Phylogeny of the industrial relevant, thermophilic genera Myceliophthora and Corynascus

Ventilator-associated pneumonia caused by a new-found opportunistic fungal pathogen-Myceliophthora heterothallica: a case report

BACKGROUND

Myceliophthora heterothallica belonging to Myceliophthora is considered as an environmental fungus and has not been reported to be pathogenic or colonizing in recent literature. The present case firstly reports a ventilation-associated pneumonia caused by Myceliophthora heterothallica among the aged adult.

CASE PRESENTATION

A 67-years-old Asian female patient suffering from a sudden disturbance of consciousness for 3 h was admitted to our hospital. Cardiac arrest occurred during emergency transport, and sinus rhythm was restored after cardiopulmonary resuscitation. Invasive mechanical ventilation was given to this patient for respiratory failure. After mechanical ventilation, the lung CT images showed multiple cuneiform nodules arranging subpleural accompanying with ground-glass opacity. On the 5th day of mechanical ventilation, Myceliophthora heterothallica was cultured from endotracheal aspirates. Two methods, namely automatic microbial identification system and internal transcribed spacer sequencing were employed to identify this fungus. The present case firstly uncovered the colonization ability and pathogenicity of Myceliophthora heterothallica in the respiratory tract. After 28d of treatment with piperacillin-tazobactam, this patient weaned from the ventilator and recovered from consciousness with lung infection disappearance.

CONCLUSIONS

This is the first case report of ventilation-associated pneumonia in the aged patient caused by Myceliophthora heterothallica. This current case is worth for the clinical diagnosis and treatment of Myceliophthora heterothallica infection, and also enriches new pathogenic species found of thermothelomyces species.

Changes in soil organic carbon components and microbial community following spent mushroom substrate application

While spent mushroom substrate (SMS) has shown promise in increasing soil organic carbon (SOC) and improving soil quality, research on the interplay between SOC components and microbial community following the application of diverse SMS types remains scant. A laboratory soil incubation experiment was conducted with application of two types of SMSs from cultivation of Pleurotus eryngii (PE) and Agaricus bisporus (AB), each at three application rates (3, 5.5, and 8%). Advanced techniques, including solid-state 13C nuclear magnetic resonance (NMR) and high-throughput sequencing, were employed to investigate on SOC fractions and chemical structure, microbial community composition and functionality. Compared to SMS-AB, SMS-PE application increased the relative abundances of carbohydrate carbon and O-alkyl C in SOC. In addition, SMS-PE application increased the relative abundance of the bacterial phylum Proteobacteria and those of the fungal phyla Basidiomycota and Ascomycota. The relative abundances of cellulose-degrading bacterial (e.g., Flavisolibacter and Agromyces) and fungal genera (e.g., Myceliophthora, Thermomyces, and Conocybe) were increased as well. The application of SMS-AB increased the aromaticity index of SOC, the relative abundance of aromatic C, and the contents of humic acid and heavy fraction organic carbon. In addition, SMS-AB application significantly increased the relative abundances of the bacterial phyla Firmicutes and Actinobacteria. Notably, the genera Actinomadura, Ilumatobacter, and Bacillus, which were positively correlated with humic acid, experienced an increase in relative abundance. Functional prediction revealed that SMS-PE application elevated carbohydrate metabolism and reduced the prevalence of fungal pathogens, particularly Fusarium. The application of high-rate SMS-AB (8%) enhanced bacterial amino acid metabolism and the relative abundances of plant pathogenic fungi. Our research provides strategies for utilizing SMS to enrich soil organic carbon and fortify soil health, facilitating the achievement of sustainable soil management.

A new species of Dictyochaeta (Sordariomycetes, Chaetosphaeriales, Chaetosphaeriaceae) from freshwater habitats in China

Background

Freshwater fungi refer to the fungi that depend on the freshwater habitats for the whole life cycle or part of their life cycle. In this context, a new aquatic hyphomycete was isolated from decaying wood in a freshwater habitat in Jiangxi Province, China.

New information

Dictyochaetajiangxiensis sp. nov., a new aquatic hyphomycete, is characterised by its unbranched, septate, base-fertile conidiophores with multisepta and single phialide at the apex, brown, sterile seta, monophialidic, subcylindrical conidiogenous cells narrowing below the funnel-shaped collarette, hyaline, unicellular, thin-walled, smooth, guttulate, falcate to subclavate conidia narrowly rounded at both ends with hair-like appendages. Phylogenetically, the new species Dictyochaetajiangxiensis clustered together with Dictyochaetabrevis MFLU 19-0216 in a well-supported clade, but formed a separate branch. In order to better define the taxonomic status of the new species, a phylogenetic tree of most closely-related taxa in Chaetosphaeriaceae was established, based on multi-locus sequences (ITS and LSU). The novel species is described and illustrated. Newly-generated molecular data of Dictyochaetajiangxiensis is also provided.

The diversity of cultivable endophytic fungi of the sand coast plant Ipomoeapes-caprae in Taiwan

Background

Ipomoeapes-caprae is a plant of sand coasts and it can tolerate stresses, such as high salinity, strong wind and sand movements and lack of nutrients. It plays an important role in coast protection and preventing erosion. Fungal endophytes show high biodiversity and have a strong influence on the survival of plants under different stress factors. Although this plant is important for sand coast ecosystems, little is known about the associated fungi. In this study, we isolated and identified endophytic fungi of Ipomoeapes-caprae, a dominant plant along the shore of Taiwan. The dataset contains 896 records, which correspond to 177 species. The geographical scope of the dataset covers the northern subtropical area of the main island of Taiwan, with its sand coasts in New Taipei, Taoyuan, Hsinchu and Taichung and two botanical gardens in Taipei and Taichung. The detailed original data of fungal diversity are rarely publicly shared under strictly formalised and, thus, reusable standards. As an example for such an approach, the complete occurrence dataset was made available in the Darwin Core Archive format via the Global Biodiversity Information Facility (GBIF) under Version 1.13, Taiwan Biodiversity Information Facility (TaiBIF) https://doi.org/10.15468/9h9rcg. In this first data paper on endophytic fungi, the scientific name and associated DNA sequence in the dataset were directly linked to other free online resource (Index Fungorum, GenBank), which shows the potential of GBIF for linking together different online data repositories.

New information

We describe a dataset, in which the diversity of endophytic fungi of the sand coast plant Ipomoeapes-caprae in Taiwan was investigated.

Species Diversity of Cordyceps-Like Fungi in the Tiankeng Karst Region of China

Tiankeng acts as a refugium for biodiversity amid a changing global climate, and a previous study has shown that some ancient (Alsophila spinulosa) and unique plants (cool-adapted plants) are present in Tiankeng. However, there are few reports on Ascomycota from the Tiankeng karst region. In this research, the species diversity of Cordyceps-like fungi in Monkey-Ear Tiankeng was investigated. Seven species in the genera Akanthomyces, Beauveria, Cordyceps, and Samsoniella were identified based on internal transcribed spacer sequences and morphological characteristics. Eight new species in the genera Akanthomyces, Cordyceps, and Samsoniella were established and described according to a multilocus phylogenetic analysis and morphological characteristics. Our results revealed that Cordyceps-like fungi were abundant in Monkey-Ear Tiankeng, providing new insights into the diversity of Ascomycota in this special eco-environment. IMPORTANCE Karst Tiankeng has a special eco-environment and acts as a refugium for biodiversity. However, there are few reports on Ascomycota from the Tiankeng karst region. In this research, seven known species and eight new species in the genera Akanthomyces, Beauveria, Cordyceps, and Samsoniella were reported. The results showed that Cordyceps-like fungi are abundant in Monkey-Ear Tiankeng. Interestingly, the month of the sampling was November, which is not an active period of growth and reproduction for Cordyceps-like fungi. These results revealed that unconventional time sampling should not be ignored, especially for a special eco-environment, and provided new insights into the diversity of Ascomycota in this special eco-environment.

Dynamics of microbial community and enzyme activities during preparation of Agaricus bisporus compost substrate

Button mushrooms (Agaricus bisporus) are grown commercially on a specialized substrate that is usually prepared from wheat straw and poultry manure in a microbially-mediated composting process. The quality and yield of the mushroom crop depends critically on the quality of this composted substrate, but details of the microbial community responsible for compost production have only emerged recently. Here we report a detailed study of microbial succession during mushroom compost production (wetting, thermophilic, pasteurization/conditioning, spawn run). The wetting and thermophilic phases were characterized by a rapid succession of bacterial and fungal communities, with maximum diversity at the high heat stage. Pasteurization/conditioning selected for a more stable community dominated by the thermophilic actinomycete Mycothermus thermophilus and a range of bacterial taxa including Pseudoxanthomonas taiwanensis and other Proteobacteria. These taxa decreased during spawn run and may be acting as a direct source of nutrition for the proliferating Agaricus mycelium, which has previously been shown to use microbial biomass in the compost for growth. Comparison of bacterial communities at five geographically separated composting yards in south-eastern Australia revealed similarities in microbial succession during composting, although the dominant bacterial taxa varied among sites. This suggests that specific microbial taxa or combinations of taxa may provide useful biomarkers of compost quality and may be applied as predictive markers of mushroom crop yield and quality.

Phylogenetic, ecological and morphological characteristics reveal two new spider-associated genera in Clavicipitaceae

Clavicipitaceous fungi are pathogenic to scale insects, white flies and other insect orders. However, a few species are spider-associated. Two new genera from China, Neoaraneomyces and Pseudometarhizium, are described based on phylogenetic, ecological and morphological characteristics. Two spider-associated species, Neoaraneomycesaraneicola, Pseudometarhiziumaraneogenum, and an insect-associated species Pseudometarhiziumlepidopterorum are included. The morphological characteristics of paecilomyces-like conidiogenous structures, present in many insect/spiders associated species make species-level identifications difficult. A phylogenetic analysis of the combined dataset (ITS, LSU, RPB2 and TEF), placed the two new genera in Clavicipitaceae. The new spider-associated species may be the result of convergent evolution to adapt to the ecological environment and may have undergone host jumping or altered their nutritional preferences.

Phylogenetic and ecological reevaluation of the order Onygenales

The order Onygenales is classified in the class Eurotiomycetes of the subphylum Pezizomycotina. Families in this order have classically been isolated from soil and dung, and two lineages contain causative agents of superficial, cutaneous and systemic infections in mammals. The ecology and habitat choices of the species are driven mainly by the keratin and cellulose degradation abilities. The present study aimed to investigate whether the ecological trends of the members of Onygenales can be interpreted in an evolutionary sense, linking phylogenetic parameters with habitat preferences, to achieve polyphasic definitions of the main taxonomic groups. Evolutionary processes were estimated by multiple gene genealogies and divergence time analysis. Previously described families, namely, Arthrodermataceae, Ajellomycetaceae, Ascosphaeraceae, Eremascaceae, Gymnoascaceae, Onygenaceae and Spiromastigoidaceae, were accepted in Onygenales, and two new families, Malbrancheaceae and Neogymnomycetaceae, were introduced. A number of species could not be assigned to any of the defined families. Our study provides a revised overview of the main lines of taxonomy of Onygenales, supported by multilocus analyses of ITS, LSU, TUB, TEF1, TEF3, RPB1, RPB2, and ribosomal protein 60S L10 (L1) (RP60S) sequences, combined with available data on ecology, physiology, morphology, and genomics.

Cryptic Diversity of Isaria-like Species in Guizhou, China

Many Isaria-like species have recently been moved into more appropriate genera. However, more robust molecular phylogenetic analyses are still required for Isaria-like fungi to ensure accurate taxonomic identification. We analyzed these Isaria-like strains using multi-gene phylogenetics. Cryptic diversity was discovered in several Isaria farinosa strains, and two new species, Samsoniella pseudogunnii and S. pupicola, are proposed. Our results reveal that more attention needs to be paid to cryptic intraspecific diversity across different isolates and genotypes of the Isaria-like species, some of which will need to be transferred to Samsoniella. Interestingly, S. hepiali, with a very broad host distribution, has been widely used as a medicinal and edible cordycipitoid fungus.

Effects of chloropicrin fumigation combined with biochar on soil bacterial and fungal communities and Fusarium oxysporum

Chloropicrin (CP) can cause long-term damage to beneficial microbes which reduces soil health. Biochar (BC) can mitigate against the effects of CP by reducing the time for beneficial microbes to recover after CP fumigation. In this study, we used Real-Time Quantitative PCR to determine the effects of different rates of BC added to CP-fumigated soil on the speed of recovery of bacteria and fungi population and on changes to gene copy number of the target pathogen Fusarium oxysporum. And then we compared the structure and composition of the beneficial microbial community in the different treatments soil by using High throughput Illumina sequencing. As the results shown, adding 1 or 3% BC after CP fumigation accelerated the recovery of bacterial and fungal populations without increasing F. oxysporum abundance. BC also promoted the recovery of beneficial bacteria Rokubacteria and Latescibacteria damaged by CP. And these two bacteria may be related to the immunity of soil to F. oxysporum. In CP-fumigated soil, BC improved the disease resistance of the soil by increasing beneficial microbes, such as Steroidobacter, Sphingomonas, Purpureocillium and Mortierella. This combination of CP and BC is a new concept that could encourages the development of a healthy and sustainable soil ecosystems while controlling plant pathogens.

Taxonomic and phylogenetic characterizations reveal four new species of Simplicillium (Cordycipitaceae, Hypocreales) from Guizhou, China

Simplicillium species are commonly found from soil, seawater, rock surface, decayed wood, air and as symbiotic, endophytic, entomopathogenic and mycoparasitic fungi. Minority insect-associated species was reported. Simplicillium coccinellidae, S. hymenopterorum, S. neolepidopterorum and S. scarabaeoidea were introduced as the newly insect-associated species. The phylogenetic analyses of two combined datasets (LSU + RPB1 + TEF and SSU + ITS + LSU) revealed that S. coccinellidae and S. hymenopterorum were both nested in an independent clade. S. neolepidopterorum and S. scarabaeoidea have a close relationship with S. formicidae and S. lepidopterorum, respectively. S. neolepidopterorum can be easily distinguished from S. formicidae by ellipsoidal to cylindrical, solitary conidia which occasionally gather in short imbricate chains. S. scarabaeoidea could be easily distinguished from S. lepodopterorum by having longer phialides and larger conidia. Based on the morphological and phylogenetic conclusion, we determine the four newly generated isolates as new species of Simplicillium and a new combination is proposed in the genus Leptobacillium.

Multi-gene phylogenetic evidence indicates that Pleurodesmospora belongs in Cordycipitaceae (Hypocreales, Hypocreomycetidae) and Pleurodesmospora lepidopterorum sp. nov. on pupa from China

A new species, Pleurodesmospora lepidopterorum, isolated from a pupa, is introduced. Morphological comparisons and phylogenetic analyses based on multigene datasets (ITS+RPB1+RPB2+TEF) support the establishment of the new species. Pleurodesmospora lepidopterorum is distinguished from P. coccorum by its longer conidiogenous pegs located in the terminal or lateral conidiophores, and smaller subglobose or ellipsoidal conidia. A combined dataset of RPB1, RPB2, and TEF confirmed the taxonomic placement of Pleurodesmospora in Cordycipitaceae for the first time.

Safety evaluation of a β-mannanase enzyme preparation produced with Thermothelomyces thermophilus expressing a protein-engineered β-mannanase gene

Mannanase 19287 enzyme is an engineered β-mannanase that can be added to diets for animals raised for human consumption to hydrolyze β-mannans. Established toxicological analyses were conducted with the enzyme preparation to ensure the safety of this product for the intended use. The mannanase 19287 preparation was produced with Thermothelomyces thermophilus strain DSM 33149. In vitro toxicity studies presented here used dosages of the mannanase 19287 test articles up to 5000 μg/plate. For in vivo toxicity studies in Wistar rats, test articles were administered at 5.1 mg/L for inhalation toxicity and up to 15,000 mg/kg rat feed for oral toxicity, based on the Total Organic Solids (TOS) content in each test article. No treatment related adverse effects were reported in any study. The No Observed Adverse Effect Levels in the high dose group of the subchronic oral toxicity study were calculated as 1117–1298 mg TOS/kg bw/day in rats. Comparing these values to an Estimated Daily Intake for poultry demonstrated safety factors larger than 5000. Our results confirm that T. thermophilus fulfills the recognized safety criteria for the manufacture of food enzyme preparations and represent the first peer-reviewed safety evaluation of an enzyme preparation by T. thermophilus. The results of the toxicity studies presented herein attest to the safety of the mannanase 19287 enzyme for its intended use.

Morphological and phylogenetic characterisations reveal three new species of Samsoniella (Cordycipitaceae, Hypocreales) from Guizhou, China

Samsoniella species have been found on lepidopteran larvae or pupae buried in soil or leaf litter. Three new species, Samsoniella hymenopterorum, S. coleopterorum and S. lepidopterorum, parasitic on hymenopteran larvae, coleopteran larvae and lepidopteran pupae, respectively, are reported. Morphological comparisons with extant species and DNA-based phylogenies from analysis of a multigene (ITS, RPB1, RPB2 and TEF) dataset supported the establishment of the new species. Unusually, all three new species have mononematous conidiophores. The new species are clearly distinct from other species in Samsoniella occurring in separate subclades.

Diketopiperazines from Batnamyces globulariicola, gen. & sp. nov. (Chaetomiaceae), a fungus associated with roots of the medicinal plant Globularia alypum in Algeria

Eight diketopiperazines including five previously unreported derivatives were isolated from an endophytic fungus cultured from the medicinal plant Globularia alypum collected in Algeria. The strain was characterised by means of morphological studies and molecular phylogenetic methods and was found to represent a species of a new genus in the Chaetomiaceae, for which we propose the name Batnamyces globulariicola. The taxonomic position of the new genus, which appears phylogenetically related to Stolonocarpus and Madurella, was evaluated by a multi-locus genealogy and by morphological studies in comparison to DNA sequence data reported in the recent monographs of the family. The culture remained sterile on several culture media despite repeated attempts to induce sporulation, and only some chlamydospores were formed. After fermentation in submerged culture and extraction of the cultures with organic solvents, the major secondary metabolites of B. globulariicola were isolated and their chemical structures were elucidated by extensive spectral analysis including nuclear magnetic resonance (NMR) spectroscopy, high-resolution electrospray ionisation mass spectrometry (HRESIMS), and electronic circular dichroism (ECD) measurements. The isolated compounds were tested for their biological activities against various bacteria, fungi, and two mammalian cell lines, but only three of them exhibited weak cytotoxicity against KB3.1 cells, but no antimicrobial effects were observed.

Development of genetic tools for the thermophilic filamentous fungus Thermoascus aurantiacus

BACKGROUND

Fungal enzymes are vital for industrial biotechnology, including the conversion of plant biomass to biofuels and bio-based chemicals. In recent years, there is increasing interest in using enzymes from thermophilic fungi, which often have higher reaction rates and thermal tolerance compared to currently used fungal enzymes. The thermophilic filamentous fungus Thermoascus aurantiacus produces large amounts of highly thermostable plant cell wall-degrading enzymes. However, no genetic tools have yet been developed for this fungus, which prevents strain engineering efforts. The goal of this study was to develop strain engineering tools such as a transformation system, a CRISPR/Cas9 gene editing system and a sexual crossing protocol to improve the enzyme production.

RESULTS

Here, we report Agrobacterium tumefaciens-mediated transformation (ATMT) of T. aurantiacus using the hph marker gene, conferring resistance to hygromycin B. The newly developed transformation protocol was optimized and used to integrate an expression cassette of the transcriptional xylanase regulator xlnR, which led to up to 500% increased xylanase activity. Furthermore, a CRISPR/Cas9 gene editing system was established in this fungus, and two different gRNAs were tested to delete the pyrG orthologue with 10% and 35% deletion efficiency, respectively. Lastly, a sexual crossing protocol was established using a hygromycin B- and a 5-fluoroorotic acid-resistant parent strain. Crossing and isolation of progeny on selective media were completed in a week.

CONCLUSION

The genetic tools developed for T. aurantiacus can now be used individually or in combination to further improve thermostable enzyme production by this fungus.

She Loves Me, She Loves Me Not: On the Dualistic Asexual/Sexual Nature of Dermatophyte Fungi

Dermatophytes are ascomycetous fungi whose sexuality is greatly influenced by their ecology. Sexual reproduction is ubiquitous among soil-related geophiles and some animal-associated zoophiles. In contrast, anthropophiles are generally present as a single mating type in the population and appear to reproduce asexually. In this article, the current knowledge on the sexuality of dermatophytes including reproduction modes, mating conditions, mating type distributions and the mating type (MAT) locus is presented in the context of revised taxonomy and discussed from an evolutionary perspective.

Three novel insect-associated species of Simplicillium (Cordycipitaceae, Hypocreales) from Southwest China

In this paper, we introduce three new species of Simplicillium, viz. S. cicadellidae, S. formicidae and S. lepidopterorum, which were isolated from an infected leafhopper, ant and carpenterworm, respectively. Morphological comparisons and phylogenetic analyses based on multigene datasets (LSU+RPB1+RPB2+TEF and ITS+LSU) support the establishment of the three new species. Simplicillium cicadellidae was distinguished from other species in morphological characteristics by having smaller phialides and ellipsoidal conidia, and lacking octahedral crystals. The reverse of colonies were yellowish (#FFBF00), especially in the middle, and radially sulcate. Simplicillium formicidae was morphologically distinguished from other by having longer phialides and filiform to fusoid conidia, and by lacking octahedral crystals. Simplicillium lepidopterorum was morphologically distinguished from other species by having smaller, ellipsoidal to fusiform conidia, and by lacking octahedral crystals. The reverse of the colony was pale white. The three new species are likely to be nourished by plant to animal (especially insect) nutrients based on the evolutionary pattern of the Hypocreales, and they are described herein as being clearly distinct from other species in Simplicillium.

Phylogenetic re-evaluation of Thielavia with the introduction of a new family Podosporaceae

The genus Thielavia is morphologically defined by having non-ostiolate ascomata with a thin peridium composed of textura epidermoidea, and smooth, single-celled, pigmented ascospores with one germ pore. Thielavia is typified with Th. basicola that grows in close association with a hyphomycete which was traditionally identified as Thielaviopsis basicola. Besides Th. basicola exhibiting the mycoparasitic nature, the majority of the described Thielavia species are from soil, and some have economic and ecological importance. Unfortunately, no living type material of Th. basicola exists, hindering a proper understanding of the classification of Thielavia. Therefore, Thielavia basicola was neotypified by material of a mycoparasite presenting the same ecology and morphology as described in the original description. We subsequently performed a multi-gene phylogenetic analyses (rpb2, tub2, ITS and LSU) to resolve the phylogenetic relationships of the species currently recognised in Thielavia. Our results demonstrate that Thielavia is highly polyphyletic, being related to three family-level lineages in two orders. The redefined genus Thielavia is restricted to its type species, Th. basicola, which belongs to the Ceratostomataceae (Melanosporales) and its host is demonstrated to be Berkeleyomyces rouxiae, one of the two species in the "Thielaviopsis basicola" species complex. The new family Podosporaceae is sister to the Chaetomiaceae in the Sordariales and accommodates the re-defined genera Podospora, Trangularia and Cladorrhinum, with the last genus including two former Thielavia species (Th. hyalocarpa and Th. intermedia). This family also includes the genetic model species Podospora anserina, which was combined in Triangularia (as Triangularia anserina). The remaining Thielavia species fall in ten unrelated clades in the Chaetomiaceae, leading to the proposal of nine new genera (Carteria, Chrysanthotrichum, Condenascus, Hyalosphaerella, Microthielavia, Parathielavia, Pseudothielavia, Stolonocarpus and Thermothielavioides). The genus Canariomyces is transferred from Microascaceae (Microascales) to Chaetomiaceae based on its type species Can. notabilis. Canariomyces is closely related to the human-pathogenic genus Madurella, and includes three thielavia-like species and one novel species. Three monotypic genera with a chaetomium-like morph (Brachychaeta, Chrysocorona and Floropilus) are introduced to better resolve the Chaetomiaceae and the thielavia-like species in the family. Chrysocorona lucknowensis and Brachychaeta variospora are closely related to Acrophialophora and three newly introduced genera containing thielavia-like species; Floropilus chiversii is closely related to the industrially important and thermophilic species Thermothielavioides terrestris (syn. Th. terrestris). This study shows that the thielavia-like morph is a homoplastic form that originates from several separate evolutionary events. Furthermore, our results provide new insights into the taxonomy of Sordariales and the polyphyletic Lasiosphaeriaceae.

Diversity of Onygenalean Fungi in Keratin-Rich Habitats of Maharashtra (India) and Description of Three Novel Taxa

Extensive survey was carried out in the state of Maharashtra, India, as part of a 3-year project to explore keratinophilic fungal diversity for conservation and biotechnological potential. A total of 578 soil samples were collected from keratin-rich habitats across 24 districts of Maharashtra State. Hair-baiting technique and micro-dilution drop-trail method were employed for isolation and purification of keratinophilic fungi from soil. A total of 66 species belonging to 17 genera of order Onygenales were recorded in hair baits. Eleven taxa were found to be new to science, most of which were rare as they were recorded in only one sample out of the > 500 samples analyzed. Three novel taxa have been characterized at morphological and molecular level and described here as new to science. These taxa include Currahmyces indicus gen. et sp. nov., Canomyces reticulatus gen. et sp. nov., Ctenomyces indicus sp. nov. All these novel taxa are morphologically and phylogenetically distinct from known taxa of order Onygenales. The study indicates that systematic sampling of a larger area is needed to uncover the hidden (unknown) diversity of keratinophilic fungi which is overlooked in sporadic samplings as evident from previous studies.

Characterization and Dye Decolorization Potential of Two Laccases from the Marine-Derived Fungus Pestalotiopsis sp

Two laccase-encoding genes from the marine-derived fungus Pestalotiopsis sp. have been cloned in Aspergillus niger for heterologous production, and the recombinant enzymes have been characterized to study their physicochemical properties, their ability to decolorize textile dyes for potential biotechnological applications, and their activity in the presence of sea salt. The optimal pH and temperature of PsLac1 and PsLac2 differed in relation to the substrates tested, and both enzymes were shown to be extremely stable at temperatures up to 50 °C, retaining 100% activity after 3 h at 50 °C. Both enzymes were stable between pH 4–6. Different substrate specificities were exhibited, and the lowest K_m and highest catalytic efficiency values were obtained against syringaldazine and 2,6-dimethoxyphenol (DMP) for PsLac1 and PsLac2, respectively. The industrially important dyes—Acid Yellow, Bromo Cresol Purple, Nitrosulfonazo III, and Reactive Black 5—were more efficiently decolorized by PsLac1 in the presence of the redox mediator 1-hydroxybenzotriazole (HBT). Activities were compared in saline conditions, and PsLac2 seemed more adapted to the presence of sea salt than PsLac1. The overall surface charges of the predicted PsLac three-dimensional models showed large negatively charged surfaces for PsLac2, as found in proteins for marine organisms, and more balanced solvent exposed charges for PsLac1, as seen in proteins from terrestrial organisms.

Surveying of acid-tolerant thermophilic lignocellulolytic fungi in Vietnam reveals surprisingly high genetic diversity

Thermophilic fungi can represent a rich source of industrially relevant enzymes. Here, 105 fungal strains capable of growing at 50 °C and pH 2.0 were isolated from compost and decaying plant matter. Maximum growth temperatures of the strains were in the range 50 °C to 60 °C. Sequencing of the internal transcribed spacer (ITS) regions indicated that 78 fungi belonged to 12 species of Ascomycota and 3 species of Zygomycota, while no fungus of Basidiomycota was detected. The remaining 27 strains could not be reliably assigned to any known species. Phylogenetically, they belonged to the genus Thielavia, but they represented 23 highly divergent genetic groups different from each other and from the closest known species by 12 to 152 nucleotides in the ITS region. Fungal secretomes of all 105 strains produced during growth on untreated rice straw were studied for lignocellulolytic activity at different pH and temperatures. The endoglucanase and xylanase activities differed substantially between the different species and strains, but in general, the enzymes produced by the novel Thielavia spp. strains exhibited both higher thermal stability and tolerance to acidic conditions. The study highlights the vast potential of an untapped diversity of thermophilic fungi in the tropics.

Phylogeny and taxonomy of three new Ctenomyces (Arthrodermataceae, Onygenales) species from China

Twelve Ctenomyces (Arthrodermataceae, Onygenales) strains were obtained and identified during a survey of keratinophilic fungi in soils from China. We used molecular identification combined with morphological evidence to delimit species, circumscribing five species in the genus. Three new species are herein described: C.albus sp. nov., C.obovatus sp. nov. and C.peltricolor sp. nov. We also described, illustrated and compared the novel species with related species in the morphology.

Lecanicilliumcauligalbarum sp. nov. (Cordycipitaceae, Hypocreales), a novel fungus isolated from a stemborer in the Yao Ren National Forest Mountain Park, Guizhou

A new species of entomopathogenic fungi, Lecanicilliumcauligalbarum, was discovered from a survey of invertebrate-associated fungi in the Yao Ren National Forest Mountain Park in China. The synnemata of this species emerged from the corpse of a stemborer (Lepidoptera), which was hidden amongst pieces of wood on the forest floor. It differs from morphologically similar Lecanicillium species mainly in its short conidiogenous cells and ellipsoid to ovoid and aseptate conidia. Phylogenetic analysis of a combined data set comprising ITS, SSU, LSU, TEF, RPB1 and RPB2 sequence data supported the inclusion of L.cauligalbarum in the Lecanicillium genus and its recognition as a distinct species.

The Genome of a Thermo Tolerant, Pathogenic Albino Aspergillus fumigatus

Biotechnologists are interested in thermo tolerant fungi to manufacture enzymes active and stable at high temperatures, because they provide improved catalytic efficiency, strengthen enzyme substrate interactions, accelerate substrate enzyme conversion rates, enhance mass transfer, lower substrate viscosity, lessen contamination risk and offer the potential for enzyme recycling. Members of the genus Aspergillus live a wide variety of lifestyles, some embrace GRAS status routinely employed in food processing while others such as Aspergillus fumigatus are human pathogens. A. fumigatus produces melanins, pyomelanin protects the fungus against reactive oxygen species and DHN melanin produced by the pksP gene cluster confers the gray-greenish color. pksP mutants are attenuated in virulence. Here we report on the genomic DNA sequence of a thermo tolerant albino Aspergillus isolated from rain forest composted floors. Unexpectedly, the nucleotide sequence was 95.7% identical to the reported by Aspergillus fumigatus Af293. Genome size and predicted gene models were also highly similar, however differences in DNA content and conservation were observed. The albino strain, classified as Aspergillus fumigatus var. niveus, had 160 gene models not present in A. fumigatus Af293 and A. fumigatus Af293 had 647 not found in the albino strain. Furthermore, the major pigment generating gene cluster pksP appeared to have undergone genomic rearrangements and a key tyrosinase present in many aspergilli was missing from the genome. Remarkably however, despite the lack of pigmentation A. fumigatus var. niveus killed neutropenic mice and survived macrophage engulfment at similar rates as A. fumigatus Af293.

Management of enzyme diversity in high-performance cellulolytic cocktails

BACKGROUND

Modern biorefineries require enzymatic cocktails of improved efficiency to generate fermentable sugars from lignocellulosic biomass. Cellulolytic fungi, among other microorganisms, have demonstrated the highest potential in terms of enzymatic productivity, complexity and efficiency. On the other hand, under cellulolytic-inducing conditions, they often produce a considerable diversity of carbohydrate-active enzymes which allow them to adapt to changing environmental conditions. However, industrial conditions are fixed and adjusted to the optimum of the whole cocktail, resulting in underperformance of individual enzymes.

RESULTS

One of these cellulolytic cocktails from Myceliophthora thermophila has been analyzed here by means of LC-MS/MS. Pure GH6 family members detected have been characterized, confirming previous studies, and added to whole cocktails to compare their contribution in the hydrolysis of industrial substrates. Finally, independent deletions of two GH6 family members, as an example of the enzymatic diversity management, led to the development of a strain producing a more efficient cellulolytic cocktail.

CONCLUSIONS

These data indicate that the deletion of noncontributive cellulases (here EG VI) can increase the cellulolytic efficiency of the cocktail, validating the management of cellulase diversity as a strategy to obtain improved fungal cellulolytic cocktails.

Development of a genome-editing CRISPR/Cas9 system in thermophilic fungal Myceliophthora species and its application to hyper-cellulase production strain engineering

BACKGROUND

Over the past 3 years, the CRISPR/Cas9 system has revolutionized the field of genome engineering. However, its application has not yet been validated in thermophilic fungi. Myceliophthora thermophila, an important thermophilic biomass-degrading fungus, has attracted industrial interest for the production of efficient thermostable enzymes. Genetic manipulation of Myceliophthora is crucial for metabolic engineering and to unravel the mechanism of lignocellulose deconstruction. The lack of a powerful, versatile genome-editing tool has impeded the broader exploitation of M. thermophila in biotechnology.

RESULTS

In this study, a CRISPR/Cas9 system for efficient multiplexed genome engineering was successfully developed in the thermophilic species M. thermophila and M. heterothallica. This CRISPR/Cas9 system could efficiently mutate the imported amdS gene in the genome via NHEJ-mediated events. As a proof of principle, the genes of the cellulase production pathway, including cre-1, res-1, gh1-1, and alp-1, were chosen as editing targets. Simultaneous multigene disruptions of up to four of these different loci were accomplished with neomycin selection marker integration via a single transformation using the CRISPR/Cas9 system. Using this genome-engineering tool, multiple strains exhibiting pronounced hyper-cellulase production were generated, in which the extracellular secreted protein and lignocellulase activities were significantly increased (up to 5- and 13-fold, respectively) compared with the parental strain.

CONCLUSIONS

A genome-wide engineering system for thermophilic fungi was established based on CRISPR/Cas9. Successful expansion of this system without modification to M. heterothallica indicates it has wide adaptability and flexibility for use in other Myceliophthora species. This system could greatly accelerate strain engineering of thermophilic fungi for production of industrial enzymes, such as cellulases as shown in this study and possibly bio-based fuels and chemicals in the future.

Genetics of mating in members of the Chaetomiaceae as revealed by experimental and genomic characterization of reproduction in Myceliophthora heterothallica

Members of the Chaetomiaceae are among the most studied fungi in industry and among the most reported in investigations of biomass degradation in both natural and laboratory settings. The family is recognized for production of carbohydrate-active enzymes and antibiotics. Thermophilic species are of special interest for their abilities to produce thermally stable enzymes and to be grown under conditions that are unsuitable for potential contaminant microorganisms. Such interests led to the recent acquisition of genome sequences from several members of the family, including thermophilic species, several of which are reported here for the first time. To date, however, thermophilic fungi in industry have served primarily as parts reservoirs and there has been no good genetic model for species in the family Chaetomiaceae or for thermophiles in general. We report here on the reproductive biology of the thermophile Myceliophthora heterothallica, which is heterothallic, unlike most described species in the family. We confirmed heterothallism genetically by following the segregation of mating type idiomorphs and other markers. We have expanded the number of known sexually-compatible individuals from the original isolates from Indiana and Germany to include several isolates from New Mexico. An interesting aspect of development in M. heterothallica is that ascocarp formation is optimal at approximately 30 °C, whereas vegetative growth is optimal at 45 °C. Genome sequences obtained from several strains, including isolates of each mating type, revealed mating-type regions whose genes are organized similarly to those of other members of the Sordariales, except for the presence of a truncated version of the mat A-1 (MAT1-1-1) gene in mating-type a (MAT1-2) strains. In M. heterothallica and other Chaetomiaceae, mating-type A (MAT1-1) strains have the full-length version of mat A-1 that is typical of mating-type A strains of diverse Ascomycota, whereas a strains have only the truncated version. This truncated mat A-1 has an intact open reading frame and a derived start codon that is not present in mat A-1 from A strains. The predicted protein contains a region that is conserved across diverse mat A-1 genes, but it lacks the major alpha1 domain, which characterizes proteins in this family and is known to be required for fertility in A strains from other Ascomycota. Finally, we have used genes from M. heterothallica to probe for mating genes in other homothallic and heterothallic members of the Chaetomiaceae. The majority of homothallic species examined have a typical mat A-1,2,3 (MAT1-1-1,2,3) region in addition to an unlinked mat a-1 (MAT1-2-1) gene, reflecting one type of homothallism commonly observed in diverse Ascomycota.

Thermophilic growth and enzymatic thermostability are polyphyletic traits within Chaetomiaceae

Thermophilic fungi have the potential to produce industrial-relevant thermostable enzymes, in particular for the degradation of plant biomass. Sordariales is one of the few fungal orders containing several thermophilic taxa, of which many have been associated with the production of thermostable enzymes. The evolutionary affiliation of Sordariales fungi, especially between thermophiles and non-thermophilic relatives, is however poorly understood. Phylogenetic analysis within the current study was based on sequence data, derived from a traditional Sanger and highly multiplexed targeted next generation sequencing approach of 45 isolates. The inferred phylogeny and detailed growth analysis rendered the trait 'thermophily' as polyphyletic within Chaetomiaceae (Sordariales, Sordariomycetes), and characteristic to: Myceliophthora spp., Thielavia terrestris, Chaetomium thermophilum, and Mycothermus thermophilus. Compared to mesophiles, the isolates within thermophilic taxa produced enzyme mixtures with the highest thermostability of known cellulase activities. Temperature profiles of the enzyme activities correlated strongly with the optimal growth temperatures of the isolates but not with their phylogenetic relationships. This strong correlation between growth and enzyme characteristics indicated that detailed analysis of growth does give predictive information on enzyme physiology. The variation in growth and enzyme characteristics reveals these fungi as an excellent platform to better understand fungal thermophily and enzyme thermostability.

Thermophilic fungi in the new age of fungal taxonomy

Thermophilic fungi are of wide interest due to their potential to produce heat-tolerant enzymes for biotechnological processes. However, the taxonomy of such organisms remains obscure, especially given new developments in the nomenclature of fungi. Here, we examine the taxonomy of the thermophilic fungi most commonly used in industry in light of the recent taxonomic changes following the adoption of the International Code of Nomenclature for Algae, Fungi and Plants and also based on the movement One Fungus = One Name. Despite the widespread use of these fungi in applied research, several thermotolerant fungi still remain classified as thermophiles. Furthermore, we found that while some thermophilic fungi have had their genomes sequenced, many taxa still do not have barcode sequences of reference strains available in public databases. This lack of basic information is a limiting factor for the species identification of thermophilic fungi and for metagenomic studies in this field. Based on next-generation sequencing, such studies generate large amounts of data, which may reveal new species of thermophilic fungi in different substrates (composting systems, geothermal areas, piles of plant material). As discussed in this study, there are intrinsic problems associated with this method, considering the actual state of the taxonomy of thermophilic fungi. To overcome such difficulties, the taxonomic classification of this group should move towards standardizing the commonly used species names in industry and to assess the possibility of including new systems for describing species based on environmental sequences.

Efficient plant biomass degradation by thermophilic fungus Myceliophthora heterothallica

Rapid and efficient enzymatic degradation of plant biomass into fermentable sugars is a major challenge for the sustainable production of biochemicals and biofuels. Enzymes that are more thermostable (up to 70°C) use shorter reaction times for the complete saccharification of plant polysaccharides compared to hydrolytic enzymes of mesophilic fungi such as Trichoderma and Aspergillus species. The genus Myceliophthora contains four thermophilic fungi producing industrially relevant thermostable enzymes. Within this genus, isolates belonging to M. heterothallica were recently separated from the well-described species M. thermophila. We evaluate here the potential of M. heterothallica isolates to produce efficient enzyme mixtures for biomass degradation. Compared to the other thermophilic Myceliophthora species, isolates belonging to M. heterothallica and M. thermophila grew faster on pretreated spruce, wheat straw, and giant reed. According to their protein profiles and in vitro assays after growth on wheat straw, (hemi-)cellulolytic activities differed strongly between M. thermophila and M. heterothallica isolates. Compared to M. thermophila, M. heterothallica isolates were better in releasing sugars from mildly pretreated wheat straw (with 5% HCl) with a high content of xylan. The high levels of residual xylobiose revealed that enzyme mixtures of Myceliophthora species lack sufficient β-xylosidase activity. Sexual crossing of two M. heterothallica showed that progenies had a large genetic and physiological diversity. In the future, this will allow further improvement of the plant biomass-degrading enzyme mixtures of M. heterothallica.