain Zygosaccharomyces parabailii MC-5K3 was used for the bioaugmentation of cTWE fermentation and it significantly influenced the microbial diversity of the fermented cTWE. Zygosaccharomyces was observed to be the only dominant fungal genus instead of some pathogenic bacterial genera, with an abundance of over 95% after four days, and still more than 80% after a week. Meanwhile, metabolomics profiling showed significant concentration decrease with regard to some flavor-improving relative metabolites, such as 3-hydroxybenzoic acid (log2FC = - 5.25) and sorbitol (log2FC = - 5.54). This finding is extrapolated to be the key influence factor on the quality of the fermented cTWE. The correlation analysis also showed that the alterations in microbial diversity in the fermented cTWE led to some important differential metabolite changes, which finally improved various properties of tobacco products.

Human adaptation and diversification in the Microsporum canis complex

The Microsporum canis complex consists of one zoophilic species, M. canis, and two anthropophilic species, M. audouinii and M. ferrugineum. These species are the most widespread zoonotic pathogens causing dermatophytosis in cats and humans worldwide. To clarify the evolutionary relationship between the three species and explore the potential host shift process, this study used phylogenetic analysis, population structure analysis, multispecies coalescent analyses, determination of MAT idiomorph distribution, sexual crosses, and macromorphology and physicochemical features to address the above questions. The complex of Microsporum canis, M. audouinii and M. ferrugineum comprises 12 genotypes. MAT1-1 was present only in M. canis, while the anthropophilic entities contained MAT1-2. The pseudocleistothecia were yielded by the mating behaviour of M. canis and M. audouinii. Growth rates and lipase, keratinolysis and urea hydrolytic capacities of zoophilic M. canis isolates were all higher than those of anthropophilic strains; DNase activity of M. ferrugineum exceeded that of M. canis. The optimum growth temperature was 28 °C, but 22 °C favoured the development of macroconidia. Molecular data, physicochemical properties and phenotypes suggest the adaptation of zoophilic M. canis to anthropophilic M. ferrugineum, with M. audouinii in an intermediate position.

A Multilocus Phylogeny Places Hymenula cerealis (syn. Cephalosporium gramineum) in the Helotiales, Leotiomycetes

The soilborne fungus Hymenula cerealis causes Cephalosporium stripe, a vascular wilt disease of wheat and other grasses in the United States and other wheat-producing countries where winter wheat is subjected to snow cover and frozen soil. No sexual stage is known for H. cerealis, and consequently, its phylogenetic position relative to other fungi has been difficult to establish. The purpose of this study was to conduct a multilocus sequence analysis to determine the phylogenetic position of H. cerealis. Sequence data for five genes, the internal transcribed spacer (ITS), partial large subunit nrDNA (LSU), partial RNA polymerase II second largest subunit region (RPB2), β-tubulin gene, and translation elongation factor 1-α (TEF1-α), from a diverse set of C. gramineum isolates and other related fungi was obtained from GenBank or directly from isolates in the Murray lab and used to construct maximum-likelihood and Bayesian trees. Based on phylogenetic analysis of the single LSU and β-tubulin genes, Cephalosporium gramineum is closely related to the Drepanopezizaceae and Ploettnerulaceae of Helotiales. Based on analyses of the DNA sequence of the ITS, RPB2, and TEF1-α genes, as well as the combined five-gene data set, C. gramineum belongs to the family Drepanopezizaceae, which is a sister taxon to the Ploettnerulaceae, and formed a well-supported clade (MLBP/BIPP = 95%/100%). In conclusion, H. cerealis belongs to the Helotiales, Leotiomycetes.

Culturable fungi from urban soils in China II, with the description of 18 novel species in Ascomycota (Dothideomycetes, Eurotiomycetes, Leotiomycetes and Sordariomycetes)

As China's urbanisation continues to advance, more people are choosing to live in cities. However, this trend has a significant impact on the natural ecosystem. For instance, the accumulation of keratin-rich substrates in urban habitats has led to an increase in keratinophilic microbes. Despite this, there is still a limited amount of research on the prevalence of keratinophilic fungi in urban areas. Fortunately, our group has conducted in-depth investigations into this topic since 2015. Through our research, we have discovered a significant amount of keratinophilic fungi in soil samples collected from various urban areas in China. In this study, we have identified and characterised 18 new species through the integration of morphological and phylogenetic analyses. These findings reveal the presence of numerous unexplored fungal taxa in urban habitats, emphasising the need for further taxonomic research in urban China.

Diagnosis of invasive fungal infections: challenges and recent developments

BACKGROUND

The global burden of invasive fungal infections (IFIs) has shown an upsurge in recent years due to the higher load of immunocompromised patients suffering from various diseases. The role of early and accurate diagnosis in the aggressive containment of the fungal infection at the initial stages becomes crucial thus, preventing the development of a life-threatening situation. With the changing demands of clinical mycology, the field of fungal diagnostics has evolved and come a long way from traditional methods of microscopy and culturing to more advanced non-culture-based tools. With the advent of more powerful approaches such as novel PCR assays, T2 Candida, microfluidic chip technology, next generation sequencing, new generation biosensors, nanotechnology-based tools, artificial intelligence-based models, the face of fungal diagnostics is constantly changing for the better. All these advances have been reviewed here giving the latest update to our readers in the most orderly flow.

MAIN TEXT

A detailed literature survey was conducted by the team followed by data collection, pertinent data extraction, in-depth analysis, and composing the various sub-sections and the final review. The review is unique in its kind as it discusses the advances in molecular methods; advances in serology-based methods; advances in biosensor technology; and advances in machine learning-based models, all under one roof. To the best of our knowledge, there has been no review covering all of these fields (especially biosensor technology and machine learning using artificial intelligence) with relevance to invasive fungal infections.

CONCLUSION

The review will undoubtedly assist in updating the scientific community's understanding of the most recent advancements that are on the horizon and that may be implemented as adjuncts to the traditional diagnostic algorithms.

OMICS and Other Advanced Technologies in Mycological Applications

Fungi play many roles in different ecosystems. The precise identification of fungi is important in different aspects. Historically, they were identified based on morphological characteristics, but technological advancements such as polymerase chain reaction (PCR) and DNA sequencing now enable more accurate identification and taxonomy, and higher-level classifications. However, some species, referred to as "dark taxa", lack distinct physical features that makes their identification challenging. High-throughput sequencing and metagenomics of environmental samples provide a solution to identifying new lineages of fungi. This paper discusses different approaches to taxonomy, including PCR amplification and sequencing of rDNA, multi-loci phylogenetic analyses, and the importance of various omics (large-scale molecular) techniques for understanding fungal applications. The use of proteomics, transcriptomics, metatranscriptomics, metabolomics, and interactomics provides a comprehensive understanding of fungi. These advanced technologies are critical for expanding the knowledge of the Kingdom of Fungi, including its impact on food safety and security, edible mushrooms foodomics, fungal secondary metabolites, mycotoxin-producing fungi, and biomedical and therapeutic applications, including antifungal drugs and drug resistance, and fungal omics data for novel drug development. The paper also highlights the importance of exploring fungi from extreme environments and understudied areas to identify novel lineages in the fungal dark taxa.

Stop black and white thinking: Russula subgenus Compactae (Russulaceae, Russulales) in Europe revised

Russula subgenus Compactae is a group of ectomycorrhizal basidiomycetes, usually with large pileate fruitbodies. European members of the group are characterised by the absence of bright colours on the surfaces of their pilei, the context turning grey to black after cutting, the abundance of short lamellulae in the hymenophore, and spores with an inamyloid suprahilar spot and with low reticulate ornamentation. Our multi-locus phylogenetic study confirmed that this morphological delimitation corresponds to a well-supported clade. Within this clade, 16 species are recognised in Europe, of which five belong to the R. albonigra lineage and were described in a previous study, while eleven are fully described in this study. The application of the names R. acrifolia, R. adusta, R. anthracina, R. atramentosa, R. densissima, R. nigricans and R. roseonigra is based on the position of sequences retrieved from types or authentic material. Based on type sequences, R. fuliginosa is synonymised with R. anthracina and two varieties of R. anthracina are considered synonyms of R. atramentosa. The application of the name R. densifolia is based on a morphological match with the traditional species interpretation and the neotype specimen. Three species are described as new, R. marxmuelleriana sp. nov., R. picrophylla sp. nov. and R. thuringiaca sp. nov. This study recognises three major lineages and two species with isolated positions within the European Compactae and a morphological barcode was assigned to the species using an analysis of 23 selected characters. A search of publicly available sequences from the UNITE database revealed that the majority of species are host tree generalists and widely distributed in temperate and Mediterranean areas of Europe. Russula adusta is the only species so far proven to form ectomycorrhiza exclusively with conifers. Citation: De Lange R, Kleine J, Hampe F, et al. 2023. Stop black and white thinking: Russula subgenus Compactae (Russulaceae, Russulales) in Europe revised. Persoonia 51: 152-193. doi: 10.3767/persoonia.2023.51.04.

Ocean crossers: a tale of disjunctions and speciation in the dwarf-fruticose Lichina (lichenized Ascomycota)

Lichens thrive in rocky coastal areas in temperate and cold regions of both hemispheres. Species of the genus Lichina, which form characteristic black fruiting thalli associated with cyanobacteria, often create distinguishable bands in the intertidal and supralittoral zones. The present study uses a comprehensive specimen dataset and four gene loci to (1) delineate and discuss species boundaries in this genus, (2) assess evolutionary relationships among species, and (3) infer the most likely causes of their current geographic distribution in the Northern and Southern hemispheres. A dated phylogeny describes the time frame in which extant disjunctions of species and populations were established. The results showed that the genus is integrated by four species, with Lichina pygmaea, L. confinis and the newly described L. canariensis from rocky seashores in the Canary Islands, occurring in the Northern Hemisphere, whereas L. intermedia is restricted to the Southern Hemisphere. Lichina intermedia hosted a much higher intraspecific genetic diversity than the other species, with subclades interpreted as species-level lineages by the different species delimitation approaches. However, a conservative taxonomic approach was adopted. This species showed a striking disjunct distribution between Australasia and southern South America. The timing for the observed interspecific and intraspecific divergences and population disjunctions postdated continental plate movements, suggesting that long-distance dispersal across body waters in the two hemispheres played a major role in shaping the current species distributions. Such ocean crossings were, as in L. canariensis, followed by speciation. New substitution rates for the nrITS of the genus Lichina were inferred using a tree spanning the major Ascomycota lineages calibrated using fossils. In conclusion, this work lays the foundation for a better understanding of the evolution through time and space of maritime lichens.

Phenotypic and Genotypic Characterization and Antifungal Susceptibility of Sporothrix schenckii sensu stricto Isolated from a Feline Sporotrichosis Outbreak in Bangkok, Thailand

Sporotrichosis, an invasive fungal infection caused by Sporothrix schenckii, has emerged in Southeast Asia, affecting cats and posing a potential zoonotic risk to humans. We evaluated 38 feline sporotrichosis cases in and around Bangkok, Thailand, from 2017 to 2021. The isolates were phenotypically and genotypically characterized. The cats infected with sporotrichosis were mainly young adults, males, and domestic short hairs with uncontrolled outdoor access, and they lived in Bangkok. All isolates showed low thermotolerance and converted to the yeast phase at 35 °C. Based on the internal transcribed spacer region of rDNA sequences, our strains belonged to S. schenckii sensu stricto and clustered with clinical clade D. Based on the concatenated tree of calmodulin and beta-tubulin genes, five groups of S. schenckii were generated, and the monophyletic clade, Group II, of Thai strains was recognized. In vitro antifungal susceptibility testing demonstrated that the MIC50 of our isolates to amphotericin B, itraconazole, and posaconazole were within the limit of the species-specific epidemiological cutoff values, suggesting that the organisms were the wild type. Addressing the outbreak of feline sporotrichosis in Thailand by providing guidelines for diagnosis and effective treatment may help control the spread of disease and reduce the risk of cat-transmitted sporotrichosis to humans.

Exploring Differences in Culturable Fungal Diversity Using Standard Freezing Incubation-A Case Study in the Limestones of Lemos Pantheon (Portugal)

In this study, we explored the biodiversity and abundance of culturable fungi in four samples associated with different biodeterioration outlines collected from the Lemos Pantheon, a limestone-built artwork in Portugal. We compared the results from prolonged standard freezing with those previously obtained from fresh samples to analyze differences in the obtained community and assess the effectiveness of the standard freezing incubation protocol in uncovering a different segment of culturable fungal diversity. Our results showed a slight decrease in culturable diversity, but over 70% of the obtained isolates were not present in the previously studied fresh samples. We also identified a high number of potential new species with this procedure. Moreover, the use of a wide variety of selective culture media positively influenced the diversity of the cultivable fungi obtained in this study. These findings highlight the importance of developing new protocols under varying conditions to accurately characterize the culturable fraction in a given sample. The identification and study of these communities and their possible contribution to the biodeterioration process is crucial knowledge for formulating effective conservation and restoration plans to prevent further damage to valuable cultural heritage assets.

Colletotrichum Species Associated with Anthracnose in Salix babylonica in China

Salix babylonica L. is a popular ornamental tree species in China and widely cultivated in Asia, Europe, and North America. Anthracnose in S. babylonica poses a serious threat to its growth and reduces its medicinal properties. In 2021, a total of 55 Colletotrichum isolates were isolated from symptomatic leaves in three provinces in China. Phylogenetic analyses using six loci (ITS, ACT, CHS-1, TUB2, CAL, and GAPDH) and a morphological characterization of the 55 isolates showed that they belonged to four species of Colletotrichum, including C. aenigma, C. fructicola, C. gloeosporioides s.s., and C. siamense. Among them, C. siamense was the dominant species, and C. gloeosporioides s.s. was occasionally discovered from the host tissues. Pathogenicity tests revealed that all the isolates of the aforementioned species were pathogenic to the host, and there were significant differences in pathogenicity or virulence among these isolates. The information on the diversity of Colletotrichum spp. that causes S. babylonica anthracnose in China is new.

Utilization of Low Molecular Weight Carbon Sources by Fungi and Saprolegniales: Implications for Their Ecology and Taxonomy

Contributions of fungal and oomycete communities to freshwater carbon cycling have received increasing attention in the past years. It has been shown that fungi and oomycetes constitute key players in the organic matter cycling of freshwater ecosystems. Therefore, studying their interactions with dissolved organic matter is crucial for understanding the aquatic carbon cycle. Therefore, we studied the consumption rates of various carbon sources using 17 fungal and 8 oomycete strains recovered from various freshwater ecosystems using EcoPlate™ and FF MicroPlate™ approaches. Furthermore, phylogenetic relationships between strains were determined via single and multigene phylogenetic analyses of the internal transcribed spacer regions. Our results indicated that the studied fungal and oomycete strains could be distinguished based on their carbon utilization patterns, as indicated by their phylogenetic distance. Thereby, some carbon sources had a higher discriminative strength to categorize the studied strains and thus were applied in a polyphasic approach. We concluded that studying the catabolic potential enables a better understanding of taxonomic relationships and ecological roles of fungal vs. oomycete strains.

To explore strange new worlds - The diversification in Tremella caloplacae was linked to the adaptive radiation of the Teloschistaceae

Lichenicolous fungi are a heterogeneous group of organisms that grow exclusively on lichens, forming obligate associations with them. It has often been assumed that cospeciation has occurred between lichens and lichenicolous fungi, but this has been seldom analysed from a macroevolutionary perspective. Many lichenicolous species are rare or are rarely observed, which results in frequent and large gaps in the knowledge of the diversity of many groups. This, in turn, hampers evolutionary studies that necessarily are based on a reasonable knowledge of this diversity. Tremella caloplacae is a heterobasidiomycete growing on various hosts from the lichen-forming family Teloschistaceae, and evidence suggests that it may represent a species complex. We combine an exhaustive sampling with molecular and ecological data to study species delimitation, cophylogenetic events and temporal concordance of this association. Tremella caloplacae is here shown to include at least six distinct host-specific lineages (=putative species). Host switch is the dominant and most plausible event influencing diversification and explaining the coupled evolutionary history in this system, although cospeciation cannot be discarded. Speciation in T. caloplacae would therefore have occurred coinciding with the rapid diversification - by an adaptive radiation starting in the late Cretaceous - of their hosts. New species in T. caloplacae would have developed as a result of specialization on diversifying lichen hosts that suddenly offered abundant new ecological niches to explore or adapt to.

Molecular advances in mycoremediation of polycyclic aromatic hydrocarbons: Exploring fungal bacterial interactions

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous high global concern environmental pollutants and tend to bioaccumulate due to hydrophobic properties. These xenobiotics, having variable concentrations along different matrices, gradually undergo various physical, chemical, and biological transformation processes. Myco-remediation aids accelerated degradation by effectively transforming complex ring structures to oxidized/hydroxylated intermediates, which can further funnel to bacterial degradation pathways. Exploitation of such complementing fungal-bacterial enzymatic activity can overcome certain limitations of incomplete bioremediation process. Furthermore, high-throughput molecular methods can be employed to unveil community structure, taxon abundance, coexisting community interactions, and metabolic pathways under stressed conditions. The present review critically discusses the role of different fungal phyla in PAHs biotransformation and application of fungal-bacterial cocultures for enhanced mineralization. Moreover, recent advances in bioassays for PAH residue detection, monitoring, developing xenobiotics stress-tolerant strains, and application of fungal catabolic enzymes are highlighted. Application of next-generation sequencing methods to reveal complex ecological networks based on microbial community interactions and data analysis bias in performing such studies is further discussed in detail. Conclusively, the review underscores the application of mixed-culture approach by critically highlighting in situ fungal-bacterial community nexus and its role in complete mineralization of PAHs for the management of contaminated sites.

Molecular Approaches for Detection of Trichoderma Green Mold Disease in Edible Mushroom Production

Due to the evident aggressive nature of green mold and the consequently huge economic damage it causes for producers of edible mushrooms, there is an urgent need for prevention and infection control measures, which should be based on the early detection of various Trichoderma spp. as green mold causative agents. The most promising current diagnostic tools are based on molecular methods, although additional optimization for real-time, in-field detection is still required. In the first part of this review, we briefly discuss cultivation-based methods and continue with the secondary metabolite-based methods. Furthermore, we present an overview of the commonly used molecular methods for Trichoderma species/strain detection. Additionally, we also comment on the potential of genomic approaches for green mold detection. In the last part, we discuss fast screening molecular methods for the early detection of Trichoderma infestation with the potential for in-field, point-of-need (PON) application, focusing on isothermal amplification methods. Finally, current challenges and future perspectives in Trichoderma diagnostics are summarized in the conclusions.

MinION Sequencing of Yeast Mock Communities To Assess the Effect of Databases and ITS-LSU Markers on the Reliability of Metabarcoding Analysis

Microbial communities play key roles both for humans and the environment. They are involved in ecosystem functions, maintaining their stability, and provide important services, such as carbon cycle and nitrogen cycle. Acting both as symbionts and as pathogens, description of the structure and composition of these communities is important. Metabarcoding uses ribosomal DNA (rDNA) (eukaryotic) or rRNA gene (prokaryotic) sequences for identification of species present in a site and measuring their abundance. This procedure requires several technical steps that could be source of bias producing a distorted view of the real community composition. In this work, we took advantage of an innovative "long-read" next-generation sequencing (NGS) technology (MinION) amplifying the DNA spanning from the internal transcribed spacer (ITS) to large subunit (LSU) that can be read simultaneously in this platform, providing more information than "short-read" systems. The experimental system consisted of six fungal mock communities composed of species present at various relative amounts to mimic natural situations characterized by predominant and low-frequency species. The influence of the sequencing platform (MinION and Illumina MiSeq) and the effect of different reference databases and marker sequences on metagenomic identification of species were evaluated. The results showed that the ITS-based database provided more accurate species identification than LSU. Furthermore, a procedure based on a preliminary identification with standard reference databases followed by the production of custom databases, including only the best outputs of the first step, is proposed. This additional step improved the estimate of species proportion of the mock communities and reduced the number of ghost species not really present in the simulated communities. IMPORTANCE Metagenomic analyses are fundamental in many research areas; therefore, improvement of methods and protocols for the description of microbial communities becomes more and more necessary. Long-read sequencing could be used for reducing biases due to the multicopy nature of rDNA sequences and short-read limitations. However, these novel technologies need to be assessed and standardized with controlled experiments, such as mock communities. The interest behind this work was to evaluate how long reads performed identification and quantification of species mixed in precise proportions and how the choice of database affects such analyses. Development of a pipeline that mitigates the effect of the barcoding sequences and the impact of the reference database on metagenomic analyses can help microbiome studies go one step further.

A Lethal Case of Disseminated Cladosporium allicinum Infection in a Captive African Bullfrog

Cladosporium infections have a poor prognosis in animals, most likely due to a lack of knowledge about diagnosis and treatment. In this study, we described a case of a lethal Cladosporium allicinum infection in a captive bullfrog (Pyxicephalus adspersus) in Europe. One adult male bullfrog was referred with clinical signs of lethargy and a cutaneous nodule. Fungal infection was suspected on cytology and confirmed by histology and cultural isolation. The mold was identified by molecular methods using partial sequencing of the TEF1α gene and the ITS region of rDNA. Climbazole antifungal treatment was started but the frog died after 30 days, and necropsy was done. Pigmented hyphae and structures consistent with muriform bodies were found on a background of diffuse granulomatous inflammation at cytological and histopathological examinations. Fungal culture revealed the presence of pigmented fungi identified as Cladosporium allicinum only by partial sequencing of the TEF1α gene. A focally extensive granuloma with intralesional hyphae and muriform bodies effacing the architecture of head, liver, kidneys, lungs, and large intestine were retrieved after necropsy. This study is the first Italian report of the occurrence of lethal C. allicinum infection in a frog and highlights the role of this Cladosporium sp. in chromoblastomycosis.

Linking processes to community functions—insights into litter decomposition combining fungal metatranscriptomics and environmental NMR profiling

In forest ecosystems, decomposition is essential for carbon and nutrient cycling and therefore a key process for ecosystem functioning. During the decomposition process, litter chemistry, involved decomposer organisms, and enzymatic activity change interdependently. Chemical composition of the litter is the most complex and dynamic component in the decomposition process and therefore challenging to assess holistically. In this study, we aimed to characterize chemical shifts during decomposition and link them to changes in decomposer fungal activity. We characterized the chemical composition of freshly fallen autumn leaves of European beech (Fagus sylvatica) and the corresponding leaf litter after 1 year of decomposition by proton nuclear magnetic resonance spectroscopy. We further tested the applicability of spiking experiments for qualitative and quantitative characterization of leaves and litter chemistry. The composition and transcriptional activity of fungal communities was assessed by high-throughput Illumina sequencing in the same litter samples. We were able to distinguish freshly fallen leaves from 1-year-old litter based on their chemical composition. Chemical composition of leaves converged among regions with progressing decomposition. Fungal litter communities differed in composition among regions, but they were functionally redundant according to the expression of genes encoding litter degrading enzymes (CAZymes). Fungi of the saprotrophic genera Mycena and Chalara correlated with transcription of litter-degrading CAZymes in 1-year-old litter. Forestry measures influenced the diversity and transcription rate of the detected CAZymes transcripts in litter. Their expression was primarily predicted by composition of the soluble chemical fraction of the litter. Environmental NMR fingerprints thus proved valuable for inferring ecological contexts. We propose and discuss a holistic framework to link fungal activity, enzyme expression, and chemical composition.

DNA-Barcoding Identification of Plant Pathogens for Disease Diagnostics

The accurate identification of plant pathogens is a critical step to prevent their spread and attenuate their impact. Among the wide range of methods available, DNA-barcoding, i.e., the identification of an organism through the PCR amplification and sequencing of a single locus, remains one of the most straightforward and accurate plant-pathogen identification techniques that can be used in a generic molecular biology lab. This chapter provides a detailed protocol for the isolation of genomic DNA of fungal and oomycete pathogens from fresh field samples and the amplification and sequencing of the internal transcribed spacer (ITS) locus for DNA-barcoding purpose. Amendments to the protocol are provided to help in resolving issues related to the analysis of complicated samples and to the lack of species resolution that can be encountered with ITS barcodes.

A pseudo-outbreak of Cyberlindnera fabianii funguria: Implication from whole genome sequencing assay

Background

Although the yeast Cyberlindnera fabianii (C. fabianii) has been rarely reported in human infections, nosocomial outbreaks caused by this organism have been documented. Here we report a pseudo-outbreak of C. fabianii in a urology department of a Chinese hospital over a two-week period.

Methods

Three patients were admitted to the urology department of a tertiary teaching hospital in Beijing, China, from Nov to Dec 2018, for different medical intervention demands. During the period Nov 28 to Dec 5, funguria occurred in these three patients, and two of them had positive urine cultures multiple times. Sequencing of rDNA internal transcribed spacer (ITS) region and MALDI-TOF MS were applied for strain identification. Further, sequencing of rDNA non-transcribed spacer (NTS) region and whole genome sequencing approaches were used for outbreak investigation purpose.

Results

All the cultured yeast strains were identified as C. fabianii by sequencing of ITS region, and were 100% identical to the C. fabianii type strain CBS 5640T. However, the MALDI-TOF MS system failed to correctly identify this yeast pathogen. Moreover, isolates from these three clustered cases shared 99.91%-100% identical NTS region sequences, which could not rule out the possibility of an outbreak. However, whole genome sequencing results revealed that only two of the C. fabianii cases were genetically-related with a pairwise SNP of 192 nt, whilst the third case had over 26,000 SNPs on its genome, suggesting a different origin. Furthermore, the genomes of the first three case strains were phylogenetically even more diverged when compared to a C. fabianii strain identified from another patient, who was admitted to a general surgical department of the same hospital 7 months later. One of the first three patients eventually passed away due to poor general conditions, one was asymptomatic, and other clinically improved.

Conclusion

In conclusion, nosocomial outbreaks caused by emerging and uncommon fungal species are increasingly being reported, hence awareness must be raised. Genotyping with commonly used universal gene targets may have limited discriminatory power in tracing the sources of infection for these organisms, requiring use of whole genome sequencing to confirm outbreak events.

DNA barcoding, an effective tool for species identification: a review

DNA barcoding is a powerful taxonomic tool to identify and discover species. DNA barcoding utilizes one or more standardized short DNA regions for taxon identification. With the emergence of new sequencing techniques, such as Next-generation sequencing (NGS), ONT MinION nanopore sequencing, and Pac Bio sequencing, DNA barcoding has become more accurate, fast, and reliable. Rapid species identification by DNA barcodes has been used in a variety of fields, including forensic science, control of the food supply chain, and disease understanding. The Consortium for Barcode of Life (CBOL) presents various working groups to identify the universal barcode gene, such as COI in metazoans; rbcL, matK, and ITS in plants; ITS in fungi; 16S rRNA gene in bacteria and archaea, and creating a reference DNA barcode library. In this article, an attempt has been made to analyze the various proposed DNA barcode for different organisms, strengths & limitations, recent advancements in DNA barcoding, and methods to speed up the DNA barcode reference library construction. This study concludes that constructing a reference library with high species coverage would be a major step toward identifying species by DNA barcodes. This can be achieved in a short period of time by using advanced sequencing and data analysis methods.

Natural infection of Chiromyzinae larvae (Diptera: Stratiomyidae) in southern Chile by Tolypocladium valdiviae sp. nov

A new species from the fungal genus Tolypocladium (Hypocreales: Ophiocordycipitaceae) that infects Stratiomyidae larva from the genus Hylorops is described: Tolypocladium valdiviae Gallardo-Pillancari, Montalva & González. The description is based on both genomic data and morphological characteristics. The sexual stage of T. valdiviae presents fleshy and visible stromata; unlike Tolypocladium ophioglossoides, it is smaller and emerges directly from its host and resembles Tolypocladium longisegmentis and Tolypocladium capitatum, both of which are parasites of deer truffle fungi of the genus Elaphomyces (Ascomycota: Eurotiales). In the anamorphic state, T. valdiviae presents conidiogenous cells similar in shape and arrangement to those of Tolypocladium inflatum, however T. valdiviae produces larger conidiogenous cells and, occasionally, produces chlamydospores. Phylogenetic evidence suggested that T. valdiviae is in a clade close to T. longisegmentis, T. inflatum and T. ophioglossoides, species also recognized to be parasites of fungi of the genus Elaphomyces. The new species is known so far only from Valdivia, southern Chile.