Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

High-elevation-induced decrease in soil pH weakens ecosystem multifunctionality by influencing soil microbiomes

Plant environmental stress response has become a global research hotspot, yet there is a lack of clear understanding regarding the mechanisms that maintain microbial diversity and their ecosystem services under environmental stress. In our research, we examined the effects of moderate elevation on the rhizosphere soil characteristics, microbial community composition, and ecosystem multifunctionality (EMF) within agricultural systems. Our findings revealed a notable negative correlation between EMF and elevation, indicating a decline in multifunctionality at higher elevations. Additionally, our analysis across bacterial and protistan communities showed a general decrease in microbial richness with increasing elevation. Using random forest models, pH was identified as the key environmental stressor influencing microbial communities. Furthermore, we found that microbial community diversity is negatively correlated with stability by mediating complexity. Interestingly, while pH was found to affect the complexity within bacterial networks, it did not significantly impact the ecosystem stability along the elevation gradients. Using a Binary-State Speciation and Extinction (BiSSE) model to explore the evolutionary dynamics, we found that Generalists had higher speciation rates and lower extinction rates compared to specialists, resulting in a skewed distribution towards higher net diversification for generalists under increasing environmental stress. Moreover, structural equation modeling (SEM) analysis highlighted a negative correlation between environmental stress and community diversity, but showed a positive correlation between environmental stress and degree of cooperation & competition. These interactions under environmental stress indirectly increased community stability and decreased multifunctionality. Our comprehensive study offers valuable insights into the intricate relationship among environmental factors, microbial communities, and ecosystem functions, especially in the context of varying elevation gradients. These findings contribute significantly to our understanding of how environmental stressors affect microbial diversity and ecosystem services, providing a foundation for future ecological research and management strategies in similar contexts.

Improving the gold standard in NCBI GenBank and related databases: DNA sequences from type specimens and type strains

Scientific names permit humans and search engines to access knowledge about the biodiversity that surrounds us, and names linked to DNA sequences are playing an ever-greater role in search-and-match identification procedures. Here, we analyze how users and curators of the National Center for Biotechnology Information (NCBI) are flagging and curating sequences derived from nomenclatural type material, which is the only way to improve the quality of DNA-based identification in the long run. For prokaryotes, 18,281 genome assemblies from type strains have been curated by NCBI staff and improve the quality of prokaryote naming. For Fungi, type-derived sequences representing over 21,000 species are now essential for fungus naming and identification. For the remaining eukaryotes, however, the numbers of sequences identifiable as type-derived are minuscule, representing only 739 species of arthropods, 1542 vertebrates, and 125 embryophytes. An increase in the production and curation of such sequences will come from (i) sequencing of types or topotypic specimens in museum collections, (ii) the March 2023 rule changes at the International Nucleotide Sequence Database Collaboration requiring more metadata for specimens, and (iii) efforts by data submitters to facilitate curation, including informing NCBI curators about a specimen's type status. We illustrate different type-data submission journeys and provide best-practice examples from a range of organisms. Expanding the number of type-derived sequences in DNA databases, especially of eukaryotes, is crucial for capturing, documenting, and protecting biodiversity.

Diversity and Pathogenicity of Botryosphaeriaceae Species Isolated from Olives in Istria, Croatia, and Evaluation of Varietal Resistance

During 2021 and 2022, a field investigation was conducted in Istria, Croatia, searching for trees exhibiting signs of Botryosphaeria dieback. Samples of symptomatic trees were collected from 26 different locations and analysed. Isolates that morphologically corresponded to species from the Botryosphaeriaceae family were selected, and detailed morphological characterisation and molecular identification of the isolates were conducted. Based on morphological characteristics and phylogenetic analysis using the internal transcribed spacer (ITS), beta-tubulin (TUB2), and translation elongation factor 1-alpha (TEF1-α) regions, six species of fungi from the Botryosphaeriaceae family were identified: Botryosphaeria dothidea (Moug. ex Fr.) Ces. & De Not.; Diplodia mutila (Fr.) Fr.; Diplodia seriata De Not.; Dothiorella iberica A.J.L. Phillips, J. Luque & A. Alves; Dothiorella sarmentorum (Fr.) A.J.L. Phillips, Alves & Luque; and Neofusicoccum parvum (Pennycook & Samuels) Crous, Slippers & A.J.L. Phillips. This is the first report of D. mutila, Do. sarmentorum, and Do. iberica causing Botryosphaeria dieback on olive trees in Croatia, and the first study investigating the resistance of Croatian olive varieties to species from the Botryosphaeriaceae family. Pathogenicity testing of selected isolates and assessment of variety resistance were conducted on four different olive varieties, namely Buža, Istarska bjelica, Leccino, and Rosinjola, using representative isolates of the mentioned species. The most aggressive species was found to be N. parvum. Olive varieties exhibited differences in susceptibility depending on the fungus they were infected with.

Foliar mycobiome remains unaltered under urban air-pollution but differentially express stress-related genes

Air pollution caused by tropospheric ozone contributes to the decline of forest ecosystems; for instance, sacred fir, Abies religiosa (Kunth) Schltdl. & Cham. forests in the peri-urban region of Mexico City. Individual trees within these forests exhibit variation in their response to ozone exposure, including the severity of visible symptoms in needles. Using RNA-Seq metatranscriptomic data and ITS2 metabarcoding, we investigated whether symptom variation correlates with the taxonomic and functional composition of fungal mycobiomes from needles collected in this highly polluted area in the surroundings of Mexico City. Our findings indicate that ozone-related symptoms do not significantly correlate with changes in the taxonomic composition of fungal mycobiomes. However, genes coding for 30 putative proteins were differentially expressed in the mycobiome of asymptomatic needles, including eight genes previously associated with resistance to oxidative stress. These results suggest that fungal communities likely play a role in mitigating the oxidative burst caused by tropospheric ozone in sacred fir. Our study illustrates the feasibility of using RNA-Seq data, accessible from global sequence repositories, for the characterization of fungal communities associated with plant tissues, including their gene expression.

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.

The Eurasian spruce bark beetle Ips typographus shapes the microbial communities of its offspring and the gallery environment

The Eurasian spruce bark beetle (Ips typographus) is currently the most economically relevant pest of Norway spruce (Picea abies). Ips typographus associates with filamentous fungi that may help it overcome the tree's chemical defenses. However, the involvement of other microbial partners in this pest's ecological success is unclear. To understand the dynamics of the bark beetle-associated microbiota, we characterized the bacterial and fungal communities of wild-collected and lab-reared beetles throughout their development by culture-dependent approaches, meta-barcoding, and quantitative PCR. Gammaproteobacteria dominated the bacterial communities, while the fungal communities were mainly composed of yeasts of the Saccharomycetales order. A stable core of microbes is shared by all life stages, and is distinct from those associated with the surrounding bark, indicating that Ips typographus influences the microbial communities of its environment and offspring. These findings coupled with our observations of maternal behavior, suggest that Ips typographus transfers part of its microbiota to eggs via deposition of an egg plug treated with maternal secretions, and by inducing an increase in abundance of a subset of taxa from the adjacent bark.

Antidiabetic Potential of a Trimeric Anthranilic Acid Peptide Isolated from Malbranchea flocciformis

Compound 3, a trimeric anthranilic acid peptide, and another three metabolites were isolated from an organic extract from the culture medium of Malbranchea flocciformis ATCC 34530. The chemical structure proposed previously for 3 was unequivocally assigned via synthesis and X-ray diffraction analysis. Tripeptide 3 showed insulinotropic properties by decreasing the postprandial peak in healthy and hyperglycemic mice. It also increased glucose-induced insulin secretion in INS-1E at 5 μM, specifically at higher glucose concentrations. These results revealed that 3 might act as an insulin sensitizer and a non-classical insulin secretagogue. Altogether, these findings are in harmony with the in vivo oral glucose tolerance test and acute oral hypoglycemic assay. Finally, the chemical composition of the extract was established by the Global Natural Products Social Molecular Network platform. Phylogenetic analysis using the internal transcribed spacer region revealed that M. flocciformis ATCC 34530 is related to the Malbrancheaceae.

Fungal Endophytes: Discovering What Lies within Some of Canada's Oldest and Most Resilient Grapevines

Plant diseases and pests reduce crop yields, accounting for global crop losses of 30% to 50%. In conventional agricultural production systems, these losses are typically controlled by applying chemical pesticides. However, public pressure is mounting to curtail agrochemical use. In this context, employing beneficial endophytic microorganisms is an increasingly attractive alternative to the use of conventional chemical pesticides in agriculture. A multitude of fungal endophytes are naturally present in plants, producing enzymes, small peptides, and secondary metabolites due to their bioactivity, which can protect hosts from pathogens, pests, and abiotic stresses. The use of beneficial endophytic microorganisms in agriculture is an increasingly attractive alternative to conventional pesticides. The aim of this study was to characterize fungal endophytes isolated from apparently healthy, feral wine grapes in eastern Canada that have grown without agrochemical inputs for decades. Host plants ranged from unknown seedlings to long-lost cultivars not widely propagated since the 1800s. HPLC-MS was used to identify unique endophyte-derived chemical compounds in the host plants, while dual-culture competition assays showed a range in endophytes' ability to suppress the mycelial growth of Botrytis, which is typically controlled in viticulture with pesticides. Twelve of the most promising fungal endophytes isolated were identified using multilocus sequencing and morphology, while DNA barcoding was employed to identify some of their host vines. These fungal endophyte isolates, which consisted of both known and putative novel strains, belonged to seven genera in six families and five orders of Ascomycota. Exploring the fungal endophytes in these specimens may yield clues to the vines' survival and lead to the discovery of novel biocontrol agents.

Taxonomic study and diversity of Postia s.lat. in Swat, Pakistan: addition of five brown rot Polypores to the country

Brown rot Polypores are ecologically significant as they play a crucial role in maintaining the carbon cycle and contribute to humus formation in forest ecosystems through their lignocellulose degradation ability. It is important to note that some species can significantly impact timber, potentially causing decay in economically valuable wood. Many Asian countries including Pakistan are still under the exploratory phase and have undocumented species diversity in Polypore fungi. In the current study, collections representing five different species belonging to two families, Postiaceae and Adustoporiaceae, were subjected to detailed morphoanatomical and molecular analyses. A combined matrix of two gene datasets (ITS and nrLSU) was analyzed using three different phylogenetic methods viz. Maximum Parsimony (MP), Maximum Likelihood (ML), and Bayesian inference (BI). Our study presents descriptions of five previously undocumented brown rot Polypore species from the country including Fuscopostia fragilis (Fr.) B.K. Cui, L.L. Shen & Y.C. Dai, Amaropostia stiptica (Pers.) B.K. Cui, L.L. Shen & Y.C. Dai, Cyanosporus piceicola B.K. Cui, L.L. Shen & Y.C. Dai, Spongiporus balsameus (Peck) A. David, Rhodonia placenta (Fr.) Niemelä, K.H. Larss. & Schigel. Regarding the molecular data, nodes of our subject sequences were substantially supported and fell under their respective species clades with high ML bootstrap values (≥ 95), MP bootstrap ≥ 74 and BI probabilities ≥ 0.98. Findings of the study will not only contribute to our understanding of local Polypores species diversity but also enhance knowledge of geographical distribution in global context.

Potential for Use of Species in the Subfamily Erynioideae for Biological Control and Biotechnology

The fungal order Entomophthorales in the Zoopagomycota includes many fungal pathogens of arthropods. This review explores six genera in the subfamily Erynioideae within the family Entomophthoraceae, namely, Erynia, Furia, Orthomyces, Pandora, Strongwellsea, and Zoophthora. This is the largest subfamily in the Entomophthorales, including 126 described species. The species diversity, global distribution, and host range of this subfamily are summarized. Relatively few taxa are geographically widespread, and few have broad host ranges, which contrasts with many species with single reports from one location and one host species. The insect orders infected by the greatest numbers of species are the Diptera and Hemiptera. Across the subfamily, relatively few species have been cultivated in vitro, and those that have require more specialized media than many other fungi. Given their potential to attack arthropods and their position in the fungal evolutionary tree, we discuss which species might be adopted for biological control purposes or biotechnological innovations. Current challenges in the implementation of these species in biotechnology include the limited ability or difficulty in culturing many in vitro, a correlated paucity of genomic resources, and considerations regarding the host ranges of different species.

Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients

BACKGROUND

The accuracy of internal-transcribed-spacer (ITS) and shotgun metagenomics has not been robustly evaluated, and the effect of diet on the composition and function of the bacterial and fungal gut microbiome in a longitudinal setting has been poorly investigated. Here we compared two approaches to study the fungal community (ITS and shotgun metagenomics), proposed an enrichment protocol to perform a reliable mycobiome analysis using a comprehensive in-house fungal database, and correlated dietary data with both bacterial and fungal communities.

RESULTS

We found that shotgun DNA sequencing after a new enrichment protocol combined with the most comprehensive and novel fungal databases provided a cost-effective approach to perform gut mycobiome profiling at the species level and to integrate bacterial and fungal community analyses in fecal samples. The mycobiome was significantly more variable than the bacterial community at the compositional and functional levels. Notably, we showed that microbial diversity, composition, and functions were associated with habitual diet composition instead of driven by global dietary changes. Our study indicates a potential competitive inter-kingdom interaction between bacteria and fungi for food foraging.

CONCLUSION

Together, our present work proposes an efficient workflow to study the human gut microbiome integrating robustly fungal, bacterial, and dietary data. These findings will further advance our knowledge of the interaction between gut bacteria and fungi and pave the way for future investigations in human mycobiome. Video Abstract.

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.

Sheptide A: an antimalarial cyclic pentapeptide from a fungal strain in the Herpotrichiellaceae

As part of ongoing efforts to isolate biologically active fungal metabolites, a cyclic pentapeptide, sheptide A (1), was discovered from strain MSX53339 (Herpotrichiellaceae). The structure and sequence of 1 were determined primarily by analysis of 2D NMR and HRMS/MS data, while the absolute configuration was assigned using a modified version of Marfey's method. In an in vitro assay for antimalarial potency, 1 displayed a pEC50 value of 5.75 ± 0.49 against malaria-causing Plasmodium falciparum. Compound 1 was also tested in a counter screen for general cytotoxicity against human hepatocellular carcinoma (HepG2), yielding a pCC50 value of 5.01 ± 0.45 and indicating a selectivity factor of ~6. This makes 1 the third known cyclic pentapeptide biosynthesized by fungi with antimalarial activity.

Current Fungal Taxonomy and Developments in the Identification System

A functional identification system is the core and basis of fungal taxonomy, which provides sufficient diagnostic characteristics for species delimitation. Phenotype-based identification systems have exhibited significant drawbacks, such as being laborious and time-consuming. Thus, a molecular-based identification system (rDNA, DNA fingerprint, etc.) is proposed for application to fungi that lack reliable morphological characteristics. High Throughput Sequencing also makes great contributions to fungal taxonomy. However, the formal naming of nonculturable fungi from environmental sequencing is a significant challenge. Biochemical profile-based identification systems have outstanding value in fungal taxonomy and can occasionally be indispensable. This method utilizes biomarker metabolites and proteins that are expected to be unequivocal and stable. Of these, Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry has become the method of choice for chemotaxonomy. In sum, these described identification systems cannot solve all problems of species delimitation, and considerable attention to the updating of fungal nomenclature, standardization of techniques, knowledge sharing, and dissemination will be necessary.

Soil microbiota plays a key regulatory role in the outbreak of tobacco root rot

Introduction

Root rot caused by the fungal pathogen Fusarium sp. poses significant challenges to tobacco cultivation in China, leading to major economic setbacks. The interplay between this pathogen and the wider soil microbial community remains poorly understood.

Methods

High-throughput sequencing technology was utilized to evaluate soil prokaryotic, fungal, and protistan communities. We compared microbial communities in infected soils to those in healthy soils from the same field. Additionally, the influence of pH on the microbial communities was assessed.

Results

Infected soils displayed elevated levels of soil nutrients but diminished observed richness across prokaryotic, fungal, and protistan groups. The pathogenic fungi Fusarium solani f sp. eumartii's abundance was notably increased in infected soils. Infection with F. solani significantly altered the soil's microbial community structure and interactions, manifested as a decrease in network scale and the number of keystone species. An evaluation of prokaryotes' role in F. solani's invasion revealed an increased number of connecting nodes in infected soils. Additionally, relationships between predatory protists and fungi were augmented, whereas predation on F. solani declined.

Discussion

The study underscores the significance of comprehending the interactions among soil microorganisms and brings to light the susceptibility of soil microbial communities to pathogen invasion. It offers insights into the multifaceted relationships and potential vulnerabilities within the soil ecosystem in the context of Fusarium sp. invasion.

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.

Redefining the Genus Corollospora Based on Morphological and Phylogenetic Approaches

The present study, initially to resolve the cryptic species within Corollospora maritima, is to determine how to attain taxonomic discrimination at species and generic levels. Multiple sequence alignments (MSAs) of the ITS, 28S, and 18S regions of the nuclear ribosomal cistron were separately subjected to pairwise distance assessments, Bayesian, and Maximum likelihood phylogenetic analyses. Morphological descriptions of 15 type strains of Corollospora species, along with MSAs involving representatives of the whole genus Corollospora (268 isolates, many from C. maritima sensu lato) totaling 355 published sequences, allowed phylogenetic assessments conducted to the following p-distance thresholds in the ITS/28S regions: ≥3%/1% for species segregation and ≥8%/2% for generic segregation. This resulted in the introduction of 10 new genera encompassing 13 new combinations of current Corollospora species: Ajigaurospora pseudopulchella, Corollosporella anglusa, Corollosporella ramulosa, Corollosporopsis portsaidica, Garethelia parvula, Honshuriella fusca, Keraliethelia pulcehlla, Nakagariella filiformis, Paracorollospora angusta, Paracorollospora luteola, Paracorollospora marina, Shirahamella gracilis, and Tokuratelia colossa. Furthermore, seven undefined genera considered putative new genera (pNGenus A to G), and 16 undefined putative new species (seven spp. come from the resolution of the C. maritima complex), await re-assessment of their morphology and additional molecular data, which may result in the recognition of new taxa.

No plant is an island

Most of the world's ecosystems are dominated by plants, and preserving the natural and agricultural landscapes that we depend on therefore requires understanding plants and their interactions at local and global scales. This is challenging because plants' ways of perceiving each other and communicating with each other and with animals are so fundamentally different from the ways we animals communicate with, and manipulate, each other. The collection of articles in the present issue of Current Biology illustrates the progress being made in deciphering some of the processes and mechanisms involved in plant interactions at different scales. While the topic of interactions with plants is very broad, any overview will require covering chemical signals and their reception; mutualisms and symbioses; interactions with pathogens; and interactions in communities. Approaches taken in these fields range from molecular biology and physiology to ecology.

Soil microbial responses to simultaneous contamination of antimony and arsenic in the surrounding area of an abandoned antimony smelter in Southwest China

Soil contamination with heavy metal(loid)s may influence microbial activities in the soil, and consequently jeopardize soil health. Microbial responses to soil contamination play an important role in ecological risk assessment. This study investigated the effect of heavy metal(loid)s contamination on microbial community structure and abundance in the surrounding soil of an abandoned antimony (Sb) smelter in Qinglong county, Guizhou province, Southwest China. A total of 46 soil samples were collected from ten sampling sites (labelled as A-I, and CK) across the study area at depths of 0-2, 2-10, 10-20, 20-30, 30-40, and 40-50 cm. The soil samples were analyzed for total and bioavailable heavy metal(loid) concentrations, bacterial, fungal, and archaeal community structures, diversities, and functions, together with soil basic physicochemical properties. Much greater ecological risk of Sb and arsenic (As) was present in the surface soil (0-2 cm) compared to that in the subsoils. The activities of dominant microorganisms tended to be associated with soil pH and heavy metal(loid)s (i.e., Sb, As, lead (Pb), cadmium (Cd), and chromium (Cr)). Bacteria associated with IMCC26256, Rhizobiales, Burkholderiales, and Gaiellales, and archaea associated with Methanocellales were estimated to be tolerant to high concentrations of Sb and As in the soil. In addition, the magnitude of soil microbial responses to Sb and As contamination was in the order of archaea > bacteria > fungi. In contrast to the negligible response of fungi and negative response of bacteria to Sb and As contamination, there was a strongly positive correlation between archaeal activity and total Sb and As concentrations in the soil. Our findings provide a theoretical basis for the remediation of Sb smelter-affected soil.

Fungal biotechnology: From yesterday to tomorrow

Fungi have been used to better the lives of everyday people and unravel the mysteries of higher eukaryotic organisms for decades. However, comparing progress and development stemming from fungal research to that of human, plant, and bacterial research, fungi remain largely understudied and underutilized. Recent commercial ventures have begun to gain popularity in society, providing a new surge of interest in fungi, mycelia, and potential new applications of these organisms to various aspects of research. Biotechnological advancements in fungal research cannot occur without intensive amounts of time, investments, and research tool development. In this review, we highlight past breakthroughs in fungal biotechnology, discuss requirements to advance fungal biotechnology even further, and touch on the horizon of new breakthroughs with the highest potential to positively impact both research and society.

A parasitic fungus employs mutated eIF4A to survive on rocaglate-synthesizing Aglaia plants

Plants often generate secondary metabolites as defense mechanisms against parasites. Although some fungi may potentially overcome the barrier presented by antimicrobial compounds, only a limited number of examples and molecular mechanisms of resistance have been reported. Here, we found an Aglaia plant-parasitizing fungus that overcomes the toxicity of rocaglates, which are translation inhibitors synthesized by the plant, through an amino acid substitution in a eukaryotic translation initiation factor (eIF). De novo transcriptome assembly revealed that the fungus belongs to the Ophiocordyceps genus and that its eIF4A, a molecular target of rocaglates, harbors an amino acid substitution critical for rocaglate binding. Ribosome profiling harnessing a cucumber-infecting fungus, Colletotrichum orbiculare, demonstrated that the translational inhibitory effects of rocaglates were largely attenuated by the mutation found in the Aglaia parasite. The engineered C. orbiculare showed a survival advantage on cucumber plants with rocaglates. Our study exemplifies a plant-fungus tug-of-war centered on secondary metabolites produced by host plants.

Metabolomic Strategies to Improve Chemical Information from OSMAC Studies of Endophytic Fungi

Metabolomics strategies are important tools to get holistic chemical information from a system, but they are scarcely applied to endophytic fungi to understand their chemical profiles of biosynthesized metabolites. Here Penicillium sp. was cultured using One Strain Many Compounds (OSMAC) conditions as a model system to demonstrate how this strategy can help in understanding metabolic profiles and determining bioactive metabolites with the application of metabolomics and statistical analyses, as well as molecular networking. Penicillium sp. was fermented in different culture media and the crude extracts from mycelial biomass (CEm) and broth (CEb) were obtained, evaluated against bacterial strains (Staphylococcus aureus and Pseudomonas aeruginosa), and the metabolomic profiles by LC-DAD-MS were obtained and chemometrics statistical analyses were applied. The CEm and CEb extracts presented different chemical profiles and antibacterial activities; the highest activities observed were against S. aureus from CEm (MIC = 16, 64, and 128 µg/mL). The antibacterial properties from the extracts were impacted for culture media from which the strain was fermented. From the Volcano plot analysis, it was possible to determine statistically the most relevant features for the antibacterial activity, which were also confirmed from biplots of PCA as strong features for the bioactive extracts. These compounds included 75 (13-oxoverruculogen isomer), 78 (austalide P acid), 87 (austalide L or W), 88 (helvamide), 92 (viridicatumtoxin A), 96 (austalide P), 101 (dihydroaustalide K), 106 (austalide k), 110 (spirohexaline), and 112 (pre-viridicatumtoxin). Thus, these features included diketopiperazines, meroterpenoids, and polyketides, such as indole alkaloids, austalides, and viridicatumtoxin A, a rare tetracycline.

Da Vinci's yeast: Blastobotrys davincii f.a., sp. nov

A new species of the yeast genus Blastobotrys was discovered during a worldwide survey of culturable xerophilic fungi in house dust. Several culture-dependent and independent studies from around the world detected the same species from a wide range of substrates including indoor air, cave wall paintings, bats, mummies, and the iconic self-portrait of Leonardo da Vinci from ca 1512. However, none of these studies identified their strains, clones, or OTUs as Blastobotrys. We introduce the new species as Blastobotrys davincii f.a., sp. nov. (holotype CBS H-24879) and delineate it from other species using morphological, phylogenetic, and physiological characters. The new species of asexually (anamorphic) budding yeast is classified in Trichomonascaceae and forms a clade along with its associated sexual state genus Trichomonascus. Despite the decade-old requirement to use a single generic name for fungi, both names are still used. Selection of the preferred name awaits a formal nomenclatural proposal. We present arguments for adopting Blastobotrys over Trichomonascus and introduce four new combinations as Blastobotrys allociferrii (≡ Candida allociferrii), B. fungorum (≡ Sporothrix fungorum), B. mucifer (≡ Candida mucifera), and Blastobotrys vanleenenianus (≡ Trichomonascus vanleenenianus). We provide a nomenclatural review and an accepted species list for the 37 accepted species in the Blastobotrys/Trichomonascus clade. Finally, we discuss the identity of the DNA clones detected on the da Vinci portrait, and the importance of using appropriate media to isolate xerophilic or halophilic fungi.

Applying a modified metabarcoding approach for the sequencing of macrofungal specimens from fungarium collections

PREMISE

Fungaria are an underutilized resource for understanding fungal biodiversity. The effort and cost of producing DNA barcode sequence data for large numbers of fungal specimens can be prohibitive. This study applies a modified metabarcoding approach that provides a labor-efficient and cost-effective solution for sequencing the fungal DNA barcodes of hundreds of specimens at once.

METHODS

We applied a two-step PCR approach using nested, barcoded primers to sequence the fungal nrITS2 region of 766 macrofungal specimens using the Illumina platform. The specimens represent a broad taxonomic sampling of the Dikarya. Of these, 382 Lactarius specimens were analyzed to identify molecular operational taxonomic units (MOTUs) using a phylogenetic approach. The raw sequences were trimmed, filtered, assessed, and analyzed using the DADA2 amplicon de-noising toolkit and Biopython. The sequences were compared to the NCBI and UNITE databases and Sanger nrITS sequences from the same specimens.

RESULTS

The taxonomic identities derived from the nrITS2 sequence data were >90% accurate across all specimens sampled. A phylogenetic analysis of the Lactarius sequences identified 20 MOTUs.

DISCUSSION

The results demonstrate the capacity of these methods to produce nrITS2 sequences from large numbers of fungarium specimens. This provides an opportunity to more effectively use fungarium collections to advance fungal diversity identification and documentation.

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.

Soil mycobiome in sustainable agriculture

The soil microbiome contributes to several ecosystem processes. It plays a key role in sustainable agriculture, horticulture and forestry. In contrast to the vast number of studies focusing on soil bacteria, the amount of research concerning soil fungal communities is limited. This is despite the fact that fungi play a crucial role in the cycling of matter and energy on Earth. Fungi constitute a significant part of the pathobiome of plants. Moreover, many of them are indispensable to plant health. This group includes mycorrhizal fungi, superparasites of pathogens, and generalists; they stabilize the soil mycobiome and play a key role in biogeochemical cycles. Several fungal species also contribute to soil bioremediation through their uptake of high amounts of contaminants from the environment. Moreover, fungal mycelia stretch below the ground like blood vessels in the human body, transferring water and nutrients to and from various plants. Recent advances in high-throughput sequencing combined with bioinformatic tools have facilitated detailed studies of the soil mycobiome. This review discusses the beneficial effects of soil mycobiomes and their interactions with other microbes and hosts in both healthy and unhealthy ecosystems. It may be argued that studying the soil mycobiome in such a fashion is an essential step in promoting sustainable and regenerative agriculture.

Expanding the geographical distribution of Blastobotrysmalaysiensis (Saccharomycetales) beyond the Asian continent - a cave fungus first reported in the Americas

Background

Saccharomycetales are ascomycetic yeasts and, amongst them, the genus Blastobotrys has approximately 30 known species. Blastobotrysmalaysiensis is a yeast species, described from cave samples, known until then only from Malaysia. In this study, we characterise a new strain and report the second occurrence record of this species. Here, Blastobotrysmalaysiensis URM 8507/SXS 675, was collected from sediments samples from a cave in the Parque Estadual de Terra Ronca (PETER) in Goiás, Brazil. Phylogenetic analyses revealed strong support with the sequence of the species type, as well as with other species of the clade. This new record contributes by providing new molecular data for the species and expanding the knowledge of its distribution beyond the Asian continent.

New information

First record of a yeast for the American continent and its second mention for the world.

Fungal names: a comprehensive nomenclatural repository and knowledge base for fungal taxonomy

Fungal taxonomy is a complex and rapidly changing subject, which makes proper naming of fungi challenging for taxonomists. A registration platform with a standardized and information-integrated database is a powerful tool for efficient research on fungal taxonomy. Fungal Names (FN, https://nmdc.cn/fungalnames/; launched in 2011) is one of the three official fungal nomenclatural repositories authorized by the International Nomenclature Committee for Fungi (NCF). Currently, FN includes >567 000 taxon names from >10 000 related journals and books published since 1596 and covers >147 000 collection records of type specimens/illustrations from >5000 preserving agencies. FN is also a knowledge base that integrates nomenclature information with specimens, culture collections and herbaria/fungaria, publications and taxonomists, and represents a summary of the history and recent advances in fungal taxonomy. Published fungal names are categorized based on well-accepted nomenclature rules and can be readily searched with different keywords and strategies. In combination with a standardized name checking tool and a sequence alignment-based identification package, FN makes the registration and typification of nomenclatural novelties of fungi convenient and accurate.

UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi

In phylogenomics the evolutionary relationship of organisms is studied by their genomic information. A common approach to phylogenomics is to extract related genes from each organism, build a multiple sequence alignment and then reconstruct evolution relations through a phylogenetic tree. Often a set of highly conserved genes occurring in single-copy, called core genes, are used for this analysis, as they allow efficient automation within a taxonomic clade. Here we introduce the Universal Fungal Core Genes (UFCG) database and pipeline for genome-wide phylogenetic analysis of fungi. The UFCG database consists of 61 curated fungal marker genes, including a novel set of 41 computationally derived core genes and 20 canonical genes derived from literature, as well as marker gene sequences extracted from publicly available fungal genomes. Furthermore, we provide an easy-to-use, fully automated and open-source pipeline for marker gene extraction, training and phylogenetic tree reconstruction. The UFCG pipeline can identify marker genes from genomic, proteomic and transcriptomic data, while producing phylogenies consistent with those previously reported, and is publicly available together with the UFCG database at https://ufcg.steineggerlab.com.

Methods used for the study of endophytic fungi: a review on methodologies and challenges, and associated tips

Endophytic fungi are microorganisms that colonize the interior of plant tissues (e.g. leaves, seeds, stem, trunk, roots, fruits, flowers) in intracellular and/or extracellular spaces without causing symptoms of disease in host plants. These microorganisms have been isolated from plant species in a wide variety of habitats worldwide, and it is estimated that all terrestrial plants are colonized by one or more species of endophytic fungus. In addition, these microorganisms have been drawing the attention of researchers because of their ability to synthesize a wide range of bioactive molecules with potential for applications in agriculture, medicine and biotechnology. However, several obstacles come up when studying the diversity and chemical potential of endophytic fungi. For example, the usage of an inappropriate surface disinfection method for plant tissue may not eliminate the epiphytic microbiota or may end up interfering with the endophytic mycobiota, which consequently generates erroneous results. Moreover, the composition of the culture medium and the culture conditions can favor the growth of certain species and inhibit others, which generates underestimated results. Other inconsistencies can arise from the fungus misidentification and consequent exploration of its chemical potential. Based on the methodological biases that may occur at all stages of studies dealing with endophytic fungi, the objective of this review is to discuss the main methods employed in these studies as well as highlight the challenges derived from the different approaches. We also report associated tips to help future studies on endophytic fungi as a contribution.

Taxonomic and Phylogenetic Reassessment of Pyrgidium (Mycocaliciales) and Investigation of Ascospore Morphology

Mycocaliciales comprise non-lichenized either saprotrophic or lichenicolous fungi which occur in temperate and tropical regions. The mazaediate, saprotrophic and monospecific genus, Pyrgidium, is currently assigned to this order, yet the phylogenetic placement of the genus has remained uncertain due to the absence of molecular data. In order to investigate the systematic position of Pyrgidium, two specimens collected in Brazil and Thailand, respectively, were used to generate mtSSU, SSU, LSU and ITS sequences. However, given that most other representatives of this order only have LSU and ITS sequences available, the phylogenetic reconstruction was limited to these two markers. The phylogenetic analyses confirmed placement of the genus within Mycocaliciales, the genus possessing a sister group relationship with the lichenicolous genus Sphinctrina. Detailed morphological descriptions and illustrations are provided, including those for type specimens of the various synonyms subsumed under the hitherto only accepted species, Pyrgidium montellicum (Beltr.) Tibell. The ascospore morphology was investigated using compound and scanning electronic microscopy (SEM). Principal component analysis (PCA) was performed for the ascospore size using PC-ORD 7. The molecular data and re-examination of the type specimens support the monospecific nature of this genus.

Production of new antimicrobial palm oil-derived sophorolipids by the yeast Starmerella riodocensis sp. nov. against Candida albicans hyphal and biofilm formation

BACKGROUND

Microbial derived-surfactants display low eco-toxicity, diverse functionality, high biodegradability, high specificity, and stability under extreme conditions. Sophorolipids are emerging as key biosurfactants of yeast origins, used in various industrial sectors to lower surface tension. Recently, sophorolipid complexes have been applied in biomedicals and agriculture to eradicate infectious problems related to human and plant fungal pathogens. This study aimed to characterize the functional properties and antifungal activities of sophorolipids produced by a newly characterized Starmerella riodocensis GT-SL1R sp. nov. strain.

RESULTS

Starmerella riodocensis GT-SL1R sp. nov. strain was belonged to Starmerella clade with 93.12% sequence similarity using the ITS technique for strain identification. Sophorolipids production was examined, using co-carbon substrates glucose and palm oil, with a yield on the substrate between 30 and 46%. Using shake-flasks, the S. riodocensis GT-SL1R strain produced biosurfactants with an emulsification activity of 54.59% against kerosene compared to the S. bombicola BCC5426 strain with an activity of 60.22%. Maximum productivities of GT-SL1R and the major sophorolipid-producer S. bombicola were similar at 0.8 gl^-1 h^-1. S. riodocensis GT-SL1R produced mixed forms of lactonic and acidic sophorolipids, shown by TCL, FTIR, and HPLC. Importantly, the complex sophorolipid mixture displayed antifungal activity against an opportunistic yeast pathogen Candida albicans by effectively reducing hyphal and biofilm formation.

CONCLUSIONS

Sophorolipids derived from S. riodocensis demonstrate potential industrial and biomedical applications as green surfactant and antifungal agent. Since numerous renewable bioresources and industrial wastes could be used by microbial cell factories in the biosynthesis of biosurfactants to reduce the production cost, sophorolipids hold a promising alternative to current antimicrobials in treatments against infectious diseases in humans, animals, and plants.

Multi-Gene Phylogenetic Approach for Identification and Diversity Analysis of Bipolaris maydis and Curvularia lunata Isolates Causing Foliar Blight of Zea mays

Bipolaris species are known to be important plant pathogens that commonly cause leaf spot, root rot, and seedling blight in a wide range of hosts worldwide. In 2017, complex symptomatic cases of maydis leaf blight (caused by Bipolaris maydis) and maize leaf spot (caused by Curvularia lunata) have become increasingly significant in the main maize-growing regions of India. A total of 186 samples of maydis leaf blight and 129 maize leaf spot samples were collected, in 2017, from 20 sampling sites in the main maize-growing regions of India to explore the diversity and identity of this pathogenic causal agent. A total of 77 Bipolaris maydis isolates and 74 Curvularia lunata isolates were screened based on morphological and molecular characterization and phylogenetic analysis based on ribosomal markers—nuclear ribosomal DNA (rDNA) internal transcribed spacer (ITS) region, 28S nuclear ribosomal large subunit rRNA gene (LSU), D1/D2 domain of large-subunit (LSU) ribosomal DNA (rDNA), and protein-coding gene-glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Due to a dearth of molecular data from ex-type cultures, the use of few gene regions for species resolution, and overlapping morphological features, species recognition in Bipolaris has proven difficult. The present study used the multi-gene phylogenetic approach for proper identification and diversity of geographically distributed B. maydis and C. lunata isolates in Indian settings and provides useful insight into and explanation of its quantitative findings.

Species Diversity, Distribution, and Phylogeny of Exophiala with the Addition of Four New Species from Thailand

The genus Exophiala is an anamorphic ascomycete fungus in the family Herpotrichiellaceae of the order Chaetothyriales. Exophiala species have been classified as polymorphic black yeast-like fungi. Prior to this study, 63 species had been validated, published, and accepted into this genus. Exophiala species are known to be distributed worldwide and have been isolated in various habitats around the world. Several Exophiala species have been identified as potential agents of human and animal mycoses. However, in some studies, Exophiala species have been used in agriculture and biotechnological applications. Here, we provide a brief review of the diversity, distribution, and taxonomy of Exophiala through an overview of the recently published literature. Moreover, four new Exophiala species were isolated from rocks that were collected from natural forests located in northern Thailand. Herein, we introduce these species as E. lamphunensis, E. lapidea, E. saxicola, and E. siamensis. The identification of these species was based on a combination of morphological characteristics and molecular analyses. Multi-gene phylogenetic analyses of a combination of the internal transcribed spacer (ITS) and small subunit (nrSSU) of ribosomal DNA, along with the translation elongation factor (tef), partial β-tubulin (tub), and actin (act) genes support that these four new species are distinct from previously known species of Exophiala. A full description, illustrations, and a phylogenetic tree showing the position of four new species are provided.

Morpho-Molecular Characterization of Microfungi Associated with Phyllostachys (Poaceae) in Sichuan, China

In the present study, we surveyed the ascomycetes from bamboo of Phyllostachys across Sichuan Province, China. A biphasic approach based on morphological characteristics and multigene phylogeny confirmed seven species, including one new genus, two new species, and five new host record species. A novel genus Paralloneottiosporina is introduced to accommodate Pa. sichuanensis that was collected from leaves of Phyllostachys violascens. Moreover, the newly introduced species Bifusisporella sichuanensis was isolated from leaves of P. edulis, and five species were newly recorded on bamboos, four species belonging to Apiospora, viz. Ap. yunnana, Ap. neosubglobosa, Ap. jiangxiensis, and Ap. hydei, and the last species, Seriascoma yunnanense, isolated from dead culms of P. heterocycla. Morphologically similar and phylogenetically related taxa were compared. Comprehensive descriptions, color photo plates of micromorphology are provided.

Publicly Available and Validated DNA Reference Sequences Are Critical to Fungal Identification and Global Plant Protection Efforts: A Use-Case in Colletotrichum

Publicly available and validated DNA reference sequences useful for phylogeny estimation and identification of fungal pathogens are an increasingly important resource in the efforts of plant protection organizations to facilitate safe international trade of agricultural commodities. Colletotrichum species are among the most frequently encountered and regulated plant pathogens at U.S. ports-of-entry. The RefSeq Targeted Loci (RTL) project at NCBI (BioProject no. PRJNA177353) contains a database of curated fungal internal transcribed spacer (ITS) sequences that interact extensively with NCBI Taxonomy, resulting in verified name-strain-sequence type associations for >12,000 species. We present a publicly available dataset of verified and curated name-type strain-sequence associations for all available Colletotrichum species. This includes an updated GenBank Taxonomy for 238 species associated with up to 11 protein coding loci and an updated RTL ITS dataset for 226 species. We demonstrate that several marker loci are well suited for phylogenetic inference and identification. We improve understanding of phylogenetic relationships among verified species, verify or improve phylogenetic circumscriptions of 14 species complexes, and reveal that determining relationships among these major clades will require additional data. We present detailed comparisons between phylogenetic and similarity-based approaches to species identification, revealing complex patterns among single marker loci that often lead to misidentification when based on single-locus similarity approaches. We also demonstrate that species-level identification is elusive for a subset of samples regardless of analytical approach, which may be explained by novel species diversity in our dataset and incomplete lineage sorting and lack of accumulated synapomorphies at these loci.

dnabarcoder: an open-source software package for analyzing and predicting DNA sequence similarity cut-offs for fungal sequence identification

The accuracy and precision of fungal molecular identification and classification are challenging, particularly in environmental metabarcoding approaches as these often trade accuracy for efficiency given the large data volumes at hand. In most ecological studies, only a single similarity cutoff value is used for sequence identification. This is not sufficient since the most commonly used DNA markers are known to vary widely in terms of inter‐ and intraspecific variability. We address this problem by presenting a new tool, dnabarcoder, to predict local similarity cutoffs and measure the resolving powers of a biomarker for sequence identification for different clades of fungi. It was shown that the predicted similarity cutoffs varied significantly between the clades of a recently released ITS DNA barcode data set from the CBS culture collection of the Westerdijk Fungal Biodiversity Institute. When classifying a large public fungal ITS data set—the UNITE database—against the barcode data set, the local similarity cutoffs assigned fewer sequences than the traditional cutoffs used in metabarcoding studies. However, the obtained accuracy and precision were significantly improved. Our study showed that it might be better to extract the ITS region from the ITS barcodes to optimize taxonomic assignment accuracy. Furthermore, 15.3, 25.6, and 26.3% of the fungal species of the barcode data set were indistinguishable by full‐length ITS, ITS1, and ITS2, respectively. Except for these indistinguishable species, the resolving powers of full‐length ITS, ITS1, and ITS2 sequences were similar at the species level. Nevertheless, the complete ITS region had a better resolving power at higher taxonomic levels.

Molecular phylogenetic analyses and micromorphology reveal placement of the enigmatic tropical discomycete Polydiscidium in Sclerococcum (Sclerococcales, Eurotiomycetes)

Polydiscidium is an enigmatic, monotypic, and rarely reported genus of Ascomycota of uncertain placement. The morphologically unique Polydiscidium martynii grows on dead wood and forms compound ascomata composed of thick, black, gelatinous somatic tissue that branches out from a common base. Multiple apothecia are located on the branches, mostly toward the tips, and are composed of 8-spored asci and paraphyses embedded in a gelatinous matrix that turns blue in Melzer's reagent. The species was previously known from only three collections from Guyana (holotype), Trinidad, and the Democratic Republic of the Congo and no sequences exist. Due to its peculiar morphology, taxonomic affinities of Polydiscidium have been debated, with different authors having placed it in Helotiaceae, Leotiaceae, or Leotiomycetes incertae sedis. Recent collections of this species resulting from long-term field work in Guyana and Cameroon led us to revisit the morphology and phylogenetic position of this fungus. Newly generated sequences of P. martynii were added to an Ascomycota-wide six-locus data set. The resulting phylogeny showed Polydiscidium to be a member of order Sclerococcales (Eurotiomycetes). Next, a four-locus (18S, ITS, 28S, mtSSU) phylogenetic reconstruction revealed that Polydiscidium is congeneric with Sclerococcum. A new combination is proposed for this species, Sclerococcum martynii. Micromorphological features, including the gelatinous hymenium composed of asci with amyloid gel cap and septate brown ascospores, are in agreement with Sclerococcum. New combinations are proposed for two additional species: Sclerococcum chiangraiensis and S. fusiformis. Finally, Dactylosporales is considered a later synonym of Sclerococcales.

Morphological and Molecular Evidence Reveal Eight New Species of Gymnopus from Northeast China

Gymnopus is a widely distributed genus consisting of about 300 species thus far, including Gymnopus fusipes as a generic type. A total of nine species from China belong to the sect. Levipedes, including eight new species—Gymnopus longisterigmaticus, Gymnopus longus, Gymnopus macrosporus, Gymnopus striatus, Gymnopus changbaiensis, Gymnopus tomentosus, Gymnopus tiliicola, and Gymnopus globulosus—which were delimited and proposed based on morphological and molecular evidence; and one new record from Jilin Province, China—Gymnopus erythropus. Detailed descriptions and illustrations are presented, as well as comparisons to similar species. Overall, our results broaden the morphological characterization of the genus. The pileipellis of sect. Levipedes typically takes on the “Dryophila structure”, while, in our findings, pileipellis terminal hyphae inflated to spherical to prolate were observed, in addition to extremely long basidia sterigma. The phylogenies inferred from the ITS and nLSU dataset supported the Gymnopus, which was defined by Oliveira et al. as a monophyletic genus, and the novel species as separate lineages within. A key to all species described in this study is also provided.

Sporobolomyces lactucae sp. nov. (Pucciniomycotina, Microbotryomycetes, Sporidiobolales): An Abundant Component of Romaine Lettuce Phylloplanes

Shifts in food microbiomes may impact the establishment of human pathogens, such as virulent lineages of Escherichia coli, and thus are important to investigate. Foods that are often consumed raw, such as lettuce, are particularly susceptible to such outbreaks. We have previously found that an undescribed Sporobolomyces yeast is an abundant component of the mycobiome of commercial romaine lettuce (Lactuca sativa). Here, we formally describe this species as Sporobolomyces lactucae sp. nov. (Pucciniomycotina, Microbotryomycetes, and Sporidiobolales). We isolated multiple strains of this yeast from commercial romaine lettuce purchased from supermarkets in Illinois and Indiana; additional isolates were obtained from various plant phylloplanes in California. S. lactucae is a red-pigmented species that is similar in appearance to other members of the genus Sporobolomyces. However, it can be differentiated by its ability to assimilate glucuronate and D-glucosamine. Gene genealogical concordance supports S. lactucae as a new species. The phylogenetic reconstruction of a four-locus dataset, comprising the internal transcribed spacer and large ribosomal subunit D1/D2 domain of the ribosomal RNA gene, translation elongation factor 1-α, and cytochrome B, places S. lactucae as a sister to the S. roseus clade. Sporobolomyces lactucae is one of the most common fungi in the lettuce microbiome.

Phosphorus and Zinc Are Strongly Associated with Belowground Fungal Communities in Wheat Field under Long-Term Fertilization

Belowground fungi are closely related to crop growth, and agricultural fertilization is widely known to affect soil fungal communities. Yet it remains unclear whether fungal communities in differing belowground habitats—root endosphere, rhizosphere soil, and bulk soil—respond differently to long-term fertilization. Here we investigated the variation in fungal communities of root endosphere, rhizosphere soil, and bulk soil under 35 years of fertilization in wheat fields. Specifically, the fertilization regimes were applied as five treatments: soils receiving NPK fertilizer, NPK and cow manure (NPK+CM), NPK and pig manure (NPK+PM), NPK and wheat straw (NPK+WS), and no fertilizer (Control). Long-term fertilization significantly impacted fungal community composition in all three habitats, and these effects were stronger in the rhizosphere and bulk soils than root endosphere. Mantel test results showed that fungal community composition was significantly correlated with phosphorus and zinc contents. Further, fungal alpha diversity was lowest in the NPK+PM treatment and was negatively correlated with both phosphorus and zinc contents. Moreover, NPK+PM treatment had the lowest complexity of fungal co-occurrence network, and in general network complexity was significantly negatively correlated with the zinc and phosphorus contents. Taken together, these results suggest that long-term fertilization can impact fungal communities not only in soils but in root endosphere, and this is strongly associated with the contents of phosphorus and zinc there, a finding important for guiding fertilization management practices and supporting sustainable agriculture.

IMPORTANCE Fungi, an essential component in nutrient cycling and plant growth, are highly sensitive to fertilization. However, there are limited studies on fungi in root endosphere under long-term fertilization management. Our research extended the study on the endophytic fungal community of crop roots under agricultural management and found that its responses were similar to the communities in soil habitats. In addition, the type of organic materials was reported as the main driver affecting soil fungal community under long-term fertilization. Our research further revealed that the underlying mechanism of affecting the fungal communities in the soils and roots was the differences in phosphorus and zinc contents caused by the application of different organic materials. Therefore, our results highlight that except for phosphorus, zinc content of the organic materials should be considered in long-term organic fertilization systems.

A long-read amplicon approach to scaling up the metabarcoding of lichen herbarium specimens

Reference sequence databases are critical to the accurate detection and identification of fungi in the environment. As repositories of large numbers of well-curated specimens, herbaria and fungal culture collections have the material resources to generate sequence data for large number of taxa, and could therefore allow filling taxonomic gaps often present in reference sequence databases. Financial resources to do that are however often lacking, so that recent efforts have focused on decreasing sequencing cost by increasing the number of multiplexed samples per sequencing run while maintaining high sequence quality. Following a previous study that aimed at decreasing sequencing cost for lichen specimens by generating fungal ITS barcodes for 96 specimens using PacBio amplicon sequencing, we present a method that further decreases lichen specimen metabarcoding costs. A total of 384 mixed DNA extracts obtained from lichen herbarium specimens, mostly from the four genera Buellia, Catillaria, Endocarpon and Parmotrema, were used to generate new fungal ITS sequences using a Sequel I sequencing platform and the PacBio M13 barcoded primers. The average success rate across all taxa was high (86.5%), with particularly high rates for the crustose saxicolous taxa (Buellia, Catillaria and others; 93.3%) and the terricolous squamulose taxa (Endocarpon and others; 96.5%). On the other hand, the success rate for the foliose genus Parmotrema was lower (60.4%). With this taxon sampling, greater specimen age did not appear to impact sequencing success. In fact, the 1966–1980 collection date category showed the highest success rate (97.3%). Compared to the previous study, the abundance-based sequence denoising method showed some limitations, but the cost of generating ITS barcodes was further decreased thanks to the higher multiplexing level. In addition to contributing new ITS barcodes for specimens of four interesting lichen genera, this study further highlights the potential and challenges of using new sequencing technologies on collection specimens to generate DNA sequences for reference databases.

The curse of the uncultured fungus

The international DNA sequence databases abound in fungal sequences not annotated beyond the kingdom level, typically bearing names such as “uncultured fungus”. These sequences beget low-resolution mycological results and invite further deposition of similarly poorly annotated entries. What do these sequences represent? This study uses a 767,918-sequence corpus of public full-length fungal ITS sequences to estimate what proportion of the 95,055 “uncultured fungus” sequences that represent truly unidentifiable fungal taxa – and what proportion of them that would have been straightforward to annotate to some more meaningful taxonomic level at the time of sequence deposition. Our results suggest that more than 70% of these sequences would have been trivial to identify to at least the order/family level at the time of sequence deposition, hinting that factors other than poor availability of relevant reference sequences explain the low-resolution names. We speculate that researchers’ perceived lack of time and lack of insight into the ramifications of this problem are the main explanations for the low-resolution names. We were surprised to find that more than a fifth of these sequences seem to have been deposited by mycologists rather than researchers unfamiliar with the consequences of poorly annotated fungal sequences in molecular repositories. The proportion of these needlessly poorly annotated sequences does not decline over time, suggesting that this problem must not be left unchecked.

Long-Reads-Based Metagenomics in Clinical Diagnosis With a Special Focus on Fungal Infections

Identification of the causative infectious agent is essential in the management of infectious diseases, with the ideal diagnostic method being rapid, accurate, and informative, while remaining cost-effective. Traditional diagnostic techniques rely on culturing and cell propagation to isolate and identify the causative pathogen. These techniques are limited by the ability and the time required to grow or propagate an agent in vitro and the facts that identification based on morphological traits are non-specific, insensitive, and reliant on technical expertise. The evolution of next-generation sequencing has revolutionized genomic studies to generate more data at a cheaper cost. These are divided into short- and long-read sequencing technologies, depending on the length of reads generated during sequencing runs. Long-read sequencing also called third-generation sequencing emerged commercially through the instruments released by Pacific Biosciences and Oxford Nanopore Technologies, although relying on different sequencing chemistries, with the first one being more accurate both platforms can generate ultra-long sequence reads. Long-read sequencing is capable of entirely spanning previously established genomic identification regions or potentially small whole genomes, drastically improving the accuracy of the identification of pathogens directly from clinical samples. Long-read sequencing may also provide additional important clinical information, such as antimicrobial resistance profiles and epidemiological data from a single sequencing run. While initial applications of long-read sequencing in clinical diagnosis showed that it could be a promising diagnostic technique, it also has highlighted the need for further optimization. In this review, we show the potential long-read sequencing has in clinical diagnosis of fungal infections and discuss the pros and cons of its implementation.

Comparison of Culturing and Metabarcoding Methods to Describe the Fungal Endophytic Assemblage of Brachypodium rupestre Growing in a Range of Anthropized Disturbance Regimes

Simple Summary

The richness (number of species) of the fungi kingdom is estimated at 1.5 million species, but the vast majority remains unknown. Many of them inhabit plants—the so-called fungal endophytes—and may establish different types of interactions with their host plant. Fungal endophytes have been traditionally studied by letting them grow in appropriate culturing media in petri dishes, but novel massive DNA sequencing techniques which do not require a cultivation step (metabarcoding) are gaining ground. Both techniques were applied and compared to characterize the mycobiome of plants of a tall grass (Brachypodium rupestre) growing in high-mountain grasslands with different plant diversity (low and high). The two methods showed similar trends comparing endophyte richness between plant tissue types (root > rhizome > shoot) and between grasslands (low-diversity > high-diversity). However, the metabarcoding identified almost six times more endophyte species than the culturing although the most isolated fungal species via culturing, Omnidemptus graminis, was not recognized via metabarcoding. We conclude that the complementation of both techniques is still the best option to obtain a complete characterization of the fungal endophytic assemblage of the plant species.

Abstract

Fungal endophytes develop inside plants without visible external signs, and they may confer adaptive advantages to their hosts. Culturing methods have been traditionally used to recognize the fungal endophytic assemblage, but novel metabarcoding techniques are being increasingly applied. This study aims to characterize the fungal endophytic assemblage in shoots, rhizomes and roots of the tall grass Brachypodium rupestre growing in a large area of natural grasslands with a continuum of anthropized disturbance regimes. Seven out of 88 taxa identified via metabarcoding accounted for 81.2% of the reads (Helotiaceae, Lachnum sp. A, Albotricha sp. A, Helotiales A, Agaricales A, Mycena sp. and Mollisiaceae C), revealing a small group of abundant endophytes and a large group of rare species. Although both methods detected the same trends in richness and fungal diversity among the tissues (root > rhizome > shoot) and grasslands (low-diversity > high-diversity grasslands), the metabarcoding tool identified 5.8 times more taxa than the traditional culturing method (15 taxa) but, surprisingly, failed to sequence the most isolated endophyte on plates, Omnidemptus graminis. Since both methods are still subject to important constraints, both are required to obtain a complete characterization of the fungal endophytic assemblage of the plant species.