Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae

Formation of high-quality mixed silage from paper mulberry and wheat bran driven by the characteristics of the microbial community

Paper mulberry (Broussonetia papyrifera) is a high-quality silage protein feed material that can help address feed shortages and support livestock development. Although some studies have investigated the relationships between microbial communities and silage quality, these relationships and the underlying community assembly processes remain complex, requiring further research to clarify them. Additionally, limited research has explored the relationship between microbial community fermentation functions and silage quality. In this study, we aimed to explore B. papyrifera and wheat bran mixed silage quality driven by the characteristics of the microbial community. After 50 days of silage fermentation, high-quality and low-quality samples were selected from every mixing ratio (90:10, 80:20, and 65:35). The silage chemical composition, lignocellulose degradation enzyme activity, microbial community composition, and potential functions were used to explore the relevance between silage quality and the characteristics of the microbial community. The contents of hemicellulose, neutral detergent fiber, pH, and the activities of endoglucanase and exoglucanase were significantly affected by mixing ratios and silage quality grade. There were higher crude protein content, lignocellulose degrading enzyme activity, and lower pH, lignin, and acid detergent fiber in the mixing of 65:35 (BP65%) samples. The PERMANOVA results showed that mixing ratios had significant impacts on microbial community composition and bacterial fermentation functions. There was a higher bacterial diversity, lower fungal diversity, and better functional potentials for fermentation and lignocellulose degradation in BP65% high-quality silage. The dominant genera were Lactobacillus, Cladosporium, and Wallemia in all samples. The relative abundance of Clostridium, Rhodococcus, Turicibacter, Ralstonia, and Burkholderia was significantly higher in BP65% high-quality samples. There was a higher abundance of Wallemia in the BP65% samples than in other mixing ratios samples. Notably, silage quality showed a close relationship with Lactobacillus, Turicibacter, Romboutsia, Wallemia, and Pichia. In summary, 65:35 was a suitable mixing ratio for B. papyrifera and wheat bran silage, but high-quality silage still required the participation of multiple specific rare microbial taxa. The higher bacterial diversity and specific microbial taxa abundance could be critical for improving B. papyrifera silage quality. We expect that our findings will provide new insights into silage quality driven by the characteristics of the microbial community.

Phylogenetic analysis shows that Pyrenula (Pyrenulaceae) diversity is larger than expected: three new species and one new record discovered in China

The lichenised fungal genus Pyrenula is a very common crustose lichen element in tropical to subtropical forests, but little research has been done on this genus in China. We carried out an integrative taxonomic study on Pyrenula in China using morphological, anatomical, chemical characters, and molecular data (ITS, nuLSU, mtSSU). Three new species with muriform ascospores containing red oil when over-mature were found: Pyrenulasubmacularis sp. nov., P.yunguiensis sp. nov. and P.rufotetraspora sp. nov. Molecular data and TLC results of P.macularis and P.breutelii are for the first time reported and show that they are not synonyms. This is the first report of P.breutelii in China. Contrary to the previous reports of this genus, we found lichen substances in all the five species in this study, seemingly terpenoids. A key for the Pyrenula species reported in China is provided.

Upgrade from aerated static pile to agitated bed systems promotes lignocellulose degradation in large-scale composting through enhanced microbial functional diversity

Composting presents a viable management solution for lignocellulose-rich municipal solid waste. However, our understanding about the microbial metabolic mechanisms involved in the biodegradation of lignocellulose, particularly in industrial-scale composting plants, remains limited. This study employed metaproteomics to compare the impact of upgrading from aerated static pile (ASP) to agitated bed (AB) systems on physicochemical parameters, lignocellulose biodegradation, and microbial metabolic pathways during large-scale biowaste composting process, marking the first investigation of its kind. The degradation rates of lignocellulose including cellulose, hemicellulose, and lignin were significantly higher in AB (8.21%-32.54%, 10.21%-39.41%, and 6.21%-26.78%) than those (5.72%-23.15%, 7.01%-33.26%, and 4.79%-19.76%) in ASP at three thermal stages, respectively. The AB system in comparison to ASP increased the carbohydrate-active enzymes (CAZymes) abundance and production of the three essential enzymes required for lignocellulose decomposition involving a mixture of bacteria and fungi (i.e., Actinobacteria, Bacilli, Sordariomycetes and Eurotiomycetes). Conversely, ASP primarily produced exoglucanase and β-glucosidase via fungi (i.e., Ascomycota). Moreover, AB effectively mitigated microbial stress caused by acetic acid accumulation by regulating the key enzymes involved in acetate conversion, including acetyl-coenzyme A synthetase and acetate kinase. Overall, the AB upgraded from ASP facilitated the lignocellulose degradation and fostered more diverse functional microbial communities in large-scale composting. Our findings offer a valuable scientific basis to guide the engineering feasibility and environmental sustainability for large-scale industrial composting plants for treating lignocellulose-rich waste. These findings have important implications for establishing green sustainable development models (e.g., a circular economy based on material recovery) and for achieving sustainable development goals.

Development of PCR-Multiplex Assays for Identification of the Herpotrichiellaceae Family and Agents Causing Chromoblastomycosis

The Herpotrichiellaceae family is an important group of dematiaceous filamentous fungi, associated with a variety of pathogenic fungal species causing chromoblastomycosis (CBM) and phaeohyphomycosis (PHM), both with polymorphic clinical manifestations and worldwide incidence. Currently, the identification of this family and determination of the causative agent is challenging due to the subjectivity of morphological identification methods, necessitating the use of molecular techniques to complement diagnosis. In this context, genetic sequencing of the Internal Transcribed Spacer (ITS) has become the norm due to a lack of alternative molecular tools for identifying these agents. Therefore, this study aimed to develop PCR-Multiplex methodologies to address this gap. Sequences from the ITS and Large Subunit (LSU) of ribosomal DNA were used, and after manual curation and in vitro analyses, primers were synthesized for the identification of the targets. The primers were optimized and validated in vitro, resulting in two PCR-Multiplex methodologies: one for identifying the Herpotrichiellaceae family and the bantiana clade, and another for determining the species Fonsecaea pedrosoi and Fonsecaea monophora. Ultimately, the assays developed in this study aim to complement other identification approaches for these agents, reducing the need for sequencing, improving the management of these infections, and enhancing the accuracy of epidemiological information.

Three new Pyrenula species with 3-septate ascospores with red or orange oil when over-mature (Ascomycota, Pyrenulales, Pyrenulaceae) from China

The lichenised fungal genus Pyrenula is a very common crustose lichen element in tropical to subtropical forests, but little research has been done on this genus in China. During our study on Pyrenula in China, based on morphological characteristics, chemical traits and molecular phylogenetic analysis (ITS and nuLSU), three new 3-septate species with red or orange oil in over-mature ascospores were found: Pyrenulainspersasp. nov., P.thailandicoidessp. nov. and P.apiculatasp. nov. Compared to the known 3-septate species of Pyrenula with red or orange oil, P.inspersa is characterised by the inspersed hamathecium; P.thailandicoides is characterised by the IKI+ red hamathecium and the existence of an unknown lichen substance; and P.apiculata is characterised by the absence of endospore layers in the spore tips and the absence of pseudocyphellae. It is reported for the first time that the presence of a gelatinous halo around the ascospores of Pyrenula is common. A word key for the Pyrenula species with red or orange oil in over-mature ascospores is provided.

The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics

Advances in genomics and transcriptomics accompanying the rapid accumulation of omics data have provided new tools that have transformed and expanded the traditional concepts of model fungi. Evolutionary genomics and transcriptomics have flourished with the use of classical and newer fungal models that facilitate the study of diverse topics encompassing fungal biology and development. Technological advances have also created the opportunity to obtain and mine large datasets. One such continuously growing dataset is that of the Sordariomycetes, which exhibit a richness of species, ecological diversity, economic importance, and a profound research history on amenable models. Currently, 3,574 species of this class have been sequenced, comprising nearly one-third of the available ascomycete genomes. Among these genomes, multiple representatives of the model genera Fusarium, Neurospora, and Trichoderma are present. In this review, we examine recently published studies and data on the Sordariomycetes that have contributed novel insights to the field of fungal evolution via integrative analyses of the genetic, pathogenic, and other biological characteristics of the fungi. Some of these studies applied ancestral state analysis of gene expression among divergent lineages to infer regulatory network models, identify key genetic elements in fungal sexual development, and investigate the regulation of conidial germination and secondary metabolism. Such multispecies investigations address challenges in the study of fungal evolutionary genomics derived from studies that are often based on limited model genomes and that primarily focus on the aspects of biology driven by knowledge drawn from a few model species. Rapidly accumulating information and expanding capabilities for systems biological analysis of Big Data are setting the stage for the expansion of the concept of model systems from unitary taxonomic species/genera to inclusive clusters of well-studied models that can facilitate both the in-depth study of specific lineages and also investigation of trait diversity across lineages. The Sordariomycetes class, in particular, offers abundant omics data and a large and active global research community. As such, the Sordariomycetes can form a core omics clade, providing a blueprint for the expansion of our knowledge of evolution at the genomic scale in the exciting era of Big Data and artificial intelligence, and serving as a reference for the future analysis of different taxonomic levels within the fungal kingdom.

Enhancing antifungal properties of chitosan by attaching isatin-piperazine-sulfonyl-acetamide pendant groups via novel imidamide linkage

World health organization listed fungi as priority pathogens in 2022 to counter their adverse effects on human well-being. The use of antimicrobial biopolymers is a sustainable alternative to toxic antifungal agents. In this study, we explore chitosan as an antifungal agent by grafting a novel compound N-(4-((4-((isatinyl)methyl)piperazin-1-yl)sulfonyl)phenyl) acetamide (IS). The acetimidamide linkage of IS to chitosan herein was confirmed by ¹³C NMR and is a new branch in chitosan pendant group chemistry. The modified chitosan films (ISCH) were studied using thermal, tensile, and spectroscopic methods. The ISCH derivatives strongly inhibit fungal pathogens of agricultural and human importance, namely Fusarium solani, Colletotrichum gloeosporioides, Myrothecium verrucaria, Penicillium oxalicum, and Candida albicans. ISCH80 showed an IC₅₀ value of 0.85 μg/ml against M. verrucaria and ISCH100 with IC₅₀ of 1.55 μg/ml is comparable to the commercial antifungal IC₅₀ values of Triadiamenol (3.6 μg/ml) and Trifloxystrobin (3 μg/ml). Interestingly, the ISCH series remained non-toxic up to 2000 μg/ml against L929 mouse fibroblast cells. The ISCH series showed long-standing antifungal action, superior to our lowest observed antifungal IC₅₀ values of plain chitosan and IS at 12.09 μg/ml and 3.14 μg/ml, respectively. ISCH films are thus suitable for fungal inhibition in an agricultural setting or food preservation.

Core endophytic mycobiome in Ulmus minor and its relation to Dutch elm disease resistance

The core microbiota of plants exerts key effects on plant performance and resilience to stress. The aim of this study was to identify the core endophytic mycobiome in U. minor stems and disentangle associations between its composition and the resistance to Dutch elm disease (DED). We also defined its spatial variation within the tree and among distant tree populations. Stem samples were taken i) from different heights of the crown of a 168-year-old elm tree, ii) from adult elm trees growing in a common garden and representing a gradient of resistance to DED, and iii) from trees growing in two distant natural populations, one of them with varying degrees of vitality. Endophyte composition was profiled by high throughput sequencing of the first internal transcribed spacer region (ITS1) of the ribosomal DNA. Three families of yeasts (Buckleyzymaceae, Trichomeriaceae and Bulleraceae) were associated to DED-resistant hosts. A small proportion (10%) of endophytic OTUs was almost ubiquitous throughout the crown while tree colonization by most fungal taxa followed stochastic patterns. A clear distinction in endophyte composition was found between geographical locations. By combining all surveys, we found evidence of a U. minor core mycobiome, pervasive within the tree and ubiquitous across locations, genotypes and health status.

Chaenothecopsis (Mycocaliciales, Ascomycota) from exudates of endemic New Zealand Podocarpaceae

The order Mycocaliciales (Ascomycota) comprises fungal species with diverse, often highly specialized substrate ecologies. Particularly within the genus Chaenothecopsis, many species exclusively occur on fresh and solidified resins or other exudates of vascular plants. In New Zealand, the only previously known species growing on plant exudate is Chaenothecopsis schefflerae, found on several endemic angiosperms in the family Araliaceae. Here we describe three new species; Chaenothecopsis matai Rikkinen, Beimforde, Tuovila & A.R. Schmidt, C. nodosa Beimforde, Tuovila, Rikkinen & A.R. Schmidt, and C. novae-zelandiae Rikkinen, Beimforde, Tuovila & A.R. Schmidt, all growing on exudates of endemic New Zealand conifers of the Podocarpaceae family, particularly on Prumnopitys taxifolia. Phylogenetic analyses based on ribosomal DNA regions (ITS and LSU) grouped them into a distinct, monophyletic clade. This, as well as the restricted host range, suggests that all three taxa are endemic to New Zealand. Copious insect frass between the ascomata contain ascospores or show an early stage of ascomata development, indicating that the fungi are spread by insects. The three new species represent the first evidence of Chaenothecopsis from any Podocarpaceae species and the first from any gymnosperm exudates in New Zealand.

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.

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.

Neoveronaea sinensis gen. & sp. nov. from Jiangxi, China

A new hyphomycete genus and species, Neoveronaea sinensis, is described from Jiangxi Province, southern China. Neoveronaea is characterized by its macronematous conidiophores, and euseptate, obovoid to ellipsoidal, pale brown, smooth conidia. Phylogenetic analyses of partial DNA sequences of internal transcribed spacer (ITS) and nuclear ribosomal large subunit (LSU), using Maximum-Likelihood and Bayesian Inference, reveal the taxonomic placement of Neoveronaea within the Herpotrichiellaceae, in which it forms a lineage distinct from other genera.

The poly-extreme tolerant black yeasts are prevalent under high ultraviolet light and climatic seasonality across soils of global biomes

Black yeasts are among the most stress‐tolerant organisms of the planet, thriving under all types of terrestrial habitats and extreme environments. Yet, their global patterns and ecology remain far less studied, limiting our capacity to identify the main environmental drivers of these important organisms across biomes. To fill this knowledge gap, we analysed topsoils from 235 terrestrial ecosystems across and within globally distributed climate groups (i.e. dry, temperate and continental). We found that soils are important repositories of black yeasts, and that ultraviolet light, fine soil texture, and precipitation seasonality are the most consistent environmental factors associated with their diversity across biomes. Finally, we identified Exophiala and Cladophialophora as the most dominant black yeasts genera in soils across the globe. These findings provide novel evidence of global distribution of black yeasts and their key environmental predictors, giving new insights for speculating the evolution and spreading of these extreme‐tolerant organisms throughout both natural and human associated extreme environments.

Characterization of fungal aerosol in a landfill and an incineration plants in Guangzhou, Southern China: The link to potential impacts

To understand the characteristics and potential impacts of fungal aerosols in waste disposal treatments, we performed observations at a landfill and an incineration plants in Guangzhou, Southern China. Size-segregated airborne fungal concentrations were measured based on culture-dependent method, and fungal compositions in PM_2.5 were obtained using high-throughput sequencing method. Concentrations of airborne fungi varied from 376 to 9318 CFU/m³ in the landfill plant and from 53 to 8491 CFU/m³ in the incineration plant, respectively. The temporal and spatial variations of fungal aerosols indicate that waste disposal operation, garbage transport, air mixing, and meteorological factors can significantly influence the variations of airborne fungi in the outdoor environment in both plants. Among the meteorological factors, light/moderate rain could significantly increase the airborne fungal concentrations while heavy rain could decrease the concentrations due to wet scavenge. We observed that culturable fungal aerosols predominantly resided in the size range of 2.1-3.3 μm. Different fungal community structures in PM_2.5 were found between the landfill and the incineration plants, suggesting the influence of different waste sorts and treatment procedures. We further identified the pathogenic/allergenic fungal taxa (e.g., Alternaria, Epicoccum sp. and Stachybotrys sp.) in the two plants, implying the potential human health risks with long-term exposure for on-site workers and surrounding residents. The fungal genera producing microbial volatile organic compounds (MVOCs, e.g., Cladosporium, Fusarium sp., Penicillium sp. and Candida) were found in both plants. These MVOCs generation related fungal genera could contribute to the odor in the plants and, more importantly, affect the downwind area after aerosolization and transportation.

New Xerophilic Species of Penicillium from Soil

Soil is one of the main reservoirs of fungi. The aim of this study was to study the richness of ascomycetes in a set of soil samples from Mexico and Spain. Fungi were isolated after 2% w/v phenol treatment of samples. In that way, several strains of the genus Penicillium were recovered. A phylogenetic analysis based on internal transcribed spacer (ITS), beta-tubulin (BenA), calmodulin (CaM), and RNA polymerase II subunit 2 gene (rpb2) sequences showed that four of these strains had not been described before. Penicillium melanosporum produces monoverticillate conidiophores and brownish conidia covered by an ornate brown sheath. Penicillium michoacanense and Penicillium siccitolerans produce sclerotia, and their asexual morph is similar to species in the section Aspergilloides (despite all of them pertaining to section Lanata-Divaricata). P. michoacanense differs from P. siccitolerans in having thick-walled peridial cells (thin-walled in P. siccitolerans). Penicillium sexuale differs from Penicillium cryptum in the section Crypta because it does not produce an asexual morph. Its ascostromata have a peridium composed of thick-walled polygonal cells, and its ascospores are broadly lenticular with two equatorial ridges widely separated by a furrow. All four new species are xerophilic. Despite the genus Penicillium containing more than 480 known species, they are rarely reported as xerophilic.

Biodiversity and ecology of microorganisms in high pressure membrane filtration systems

High-pressure membrane filtration (reverse osmosis and nanofiltration) is used to purify different water sources, including wastewater, surface water, groundwater and seawater. A major concern in membrane filtration is the accumulation and growth of micro-organisms and their secreted polymeric substances, leading to reduced membrane performance and membrane biofouling. The fundamental understanding of membrane biofouling is limited despite years of research, as the means of microbial interactions and response to the conditions on the membrane surface are complicated. Here, we discuss studies that investigated the microbial diversity of fouled high-pressure membranes. High-throughput amplicon sequencing of the 16S rRNA gene have shown that Burkholderiales, Pseudomonadales, Rhizobiales, Sphingomonadales and Xanthomonadales frequently obtain a high relative abundance on fouled membranes. The bacterial communities present in the diverse feed water types and in pre-treatment compartments are different from the communities on the membrane, because high-pressure membrane filtration provides a selective environment for certain bacterial groups. The biofilms that form within the pre-treatment compartments do not commonly serve as an inoculum for the subsequent high-pressure membranes. Besides bacteria also fungi are detected in the water treatment compartments. In contrast to bacteria, the fungal community does not change much throughout membrane cleaning. The stable fungal diversity indicates that they are more significant in membrane biofouling than previously thought. By reviewing the biodiversity and ecology of microbes in the whole high pressure membrane filtration water chain, we have been able to identify potentials to improve biofouling control. These include modulation of hydrodynamic conditions, nutrient limitation and the combination of cleaning agents to target the entire membrane microbiome.

New insights into the systematics of Bactrodesmium and its allies and introducing new genera, species and morphological patterns in the Pleurotheciales and Savoryellales (Sordariomycetes)

The newly discovered systematic placement of Bactrodesmium abruptum, the lectotype species of the genus, prompted a re-evaluation of the traditionally broadly conceived genus Bactrodesmium. Fresh material, axenic cultures and new DNA sequence data of five gene regions of six species, i.e. B. abruptum, B. diversum, B. leptopus, B. obovatum, B. pallidum and B. spilomeum, were studied. Bactrodesmium is a strongly resolved lineage in the Savoryellales (Sordariomycetes), supported by Bayesian and Maximum Likelihood methods. The genus Bactrodesmium is emended and delimited to hyphomycetes characterised by sporodochial conidiomata, mononematous often fasciculate conidiophores, holoblastic conidiogenesis and acrogenous, solitary, dry, pigmented, transversely or rarely longitudinally septate conidia. The conidia are seceding rhexolytically, exhibiting multiple secession patterns. An identification key to 35 species accepted in Bactrodesmium is given, providing the most important diagnostic characters. Novel DNA sequence data of B. longisporum and B. stilboideum confirmed their placement in the Sclerococcales (Eurotiomycetes). For other Bactrodesmium, molecular data are available for B. cubense and B. gabretae, which position them in the Dothideomycetes and Leotiomycetes, respectively. All four species are excluded from Bactrodesmium and segregated into new genera, Aphanodesmium, Gamsomyces and Kaseifertia. Classification of 20 other species and varieties not recognised in the genus is discussed. Based on new collections of Dematiosporium aquaticum, the type species of Dematiosporium, the genus is emended to accommodate monodictys-like freshwater lignicolous fungi of the Savoryellales characterised by effuse colonies, holoblastic conidiogenous cells and dictyosporous, pigmented conidia with a pore in each cell. Study of additional new collections, cultures and DNA sequence data revealed several unknown species, which are proposed as taxonomic novelties in the Savoryellales and closely related Pleurotheciales. Ascotaiwania latericolla, Helicoascotaiwania lacustris and Pleurotheciella erumpens are described from terrestrial, lentic and lotic habitats from New Zealand and France, respectively. New combinations are proposed for Helicoascotaiwania farinosa and Neoascotaiwania fusiformis. Relationships and systematics of the Savoryellales are discussed in the light of recent phylogenies and morphological patterns newly linked with the order through cultural studies.

Arboricolonus simplex gen. et sp. nov. and novelties in Cadophora, Minutiella and Proliferodiscus from Prunus wood in Germany

During a survey on fungi associated with wood necroses of Prunus trees in Germany, strains belonging to the Leotiomycetes and Eurotiomycetes were detected by preliminary analyses of ITS sequences. Multi-locus phylogenetic analyses (LSU, ITS, TUB, EF-1α, depending on genus) of 31 of the 45 strains from Prunus and reference strains revealed several new taxa, including Arboricolonus gen. nov., a new genus in the Helotiales (Leotiomycetes) with a collophorina-like asexual morph. Seven Cadophora species (Helotiales, Leotiomycetes) were treated. The 29 strains from Prunus belonged to five species, of which C. luteo-olivacea and C. novi-eboraci were dominating; C. africana sp. nov., C. prunicola sp. nov. and C. ramosa sp. nov. were revealed as new species. The genus Cadophora was reported from Prunus for the first time. Phialophora bubakii was combined in Cadophora and differentiated from C. obscura, which was resurrected. Asexual morphs of two Proliferodiscus species (Helotiales, Leotiomycetes) were described, including one new species, Pr. ingens sp. nov. Two Minutiella species (Phaeomoniellales, Eurotiomycetes) were detected, including the new species M. pruni-avium sp. nov. Prunus avium and P. domestica are reported as host plants of Minutiella.

Distinct Microbial Community of Phyllosphere Associated with Five Tropical Plants on Yongxing Island, South China Sea

The surfaces of a leaf are unique and wide habitats for a microbial community. These microorganisms play a key role in plant growth and adaptation to adverse conditions, such as producing growth factors to promote plant growth and inhibiting pathogens to protect host plants. The composition of microbial communities very greatly amongst different plant species, yet there is little data on the composition of the microbiome of the host plants on the coral island in the South China Sea. In this study, we investigated the abundances and members of a major microbial community (fungi, bacteria, and diazotrophs) on the leaves of five dominant plant species (Ipomoea pes-caprae, Wedelia chinensis, Scaevola sericea, Cocos nucifera, and Sesuvium portulacastrum) on the island using real-time quantitative polymerase chain reaction (PCR) and high-throughput amplicon sequencing. Quantitative PCR results showed that fungi and bacteria were ubiquitous and variable among different host plants. Scaevola sericea showed the lowest absolute abundance and highest diversity of fungi and bacteria, while Cocos nucifera had the lowest abundance and the highest diversity of diazotrophs compare to the other four plants. There was a small proportion of shared microorganisms among the five different plants, while unique fungi, bacteria and diazotrophs were significantly enriched for different host plant species in this study (p < 0.05). Some of the most abundant organisms found in the communities of these different host plants are involved in important biogeochemical cycles that can benefit their host, including carbon and nitrogen cycles.

Penicillium section Lanata-divaricata from acidic soil

Penicillium species in section Lanata-divaricata are common soil-inhabiting fungi, but their presence in acidic soil has rarely been investigated. In an ongoing survey of Penicillium species occurring in China, 465 strains were isolated from soil, and of which 60 belonged to section Lanata-divaricata. The majority of these strains were isolated from acidic soil. The phylogenetic relationship between these 60 isolates and accepted species of section Lanata-divaricata was studied using ITS, BenA, CaM and RPB2 sequences, which revealed the presence of seven accepted species and 13 novel lineages. Combining phylogenetic data with data generated during macro- and microscopic observations resulted in the description of 13 new species. The growth rate of the new species obtained in this study was determined under acidic, neutral and alkaline conditions (pH 4, 7, 10). With the exception of P. hainanense, which was not able to grow at pH 10, all strains were able to grow at the three examined pH levels. Eleven species (i.e. P. austrosinense, P. flaviroseum, P. globosum, P. griseoflavum, P. hainanense, P. jianfenglingense, P. laevigatum, P. rubriannulatum, P. soliforme, P. spinuliferum, P. yunnanense) grew faster at low pH (pH 4) than at pH 7 or 10, and these species are therefore referred to as acid-preferential. Penicillium viridissimum grew fastest on neutral medium and P. guangxiense grew best at pH 10, and is therefore considered to be acid-tolerant. By isolating strains from a unique environment, combined with targeted isolation using a well-designed protocol, we are able to describe new fungal diversity with specific physiological characteristics.

PRP8 Intein in Onygenales: Distribution and Phylogenetic Aspects

Inteins (internal proteins) are mobile genetic elements, inserted in housekeeping proteins, with self-splicing properties. Some of these elements have been recently pointed out as modulators of genetic expression or protein function. Herein, we evaluated, in silico, the distribution and phylogenetic patterns of PRP8 intein among 93 fungal strains of the order Onygenales. PRP8 intein(s) are present in most of the species (45/49), mainly as full-length inteins (containing both the Splicing and the Homing Endonuclease domains), and must have transferred vertically in all lineages, since their phylogeny reflects the group phylogeny. While the distribution of PRP8 intein(s) varies among species of Onygenaceae family, being absent in Coccidioides spp. and present as full and mini-intein in other species, they are consistently observed as full-length inteins in all evaluated pathogenic species of the Arthrodermataceae and Ajellomycetaceae families. This conservative and massive PRP8 intein presence in Ajellomycetacean and Arthrodermatecean species reinforces the previous idea that such genetic elements do not decrease the fungal fitness significantly and even might play some role in the host-pathogen relationship, at least in these two fungal groups. We may better position the species Ophidiomyces ophiodiicola (with no intein) in the Onygenaceae family and Onygena corvina (with a full-length intein) as a basal member in the Arthrodermataceae family.

Exophiala dermatitidis: Key issues of an opportunistic fungal pathogen

The black yeast Exophiala dermatitidis is an opportunistic pathogen, causing phaeohyphomycosis in immunosuppressed patients, chromoblastomycosis and fatal infections of the central nervous system in otherwise healthy Asian patients. In addition, it is also regularly isolated from respiratory samples from cystic fibrosis patients, with rates varying between 1% and 19%.Melanin, as part of the cell wall of black yeasts, is one major factor known contributing to the pathogenicity of E. dermatitidis and increased resistance against host defense and anti-infective therapeutics. Further virulence factors, e.g. the capability to adhere to surfaces and to form biofilm were reported. A better understanding of the pathogenicity of E. dermatitidis is essential for the development of novel preventive and therapeutic strategies. In this review, the current knowledge of E. dermatitidis prevalence, clinical importance, diagnosis, microbiological characteristics, virulence attributes, susceptibility, and resistances as well as therapeutically strategies are discussed.

Foliar-feeding insects acquire microbiomes from the soil rather than the host plant

Microbiomes of soils and plants are linked, but how this affects microbiomes of aboveground herbivorous insects is unknown. We first generated plant-conditioned soils in field plots, then reared leaf-feeding caterpillars on dandelion grown in these soils, and then assessed whether the microbiomes of the caterpillars were attributed to the conditioned soil microbiomes or the dandelion microbiome. Microbiomes of caterpillars kept on intact plants differed from those of caterpillars fed detached leaves collected from plants growing in the same soil. Microbiomes of caterpillars reared on detached leaves were relatively simple and resembled leaf microbiomes, while those of caterpillars from intact plants were more diverse and resembled soil microbiomes. Plant-mediated changes in soil microbiomes were not reflected in the phytobiome but were detected in caterpillar microbiomes, however, only when kept on intact plants. Our results imply that insect microbiomes depend on soil microbiomes, and that effects of plants on soil microbiomes can be transmitted to aboveground insects feeding later on other plants.

Leaf-feeding insect microbiomes could be influenced by the soil, the plant, or a product of the two. Here, the authors conduct a series of experiments to show that an herbivorous insect predominantly acquires its microbiome from the soil rather than the plant, and that these insect microbiomes reflect soil legacies of earlier growing plants.

Fungal aerosols at dairy farms using molecular and culture techniques

Occupational exposure to harmful bioaerosols in industrial environments is a real threat to the workers. In particular, dairy-farm workers are exposed to high levels of fungal bioaerosols on a daily basis. Associating bioaerosol exposure and health problems is challenging and adequate exposure monitoring is a top priority for aerosol scientists. Using only culture-based tools does not express the overall microbial diversity and underestimate the large spectrum of microbes in bioaerosols and therefore the extended fungal profile that farmers are exposed to. The aim of this study was to provide an in-depth characterization of fungal exposure at Eastern Canadian dairy farms using qPCR and high-throughput sequencing methods. Specific primers were used for the quantification of Penicillium/Aspergillus and Aspergillus fumigatus in dairy farms air samples. Illumina Miseq sequencing of the ITS1 region provided sequences for the diversity analyses. The minimum and maximum concentration of Penicillium/Aspergillus ranged from 4.6 × 10⁶ to 9.4 × 10⁶ gene copies/m³ and from 1 × 10⁴ gene copies/m³ to 4.8 × 10⁵ gene copies/m³ for Aspergillus fumigatus, respectively. Differences in the diversity profiles of the five dairy farms support the idea that the novel approach identifies a large number of fungal taxa. The most striking differences include Microascus, Piptoporus, Parastagonospora, Dissoconium, Microdochium, Tubilicrinis, Ganoderma, Ustilago, Phlebia and Wickerhamomyces. The presence of a diverse portrait of fungi in air may represent a health risk for workers who are exposed on a daily basis. The broad spectrum of fungi detected in this study includes many known pathogens like Aspergillus, Acremonium, Alternaria and Fusarium. Adequate monitoring of bioaerosol exposure is necessary to evaluate and minimize risks.

Fungal bioaerosols in biomethanization facilities

Biomethanization is a new technology used for green-waste valorization where organic waste is biodegraded by microbial communities under anaerobic conditions. The main product of this type of anaerobic digestion is a biogas used as an energy source. Moving and handling organic waste may lead to the emission of high concentrations of bioaerosols. High exposure levels are associated with adverse health effects amongst green environment workers. Fungal spores are suspected to play a role in many respiratory illnesses. There is a paucity of information related to the detailed fungal diversity in biomethanization facilities. The aim of this study was to provide an in-depth description of fungal bioaerosols in biomethanization work environments using a next-generation sequencing approach combined with real-time polymerase chain reaction (PCR). Two biomethanization facilities treating different wastes were visited during the sampling campaign (n = 16). Quantification of Penicillium/Aspergillus and Aspergillus fumigatus revealed a greater exposure risk during summer for both facilities visited. Concentrations of Penicillium and Aspergillus were similar in all work areas in both biomethanization facilities. Taxonomy analyses showed that the type of waste treated affects the fungal diversity of aerosols emitted. Although eight classes were evenly distributed in all samples, Eurotiomycetes were more dominant in the first facility and Agaricomycetes were dominant in the second one. A large diversity profile was observed in bioaerosols from both facilities showing the presence of pathogenic fungi. The following fungi detected are known allergens and/or are opportunistic pathogens: Aspergillus, Malassezia, Emericella, Fusarium, Acremonium, and Candida. Daily exposure to these fungi may put workers at risk. The information from this study can be used as a reference for minimizing occupational exposure in future biomethanization facilities. Implications: Biomethanization is a new technology used for green-waste valorization where organic waste is biodegraded by microbial communities. Effective waste management is increasingly recognized as a strategic approach for achieving newly created regulations concerning the disposal of organic residues; therefore, an expansion of facilities is expected. Workers' exposure to diverse fungal communities is certain, as fungi are ubiquitous and necessary in organic matter decomposition. Monitoring this occupational exposure is important in order to prevent workers' health problems.

The evolution of fungal substrate specificity in a widespread group of crustose lichens

Lichens exhibit varying degrees of specialization with regard to the surfaces they colonize, ranging from substrate generalists to strict substrate specialists. Though long recognized, the causes and consequences of substrate specialization are poorly known. Using a phylogeny of a 150-200 Mya clade of lichen fungi, we asked whether substrate niche is phylogenetically conserved, which substrates are ancestral, whether specialists arise from generalists or vice versa and how specialization affects speciation/extinction processes. We found strong phylogenetic signal for niche conservatism. Specialists evolved into generalists and back again, but transitions from generalism to specialism were more common than the reverse. Our models suggest that for this group of fungi, 'escape' from specialization for soil, rock and bark occurred, but specialization for wood foreclosed evolution away from that substrate type. In parallel, speciation models showed positive diversification rates for soil and rock dwellers but not other specialists. Patterns in the studied group suggest that fungal substrate specificity is a key determinant of evolutionary trajectory for the entire lichen symbiosis.

RNA-based analyses reveal fungal communities structured by a senescence gradient in the moss Dicranum scoparium and the presence of putative multi-trophic fungi

Diverse plant-associated fungi are thought to have symbiotrophic and saprotrophic states because they can be isolated from both dead and living plant tissues. However, such tissues often are separated in time and space, and fungal activity at various stages of plant senescence is rarely assessed directly in fungal community studies. We used fungal ribosomal RNA metatranscriptomics to detect active fungal communities across a natural senescence gradient within wild-collected gametophytes of Dicranum scoparium (Bryophyta) to understand the distribution of active fungal communities in adjacent living, senescing and dead tissues. Ascomycota were active in all tissues across the senescence gradient. By contrast, Basidiomycota were prevalent and active in senescing and dead tissues. Several fungi were detected as active in living and dead tissues, suggesting their capacity for multi-trophy. Differences in community assembly detected by metatranscriptomics were echoed by amplicon sequencing of cDNA and compared to culture-based inferences and observation of fungal fruit bodies in the field. The combination of amplicon sequencing of cDNA and metatranscriptomics is promising for studying symbiotic systems with complex microbial diversity, allowing for the simultaneous detection of their presence and activity.

Fungal communities in ancient peatlands developed from different periods in the Sanjiang Plain, China

Peatlands in the Sanjiang Plain could be more vulnerable to global warming because they are located at the southernmost boundary of northern peatlands. Unlike bacteria, fungi are often overlooked, even though they play important roles in substance circulation in the peatland ecosystems. Accordingly, it is imperative that we deepen our understanding of fungal community structure and diversity in the peatlands. In this study, high-throughput Illumina sequencing was used to study the fungal communities in three fens in the Sanjiang Plain, located at the southern edge of northern peatlands. Peat soil was collected from the three fens which developed during different periods. A total of 463,198 fungal ITS sequences were obtained, and these sequences were classified into at least six phyla, 21 classes, more than 60 orders and over 200 genera. The fungal community structures were distinct in the three sites and were dominated by Ascomycota and Basidiomycota. However, there were no significant differences between these three fens in any α-diversity index (p > 0.05). Soil age and the carbon (C) accumulation rate, as well as total carbon (TC), total nitrogen (TN), C/N ratio, and bulk density were found to be closely related to the abundance of several dominant fungal taxa. We captured a rich fungal community and confirmed that the dominant taxa were those which were frequently detected in other northern peatlands. Soil age and the C accumulation rate were found to play important roles in shaping the fungal community structure.

A next generation sequencing approach with a suitable bioinformatics workflow to study fungal diversity in bioaerosols released from two different types of composting plants

Composting is used all over the world to transform different types of organic matter through the actions of complex microbial communities. Moving and handling composting material may lead to the emission of high concentrations of bioaerosols. High exposure levels are associated with adverse health effects among compost industry workers. Fungal spores are suspected to play a role in many respiratory illnesses. There is a paucity of information related to the detailed fungal diversity in compost as well as in the aerosols emitted through composting activities. The aim of this study was to analyze the fungal diversity of both organic matter and aerosols present in facilities that process domestic compost and facilities that process pig carcasses. This was accomplished using a next generation sequencing approach that targets the ITS1 genomic region. Multivariate analyses revealed differences in the fungal community present in samples coming from compost treating both raw materials. Furthermore, results show that the compost type affects the fungal diversity of aerosols emitted. Although 8 classes were evenly distributed in all samples, Eurotiomycetes were more dominant in carcass compost while Sordariomycetes were dominant in domestic compost. A large diversity profile was observed in bioaerosols from both compost types showing the presence of a number of pathogenic fungi newly identified in bioaerosols emitted from composting plants. Members of the family Herpotrichiellaceae and Gymnoascaceae which have been shown to cause human diseases were detected in compost and air samples. Moreover, some fungi were identified in higher proportion in air compared to compost. This is the first study to identify a high level of fungal diversity in bioaerosols present in composting plants suggesting a potential exposure risk for workers. This study suggests the need for creating guidelines that address human exposure to bioaerosols. The implementation of technical and organizational measure should be a top priority. However, skin and respiratory protection for compost workers could be used to reduce the exposure as a second resort.

Emergence and loss of spliceosomal twin introns

BACKGROUND

In the primary transcript of nuclear genes, coding sequences-exons-usually alternate with non-coding sequences-introns. In the evolution of spliceosomal intron-exon structure, extant intron positions can be abandoned and new intron positions can be occupied. Spliceosomal twin introns ("stwintrons") are unconventional intervening sequences where a standard "internal" intron interrupts a canonical splicing motif of a second, "external" intron. The availability of genome sequences of more than a thousand species of fungi provides a unique opportunity to study spliceosomal intron evolution throughout a whole kingdom by means of molecular phylogenetics.

RESULTS

A new stwintron was encountered in Aspergillus nidulans and Aspergillus niger. It is present across three classes of Leotiomyceta in the transcript of a well-conserved gene encoding a putative lipase (lipS). It occupies the same position as a standard intron in the orthologue gene in species of the early divergent classes of the Pezizomycetes and the Orbiliomycetes, suggesting that an internal intron has appeared within a pre-extant intron. On the other hand, the stwintron has been lost from certain taxa in Leotiomycetes and Eurotiomycetes at several occasions, most likely by a mechanism involving reverse transcription and homologous recombination. Another ancient stwintron present across whole Pezizomycotina orders-in the transcript of the bifunctional biotin biosynthesis gene bioDA-occurs at the same position as a standard intron in many species of non-Dikarya. Nevertheless, also the bioDA stwintron has disappeared from certain lineages within the taxa where it occurs, i.e., Sordariomycetes and Botryosphaeriales. Intriguingly, only the internal intron was lost from the Sordariomycetes bioDA stwintron at all but one occasion, leaving a standard intron in the same position, while where the putative lipase stwintron was lost, no intronic sequences remain.

CONCLUSIONS

Molecular phylogeny of the peptide product was used to monitor the existence and fate of a stwintron in the transcripts of two neatly defined fungal genes, encoding well conserved proteins. Both defining events-stwintron emergence and loss-can be explained with extant models for intron insertion and loss. We thus demonstrate that stwintrons can serve as model systems to study spliceosomal intron evolution.

Microbial Community Structure and Functions in Ethanol-Fed Sulfate Removal Bioreactors for Treatment of Mine Water

Sulfate-rich mine water must be treated before it is released into natural water bodies. We tested ethanol as substrate in bioreactors designed for biological sulfate removal from mine water containing up to 9 g L⁻¹ sulfate, using granular sludge from an industrial waste water treatment plant as inoculum. The pH, redox potential, and sulfate and sulfide concentrations were measured twice a week over a maximum of 171 days. The microbial communities in the bioreactors were characterized by qPCR and high throughput amplicon sequencing. The pH in the bioreactors fluctuated between 5.0 and 7.7 with the highest amount of up to 50% sulfate removed measured around pH 6. Dissimilatory sulfate reducing bacteria (SRB) constituted only between 1% and 15% of the bacterial communities. Predicted bacterial metagenomes indicated a high prevalence of assimilatory sulfate reduction proceeding to formation of l-cystein and acetate, assimilatory and dissimilatory nitrate reduction, denitrification, and oxidation of ethanol to acetaldehyde with further conversion to ethanolamine, but not to acetate. Despite efforts to maintain optimal conditions for biological sulfate reduction in the bioreactors, only a small part of the microorganisms were SRB. The microbial communities were highly diverse, containing bacteria, archaea, and fungi, all of which affected the overall microbial processes in the bioreactors. While it is important to monitor specific physicochemical parameters in bioreactors, molecular assessment of the microbial communities may serve as a tool to identify biological factors affecting bioreactor functions and to optimize physicochemical attributes for ideal bioreactor performance.

RNA editing of the AMD1 gene is important for ascus maturation and ascospore discharge in Fusarium graminearum

Ascospores are the primary inoculum in the wheat scab fungus Fusarium graminearum that was recently shown to have sexual stage-specific A-to-I RNA editing. One of the genes with premature-stop-codons requiring A-to-I editing to encode full-length functional proteins is AMD1 that encodes a protein with a major facilitator superfamily (MFS) domain. Here, we characterized the functions of AMD1 and its UAG to UGG editing event. The amd1 deletion mutant was normal in growth and conidiation but defective in ascospore discharge due to the premature breakdown of its ascus wall in older perithecia, which is consistent with the specific expression of AMD1 at later stages of sexual development. Expression of the wild-type or edited allele of AMD1 but not un-editable allele rescued the defects of amd1 in ascospore discharge. Furthermore, Amd1-GFP localized to the ascus membrane and Amd1 orthologs are only present in ascocarp-forming fungi that physically discharge ascospores. Interestingly, deletion of AMD1 results in the up-regulation of a number of genes related to transporter activity and membrane functions. Overall, these results indicated that Amd1 may play a critical role in maintaining ascus wall integrity during ascus maturation, and A-to-I editing of its transcripts is important for ascospore discharge in F. graminearum.

Phylogeny of saprobic microfungi from Southern Europe

During a survey of saprophytic microfungi on decomposing woody, herbaceous debris and soil from different regions in Southern Europe, a wide range of interesting species of asexual ascomycetes were found. Phylogenetic analyses based on partial gene sequences of SSU, LSU and ITS proved that most of these fungi were related to Sordariomycetes and Dothideomycetes and to lesser extent to Leotiomycetes and Eurotiomycetes. Four new monotypic orders with their respective families are proposed here, i.e. Lauriomycetales, Lauriomycetaceae; Parasympodiellales, Parasympodiellaceae; Vermiculariopsiellales, Vermiculariopsiellaceae and Xenospadicoidales, Xenospadicoidaceae. One new order and three families are introduced here to accommodate orphan taxa, viz. Kirschsteiniotheliales, Castanediellaceae, Leptodontidiaceae and Pleomonodictydaceae. Furthermore, Bloxamiaceae is validated. Based on morphology and phylogenetic affinities Diplococcium singulare, Trichocladium opacum and Spadicoides atra are moved to the new genera Paradiplococcium, Pleotrichocladium and Xenospadicoides, respectively. Helicoon fuscosporum is accommodated in the genus Magnohelicospora. Other novel genera include Neoascotaiwania with the type species N. terrestris sp. nov., and N. limnetica comb. nov. previously accommodated in Ascotaiwania; Pleomonodictys with P. descalsii sp. nov. as type species, and P. capensis comb. nov. previously accommodated in Monodictys; Anapleurothecium typified by A. botulisporum sp. nov., a fungus morphologically similar to Pleurothecium but phylogenetically distant; Fuscosclera typified by F. lignicola sp. nov., a meristematic fungus related to Leotiomycetes; Pseudodiplococcium typified by P. ibericum sp. nov. to accommodate an isolate previously identified as Diplococcium pulneyense; Xyladictyochaeta typified with X. lusitanica sp. nov., a foliicolous fungus related to Xylariales and similar to Dictyochaeta, but distinguished by polyphialidic conidiogenous cells produced on setiform conidiophores. Other novel species proposed are Brachysporiella navarrica, Catenulostroma lignicola, Cirrenalia iberica, Conioscypha pleiomorpha, Leptodontidium aureum, Pirozynskiella laurisilvatica, Parasympodiella lauri and Zanclospora iberica. To fix the application of some fungal names, lectotypes and/or epitypes are designated for Magnohelicospora iberica, Sporidesmium trigonellum, Sporidesmium opacum, Sporidesmium asperum, Camposporium aquaticum and Psilonia atra.

Biochar decreased microbial metabolic quotient and shifted community composition four years after a single incorporation in a slightly acid rice paddy from southwest China

While numerous studies both in laboratory and field have showed short term impacts of biochar on soil microbial community, there have been comparatively few reports addressing its long term impacts particular in field condition. This study investigated the changes of microbial community activity and composition in a rice paddy four years after a single incorporation of biochar at 20 and 40t/ha. The results indicated that biochar amendment after four years increased soil pH, soil organic C (SOC), total N and C/N ratio and decreased bulk density, particularly for the 40t/ha treatment compared to the control (0t/ha). Though no significant difference was observed in soil basal respiration, biochar amendment increased soil microbial biomass C and resulted in a significantly lower metabolic quotient. Besides, dehydrogenase and β-glucosidase activities were significantly decreased under biochar amendment relative to the control. The results of Illumina Miseq sequencing showed that biochar increased α-diversity of bacteria but decreased that of fungi and changed both bacterial and fungal community structures significantly. Biochar did not change the relative abundances of majority of bacteria at phylum level with the exception of a significant reduction of Actinobacteria, but significantly changed most of bacterial groups at genus level, particularly at 40t/ha. In contrast, biochar significantly decreased the relative abundances of Ascomycota and Basidiomycota by 11% and 66% and increased the relative abundances of Zygomycota by 147% at 40t/ha compared to the non-amended soil. Redundancy analysis (RDA) indicated that biochar induced changes in soil chemical properties, such as pH, SOC and C/N, were important factors driving community composition shifts. This study suggested that biochar amendment may increase microbial C use efficiency and reduce some microorganisms that are capable of decomposing more recalcitrant soil C, which may help stabilization of soil organic matter in paddy soil in long term.

More Than Just Oligomannose: An N-glycomic Comparison of Penicillium Species

N-glycosylation is an essential set of post-translational modifications of proteins; in the case of filamentous fungi, N-glycans are present on a range of secreted and cell wall proteins. In this study, we have compared the glycans released by peptide/N-glycosidase F from proteolysed cell pellets of three Penicillium species (P. dierckxii, P. nordicum and P. verrucosum that all belong to the Eurotiomycetes). Although the major structures are all within the range Hex(5-11)HexNAc(2) as shown by mass spectrometry, variations in reversed-phase chromatograms and MS/MS fragmentation patterns are indicative of differences in the actual structure. Hydrofluoric acid and mannosidase treatments revealed that the oligomannosidic glycans were not only in part modified with phosphoethanolamine residues and outer chain och1-dependent mannosylation, but that bisecting galactofuranose was present in a species-dependent manner. These data are the first to specifically show the modification of N-glycans in fungi with zwitterionic moieties. Furthermore, our results indicate that mere mass spectrometric screening is insufficient to reveal the subtly complex nature of N-glycosylation even within a single fungal genus.

Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria-rich microbiome

Many obligate symbiotic fungi are difficult to maintain in culture, and there is a growing need for alternative approaches to obtaining tissue and subsequent genomic assemblies from such species. In this study, the genome of Elaphomyces granulatus was sequenced from sporocarp tissue. The genome assembly remains on many contigs, but gene space is estimated to be mostly complete. Phylogenetic analyses revealed that the Elaphomyces lineage is most closely related to Talaromyces and Trichocomaceae s.s. The genome of E. granulatus is reduced in carbohydrate-active enzymes, despite a large expansion in genome size, both of which are consistent with what is seen in Tuber melanosporum, the other sequenced ectomycorrhizal ascomycete. A large number of transposable elements are predicted in the E. granulatus genome, especially Gypsy-like long terminal repeats, and there has also been an expansion in helicases. The metagenome is a complex community dominated by bacteria in Bradyrhizobiaceae, and there is evidence to suggest that the community may be reduced in functional capacity as estimated by KEGG pathways. Through the sequencing of sporocarp tissue, this study has provided insights into Elaphomyces phylogenetics, genomics, metagenomics and the evolution of the ectomycorrhizal association.

International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database--the quality controlled standard tool for routine identification of human and animal pathogenic fungi

Human and animal fungal pathogens are a growing threat worldwide leading to emerging infections and creating new risks for established ones. There is a growing need for a rapid and accurate identification of pathogens to enable early diagnosis and targeted antifungal therapy. Morphological and biochemical identification methods are time-consuming and require trained experts. Alternatively, molecular methods, such as DNA barcoding, a powerful and easy tool for rapid monophasic identification, offer a practical approach for species identification and less demanding in terms of taxonomical expertise. However, its wide-spread use is still limited by a lack of quality-controlled reference databases and the evolving recognition and definition of new fungal species/complexes. An international consortium of medical mycology laboratories was formed aiming to establish a quality controlled ITS database under the umbrella of the ISHAM working group on "DNA barcoding of human and animal pathogenic fungi." A new database, containing 2800 ITS sequences representing 421 fungal species, providing the medical community with a freely accessible tool at http://www.isham.org/ and http://its.mycologylab.org/ to rapidly and reliably identify most agents of mycoses, was established. The generated sequences included in the new database were used to evaluate the variation and overall utility of the ITS region for the identification of pathogenic fungi at intra-and interspecies level. The average intraspecies variation ranged from 0 to 2.25%. This highlighted selected pathogenic fungal species, such as the dermatophytes and emerging yeast, for which additional molecular methods/genetic markers are required for their reliable identification from clinical and veterinary specimens.

Production of the alkaloid swainsonine by a fungal endosymbiont of the Ascomycete order Chaetothyriales in the host Ipomoea carnea

Some plant species within the Convolvulaceae (morning glory family) from South America, Africa, and Australia cause a neurologic disease in grazing livestock caused by swainsonine. These convolvulaceous species including Ipomoea carnea contain the indolizidine alkaloid swainsonine, an inhibitor of α-mannosidase and mannosidase II, and polyhydroxy nortropane alkaloids, the calystegines which are glycosidase inhibitors. Swainsonine has been shown to be produced by a fungal endosymbiont in legumes of the Astragalus and Oxytropis genera, where it causes a similar neurologic disease in grazing livestock called locoism. Here we demonstrate that I. carnea plants are infected with a fungal endosymbiont that was cultured from its seeds and which produced swainsonine in pure culture but not the calystegines. The same fungal endosymbiont was detected by PCR and by culturing in I. carnea plants containing swainsonine. The fungal endosymbiont belongs to the Ascomycete order Chaetothyriales. Plants derived from fungicide-treated seeds lacked swainsonine, but calystegine concentrations were unaltered.