European species of Hypocrea Part I. The green-spored species

Synergistic effect of cellulo-xylanolytic and laccase enzyme consortia for improved deinking of waste papers

This study reports the cellulo-xylanolytic cocktail production from Hypocrea lixii GGRK4 using multi-objective genetic algorithm-artificial neural network tool, resulting in 8.32 ± 1.07 IU/mL, 51.53 ± 3.78 IU/mL activity of CMCase and xylanase, respectively with more than 85 % residual activity at 60 °C and pH 6.0. Interestingly, metal ions viz. K+ and Ca2+ stimulated the enzyme activity, whereas Fe2+ and Cu2+ reduced the activity. Significant amounts of hydrophobic compounds, chromophores, and phenolics were released after wastepapers deinking. The deinking efficiency of 73.60 ± 2.45 % and 38.60 ± 1.34 % was obtained for photocopier paper and newspaper, respectively, whereas brightness of 89.90 ± 2.10 % ISO and 44.90 ± 1.63 % ISO was reported for both types of waste papers. The physical strength of deinked photocopier paper and newspapers, i.e., tensile index (3.10 and 0.50 %), tearing index (7.10 and 4.83 %), and burst factor (8.61) were enhanced whereas double fold property was decreased proving wastepaper reusability. This consortium showed effective and significant enzymatic deinking efficiency for recycled wastepapers.

Sclerotia degradation by Trichoderma-mycoparasitic; an effective and sustainable trend in the drop lettuce disease control caused by Sclerotinia sclerotiorum

Controlling the hazard of sclerotia produced by the Sclerotinia sclerotiorum is very complex, and it is urgent to adopt an effective method that is harmonious environmentally to control the disease. Among the six isolates isolated from the rhizosphere of lettuce, the isolate HZA84 demonstrated a high activity in its antagonism towards Sclerotinia sclerotiorum in vitro, and produces siderophore. By amplification of internal transcribed spacer (ITS), translation elongation factor 1-alpha (TEF1-α), and RNA polymerase II subunit (RPB2) genes, the isolate HZA84 was identified as Trichoderma asperellum, which was confirmed by analysis of phylogenetic tree. The Scanning electron microscope monitoring detected that the isolate HZA84 spread over the sclerotial surface, thus, damaging, decomposing, and distorting the globular cells of the outer cortex of the sclerotia. The Real-time polymerase chain reaction (RT-qPCR) analysis disclosed the overexpression of two genes (chit33 and chit37) encoding the endochitinase in addition to one gene (prb1) encoding the proteinase during 4 and 8 days of the parasitism behavior of isolate HZA84 on the sclerotia surface. These enzymes aligned together in the sclerotia destruction by hyperparasitism. On the other hand, the pots trial revealed that spraying of isolate HZA84 reduced the drop disease symptoms of lettuce. The disease severity was decreased by 19.33 and the biocontrol efficiency was increased by 80.67% within the fourth week of inoculation. These findings magnify the unique role of Trichoderma in disrupting the development of plant diseases in sustainable ways.

Genetic diversity and antagonistic properties of Trichoderma strains from the crop rhizospheres in southern Rajasthan, India

There are fewer studies on Trichoderma diversity in agricultural fields. The rhizosphere of 16 crops was analyzed for Trichoderma species in 7 districts of Rajasthan state of India. Based on DNA sequence of translation elongation factor 1α (tef-1α), and morphological characteristics, 60 isolates were identified as 11 species: Trichoderma brevicompactum, species in Harzianum clade identified as T. afroharzianum, T. inhamatum, T. lentiforme, T. camerunense, T. asperellum, T. asperelloides, T. erinaceum, T. atroviride, T. ghanense, and T. longibrachiatum. T. brevicompactum is the most commonly occurring strain followed by T. afroharzianum. No new species were described in this study. T. lentiforme, showed its first occurrence outside the South American continent. The morphological and cultural characteristics of the major species were observed, described, and illustrated in detail. The isolates were tested for their antagonistic effect against three soilborne plant pathogens fungi: Sclerotium rolfsii, Rhizoctonia solani, and Fusarium verticillioides in plate culture assays. One of the most potent strains was T. afroharzianum BThr29 having a maximum in vitro inhibition of S. rolfsii (76.6%), R. solani (84.8%), and F. verticillioides (85.7%). The potential strain T. afroharzianum BThr29 was also found to be efficient antagonists against soil borne pathogens in in vivo experiment. Such information on crop selectivity, antagonistic properties, and geographic distribution of Trichoderma species will be beneficial for developing efficient Trichoderma-based biocontrol agents.

Endophyte genomes support greater metabolic gene cluster diversity compared with non-endophytes in Trichoderma

Trichoderma is a cosmopolitan genus with diverse lifestyles and nutritional modes, including mycotrophy, saprophytism, and endophytism. Previous research has reported greater metabolic gene repertoires in endophytic fungal species compared to closely-related non-endophytes. However, the extent of this ecological trend and its underlying mechanisms are unclear. Some endophytic fungi may also be mycotrophs and have one or more mycoparasitism mechanisms. Mycotrophic endophytes are prominent in certain genera like Trichoderma, therefore, the mechanisms that enable these fungi to colonize both living plants and fungi may be the result of expanded metabolic gene repertoires. Our objective was to determine what, if any, genomic features are overrepresented in endophytic fungi genomes in order to undercover the genomic underpinning of the fungal endophytic lifestyle. Here we compared metabolic gene cluster and mycoparasitism gene diversity across a dataset of thirty-eight Trichoderma genomes representing the full breadth of environmental Trichoderma's diverse lifestyles and nutritional modes. We generated four new Trichoderma endophyticum genomes to improve the sampling of endophytic isolates from this genus. As predicted, endophytic Trichoderma genomes contained, on average, more total biosynthetic and degradative gene clusters than non-endophytic isolates, suggesting that the ability to create/modify a diversity of metabolites potential is beneficial or necessary to the endophytic fungi. Still, once the phylogenetic signal was taken in consideration, no particular class of metabolic gene cluster was independently associated with the Trichoderma endophytic lifestyle. Several mycoparasitism genes, but no chitinase genes, were associated with endophytic Trichoderma genomes. Most genomic differences between Trichoderma lifestyles and nutritional modes are difficult to disentangle from phylogenetic divergences among species, suggesting that Trichoderma genomes maybe particularly well-equipped for lifestyle plasticity. We also consider the role of endophytism in diversifying secondary metabolism after identifying the horizontal transfer of the ergot alkaloid gene cluster to Trichoderma.

Taxonomy and systematics of the fungus-growing ant associate Escovopsis (Hypocreaceae)

Escovopsis is a symbiont of fungus-growing ant colonies. Unstandardised taxonomy prevented the evaluation of the morphological diversity of Escovopsis for more than a century. The aim of this study is to create a standardised taxonomic framework to assess the morphological and phylogenetic diversity of Escovopsis. Therefore, to set the foundation for Escovopsis taxonomy and allow interspecific comparisons within the genus, we redescribe the ex-type cultures of Escovopsis aspergilloides, E. clavata, E. lentecrescens, E. microspora, E. moelleri, E. multiformis, and E. weberi. Thus, based on the parameters adopted in this study combined with phylogenetic analyses using five molecular markers, we synonymize E. microspora with E. weberi, and introduce 13 new species isolated from attine nests collected in Argentina, Brazil, Costa Rica, Mexico, and Panama: E. breviramosa, E. chlamydosporosa, E. diminuta, E. elongatistipitata, E. gracilis, E. maculosa, E. papillata, E. peniculiformis, E. phialicopiosa, E. pseudocylindrica, E. rectangula, E. rosisimilis, and E. spicaticlavata. Our results revealed a great interspecific morphological diversity throughout Escovopsis. Notwithstanding, colony growth rates at different temperatures, as well as vesicle shape, appear to be the most outstanding features distinguishing species in the genus. This study fills an important gap in the systematics of Escovopsis that will allow future researchers to unravel the genetic and morphological diversity and species diversification of these attine ant symbionts. Taxonomic novelties: New species: Escovopsis breviramosa Q.V. Montoya, M.J.S. Martiarena & A. Rodrigues, E. chlamydosporosa Q.V. Montoya, M.J.S. Martiarena & A. Rodrigues, E. diminuta Q.V. Montoya, M.J.S. Martiarena & A. Rodrigues, E. elongatistipitata Q.V. Montoya, M.J.S. Martiarena & A. Rodrigues, E. gracilis Q.V. Montoya, M.J.S. Martiarena & A. Rodrigues, E. maculosa Q.V. Montoya, M.J.S. Martiarena & A. Rodrigues, E. papillata Q.V. Montoya, M.J.S. Martiarena & A. Rodrigues, E. peniculiformis Q.V. Montoya, M.J.S. Martiarena & A. Rodrigues, E. phialicopiosa Q.V. Montoya, M.J.S. Martiarena & A. Rodrigues, E. pseudocylindrica Q.V. Montoya, M.J.S. Martiarena & A. Rodrigues, E. rectangula Q.V. Montoya, M.J.S. Martiarena & A. Rodrigues, E. rosisimilis Q.V. Montoya, M.J.S. Martiarena & A. Rodrigues, E. spicaticlavata Q.V. Montoya, M.J.S. Martiarena & A. Rodrigues. Citation: Montoya QV, Martiarena MJS, Rodrigues A (2023). Taxonomy and systematics of the fungus-growing ant associate Escovopsis (Hypocreaceae). Studies in Mycology 106: 349-397. doi: 10.3114/sim.2023.106.06.

Characterization and fungicide sensitivity of Trichoderma species causing green mold of Ganoderma sichuanense in China

Green mold disease, caused by Trichoderma spp., is one of the most devastating diseases of mushrooms in China. The application of fungicides remains one of the important control methods among the integrated pest management tools for disease management in mushroom farms. This study aimed to identify Trichoderma spp., isolated from G. sichuanense fruiting bodies displaying green mold symptoms collected from mushroom farms in Zhejiang, Hubei, and Jilin Province, China, and evaluate their in vitro sensitivity to six fungicides. A total of 47 isolates were obtained and classified into nine Trichoderma spp. namely, T. asperellum, T. citrinoviride, T. ganodermatiderum, T. guizhouense, T. hamatum, T. harzianum, T. koningiopsis, T. paratroviride, and T. virens, through morphological characteristics and phylogenetic analysis of concatenated sequences of translation elongation factor 1-alpha (TEF) and DNA-dependent RNA polymerase II subunit (RPB2) genes. The pathogenicity test was repeated two times, and re-isolation of the nine Trichoderma spp. from the fruiting bodies of G. sichuanense fulfilled Koch's postulates. Prochloraz manganese showed the best performance against most species. This research contributes to our understanding of green mold disease, reveals the phylogenetic relationships among Trichoderma species, and expands our knowledge of Trichoderma species diversity associated with green mold disease in G. sichuanense.

Structures and Biological Activities of Secondary Metabolites from the Trichoderma genus (Covering 2018-2022)

Trichoderma, a genus with more than 400 species, has a long history of use as an industrial bioreactor, biofertilizer, and biocontrol agent. It is considered a significant source of secondary metabolites (SMs) that possess unique structural features and a wide range of bioactivities. In recent years, numerous secondary metabolites of Trichoderma, including terpenoids, polyketides, peptides, alkaloids, and steroids, have been identified. Most of these SMs displayed antimicrobial, cytotoxic, and antifungal effects. This review focuses on the structural diversity, biological activities, and structure-activity relationships (SARs) of the SMs isolated from Trichoderma covered from 2018 to 2022. This study provides insights into the exploration and utilization of bioactive compounds from Trichoderma species in the agriculture or pharmaceutical industry.

Biocontrol Potential of Trichoderma asperellum Strain 576 against Exserohilum turcicum in Zea mays

Maize is a crucial cereal crop in China, serving both as a staple food and an essential industrial resource. Northern corn leaf blight (NCLB) is a disease of corn caused by a fungus, Exserohilum turcicum (sexual stage Setosphaeria turcica). This study aimed to assess the biocontrol potential of various Trichoderma strains against Exserohilum turcicum 101 in Jilin, China. Through dual culture tests, the Trichoderma strains were categorized into four groups based on their antagonistic abilities. Eleven Trichoderma strains exhibited strong antagonistic behavior, with comparable or faster growth rates than E. turcicum 101. Microscopic observations confirmed that T. asperellum 576 hyphae effectively encircled E. turcicum 101 hyphae, reinforcing their antagonistic behavior. The production of non-volatile and volatile substances by the Trichoderma strains was evaluated, with T. asperellum 576 showing the highest potency in producing non-volatile and volatile substances, leading to an impressive 80.81% and 65.86% inhibition of E. turcicum 101 growth. Remarkably, co-culture suspensions of T. asperellum 576 + E. turcicum 101 and T. atroviride 393 + E. turcicum 101 exhibited strong antifungal activity. Furthermore, the activities of chitinase, β-1.3-glucanase, and cellulase were evaluated using the 3, 5-dinitrosalicylic acid (DNS) method. T. asperellum 576 + E. turcicum 101 displayed stronger cell wall degradation enzyme activity compared to T. atroviride 393 + E. turcicum 101, with values of 8.34 U/mL, 3.42 U/mL, and 7.75 U/mL, respectively. In greenhouse conditions, the application of a 107 spores/mL conidia suspension of T. asperellum 576 significantly enhanced maize seed germination and plant growth while effectively suppressing E. turcicum 101 infection. Maize seedlings inoculated/treated with both E. turcicum 101 and T. asperellum 576 demonstrated substantial improvements compared to those inoculated solely with E. turcicum 101. The T. asperellum 576 treatment involved a 107 spores/mL conidia suspension applied through a combination of foliar spray and soil drench. These findings highlight T. asperellum 576 as a promising biocontrol candidate against northern leaf blight in maize. Its antagonistic behavior, production of inhibitory compounds, and promotion of plant growth all contribute to its potential as an effective biocontrol agent for disease management.

Two new Trichoderma species (Hypocreales, Hypocreaceae) isolated from decaying tubers of Gastrodiaelate

Species of Trichoderma are widely distributed around the world. In this study, two new species in Trichoderma, named as T.albidum and T.variegatum, were introduced and illustrated. These species were isolated from diseased tubers of Gastrodiaelata in China and identified based on morphological characteristics and multi-gene sequence analyses of three loci that is the internal transcribed spacer regions of the ribosomal DNA (ITS), the translation elongation factor 1-α encoding gene (tef1-α) and the gene encoding the second largest nuclear RNA polymerase subunit (rpb2). Distinctions between the new species and their close relatives were discussed. According to results of the phylogenetic analyses, T.albidum belonged to the Harzianum clade and T.variegatum are grouped with species of the Spirale clade. The expansion of two clades provided research foundations for the prevention and control of tuber diseases in G.elata.

Identification of a pathogen causing fruiting body rot of Sanghuangporus vaninii

Sanghuangporus vaninii is a medicinal macrofungus that is increasingly cultivated in China. During cultivation, it was found that the fruiting body of S. vaninii was susceptible to pathogenic fungi, resulting in significant economic losses to the industry. The symptoms of the disease occur in the initial stage of fruiting body development. The isolate YZB-1 was obtained from the junction of the diseased and healthy areas of the fruiting body. In order to verify the pathogenicity of YZB-1, its purified spore suspension was inoculated into the exposed area nearby the developing fruiting body of S. vaninii. After 10 days, the same disease symptoms appeared in the inoculated area. Morphological identification and molecular analysis of rDNA ITS region confirmed that the isolate YZB-1 was identified as Trichoderma virens. The temperature stability assay revealed that the mycelia of YZB-1 grew the fastest at 25 °C, with growth slowing down gradually as the temperature increased or decreased. Dual-culture tests of T. virens and S. vaninii showed that the inhibition rate of T. virens on S. vaninii mycelium was the highest (79.01 ± 2.79%) at 25 °C, and more green spores were produced at the intersection of T. virens and S. vaninii.

Trichoderma Species from Soil of Pernambuco State, Brazil

Trichoderma is an important fungal genus, known mainly for its potential for the biological control of phytopathogens. Accurate identification of these fungi is essential for research and applications involving them, to be addressed correctly. The objectives of this study were to isolate, identify, and report the species richness of Trichoderma species that occur in the soil of different regions of Pernambuco, Brazil. DNA sequences of portions of the translation elongation factor 1-α (TEF1) gene region were generated for 56 isolates of Trichoderma, obtained from the Zona da Mata, Agreste, and Sertão regions of Pernambuco. According to the phylogenetic analysis based on these sequences, these fungi belong to two Sections-Trichoderma (35 isolates) and Pachybasidium (21 isolates). These fungi have been resolved in nine species, including Trichoderma afroharzianum, Trichoderma asperelloides, Trichoderma asperellum, Trichoderma koningiopsis, and five possible new species to be confirmed in further studies. This study shows that the soils of Pernambuco host a diversity of Trichoderma species and consequently of biological resources with potential for application in agriculture.

Endophytic Trichoderma species from rubber trees native to the Brazilian Amazon, including four new species

Fungi belonging to the genus Trichoderma have been widely recognized as efficient controllers of plant diseases. Although the majority of isolates currently deployed, thus far, have been isolated from soil, endophytic Trichoderma spp. is considered to be a promising option for application in biocontrol. In this study, 30 endophytic Trichoderma isolates-obtained from the leaves, stems, and roots of wild Hevea spp. in the Brazilian Amazon-were analyzed using specific DNA barcodes: sequences of internal transcribed spacers 1 and 2 of rDNA (ITS region), genes encoding translation elongation factor 1-α (TEF1-α), and the second largest subunit of RNA polymerase II (RPB2). The genealogical concordance phylogenetic species recognition (GCPSR) concept was used for species delimitation. A phylogenetic analysis showed the occurrence of Trichoderma species, such as T. erinaceum, T. ovalisporum, T. koningiopsis, T. sparsum, T. lentiforme, T. virens, and T. spirale. Molecular and morphological features resulted in the discovery of four new species, such as T. acreanum sp. nov., T. ararianum sp. nov., T. heveae sp. nov., and T. brasiliensis sp. nov. The BI and ML analyses shared a similar topology, providing high support to the final trees. The phylograms show three distinct subclades, namely, T. acreanum and T. ararianum being paraphyletic with T. koningiopsis; T. heveae with T. subviride; and T. brasiliensis with T. brevicompactum. This study adds to our knowledge of the diversity of endophytic Trichoderma species in Neotropical forests and reveals new potential biocontrol agents for the management of plant diseases.

Trichoderma Species: Our Best Fungal Allies in the Biocontrol of Plant Diseases-A Review

Biocontrol agents (BCA) have been an important tool in agriculture to prevent crop losses due to plant pathogens infections and to increase plant food production globally, diminishing the necessity for chemical pesticides and fertilizers and offering a more sustainable and environmentally friendly option. Fungi from the genus Trichoderma are among the most used and studied microorganisms as BCA due to the variety of biocontrol traits, such as parasitism, antibiosis, secondary metabolites (SM) production, and plant defense system induction. Several Trichoderma species are well-known mycoparasites. However, some of those species can antagonize other organisms such as nematodes and plant pests, making this fungus a very versatile BCA. Trichoderma has been used in agriculture as part of innovative bioformulations, either just Trichoderma species or in combination with other plant-beneficial microbes, such as plant growth-promoting bacteria (PGPB). Here, we review the most recent literature regarding the biocontrol studies about six of the most used Trichoderma species, T. atroviride, T. harzianum, T. asperellum, T. virens, T. longibrachiatum, and T. viride, highlighting their biocontrol traits and the use of these fungal genera in Trichoderma-based formulations to control or prevent plant diseases, and their importance as a substitute for chemical pesticides and fertilizers.

Diversity of Trichoderma species associated with soil in the Zoige alpine wetland of Southwest China

The ecology of soil fungi is poorly understood, and recent comprehensive reports on Trichoderma are unavailable for any region, including the Zoige alpine wetland ecological region in China. One hundred soil samples were collected from different soil types and soil layers in Zoige alpine wetland ecological regions. Using the traditional suspension plating method, 80 Trichoderma strains were chosen to analyze species diversity. After a preliminary classification of morphological characteristics and the genes glyceraldehyde-3-phosphate dehydrogenase (gpd), 57 representative strains were selected and eventually identified as seven species via phylogenetic analyses of multilocus sequences based on the genes transcription elongation factor 1 alpha (tef1), encoding RNA polymerase II subunit B (rpb2) and ATP citrate lyase (acl1). Among them, T. harzianum was the dominant species isolated from five soil layers and four soil types, and had the highest isolation frequency (23%) in this zone, while T. polysporum and T. pyramidale were rare species, with isolation frequencies of less than 1%. Our detailed morphological observation and molecular phylogenetic analyses support the recognition of Trichoderma zoigense was described for the first time as a new species, while T. atrobrunneum as a new record for China was found. Our results will be used as a reference for a greater understanding of soil microbial resources, ecological rehabilitation and reconstructions in the Zoige alpine wetland.

Five Previously Unrecorded Fungal Species Isolated from Marine Plastic Wastes in South Korea

Plastic wastes have a negative impact on marine environments; however, they can be used as carbon sources and habitats by certain microbes. Microbes in the marine plastisphere can migrate worldwide through the ocean and cause serious environmental problems when they encounter suitable environments. Therefore, efforts to investigate the microbes inhabiting the marine plastisphere are increasing. In the present study, fungal strains were isolated from plastic wastes buried in Korean sea sands and mudflats and identified using molecular and morphological analyses. Five species were identified that were previously unrecorded from South Korea: Cladosporium funiculosum, Neosetophoma poaceicola, Neosetophoma rosigena, Parasarocladium gamsii, and Trichoderma fomiticola. Their molecular phylogenies and morphological characteristics are described in this study.

Taxonomy and control of Trichoderma hymenopellicola sp. nov. responsible for the first green mold disease on Hymenopellis raphanipes

Trichoderma spp. are a group of widespread fungi with important applications in many aspects of human life, but they are also pathogens that cause green mold disease on mushrooms. During a survey of mushroom cultivation in Guizhou, China, five strains of Trichoderma from three different localities were isolated from soil in mushroom bags of Hymenopellis raphanipes. The typical morphology of having gregarious, reddish stromata and gregarious phialides and the results of phylogenetic analyses based on a combined dataset of RPB2, TEF, and ITS gene sequences demonstrated that these green-spored Trichoderma belong to a new taxon, Trichoderma hymenopellicola. Pathogenicity tests by covering fungal mycelial blocks or soil mixed with spore suspension in mushroom bags showed similar symptoms to those in the field, and the same fungal pathogen had been observed and re-isolated from these symptoms, which fulfill Koch’s postulates. A primary screening test of nine common fungicides indicated that prochloraz-manganese chloride complex and propiconazole are the top two effective fungicides inhibiting the pathogen, whereas the former was further indicated as a suitable fungicide to control Trichoderma hymenopellicola, with a high inhibition ratio to the pathogen and low toxicity to the mushroom.

Phylogenetic Analysis of Trichoderma Species Associated with Green Mold Disease on Mushrooms and Two New Pathogens on Ganoderma sichuanense

Edible and medicinal mushrooms are extensively cultivated and commercially consumed around the world. However, green mold disease (causal agent, Trichoderma spp.) has resulted in severe crop losses on mushroom farms worldwide in recent years and has become an obstacle to the development of the Ganoderma industry in China. In this study, a new species and a new fungal pathogen on Ganoderma sichuanense fruitbodies were identified based on the morphological characteristics and phylogenetic analysis of two genes, the translation elongation factor 1-α (TEF1) and the second-largest subunit of RNA polymerase II (RPB2) genes. The new species, Trichoderma ganodermatigerum sp. nov., belongs to the Harzianum clade, and the new fungal pathogen was identified as Trichoderma koningiopsis. Furthermore, in order to better understand the interaction between Trichoderma and mushrooms, as well as the potential biocontrol value of pathogenic Trichoderma, we summarized the Trichoderma species and their mushroom hosts as best as possible, and the phylogenetic relationships within mushroom pathogenic Trichoderma species were discussed.

Trichoderma spp. Genes Involved in the Biocontrol Activity Against Rhizoctonia solani

Rhizoctonia solani is a pathogen that causes considerable harm to plants worldwide. In the absence of hosts, R. solani survives in the soil by forming sclerotia, and management methods, such as cultivar breeding, crop rotations, and fungicide sprays, are insufficient and/or inefficient in controlling R. solani. One of the most challenging problems facing agriculture in the twenty-first century besides with the impact of global warming. Environmentally friendly techniques of crop production and improved agricultural practices are essential for long-term food security. Trichoderma spp. could serve as an excellent example of a model fungus to enhance crop productivity in a sustainable way. Among biocontrol mechanisms, mycoparasitism, competition, and antibiosis are the fundamental mechanisms by which Trichoderma spp. defend against R. solani, thereby preventing or obstructing its proliferation. Additionally, Trichoderma spp. induce a mixed induced systemic resistance (ISR) or systemic acquired resistance (SAR) in plants against R. solani, known as Trichoderma-ISR. Stimulation of every biocontrol mechanism involves Trichoderma spp. genes responsible for encoding secondary metabolites, siderophores, signaling molecules, enzymes for cell wall degradation, and plant growth regulators. Rhizoctonia solani biological control through genes of Trichoderma spp. is summarized in this paper. It also gives information on the Trichoderma-ISR in plants against R. solani. Nonetheless, fast-paced current research on Trichoderma spp. is required to properly utilize their true potential against diseases caused by R. solani.

Recent Developments in Biological Processing Technology for Palm Oil Mill Effluent Treatment-A Review

Simple Summary

Palm oil mill effluent (POME) requires treatment prior to discharge to the environment. Biological processing technology is highly preferable due to its advantages of environmentally friendliness, cost effectiveness, and practicality. These methods utilized various designs and modifications of bioreactors fostering effective fermentation technology in the presence of fungi, bacteria, microalgae, and a consortium of microorganisms. This review highlights the recent biological processing technology for POME treatment as a resource utilization.

Abstract

POME is the most voluminous waste generated from palm oil milling activities. The discharge of POME into the environment without any treatment processing could inflict an undesirable hazard to humans and the environment due to its high amount of toxins, organic, and inorganic materials. The treatment of POME prior to discharge into the environment is utmost required to protect the liability for human health and the environment. Biological treatments are preferable due to eco-friendly attributes that are technically and economically feasible. The goal of this review article is to highlight the current state of development in the biological processing technologies for POME treatment. These biological processing technologies are conducted in the presence of fungi, bacteria, microalgae, and a consortium of microorganisms. Numerous microbes are listed to identify the most efficient strain by monitoring the BOD, COD, working volume of the reactor, and treatment time. The most effective processing technology for POME treatment uses an upflow anaerobic sludge blanket reactor with the COD value of 99%, hydraulic retention time of 7.2 days, and a working volume of 4.7 litres. Biological processing technologies are mooted as an efficient and sustainable management practice of POME waste.

New species, combinations and records of Thyronectria, with a key to species

The new species Thyronectria ulmi is described from Ulmus laevis and U. minor collected in Austria, the Czech Republic and Slovakia. It is morphologically and phylogenetically close to the North American T. chrysogramma, which also occurs on Ulmus and shares olive green to brown muriform ascospores, but differs from the latter by geographic distribution, narrower asci, smaller ascospores with fewer septa and DNA sequence data from seven loci (ITS and LSU regions of nu rDNA, ACT1, RPB1, RPB2, TEF1 and TUB2 genes). As in many other Thyronectria species, ascomata of T. ulmi were closely associated with Diplodia, indicating a fungicolous habit. The genus Neothyronectria is synonymised with Thyronectria based on morphological and molecular phylogenetic data, and the new combinations T. citri and T. sophorae are proposed. A key to 45 accepted species of Thyronectria is provided. The recently described T. abieticola, previously known from the Czech Republic and France, is newly reported from Austria and Slovakia; its pycnidial anamorph is recorded, described and illustrated from natural substrates for the first time. A sporodochial anamorph is reported from natural substrates for T. aurigera, a new record for Austria as well. New host and distribution records include T. rhodochlora on Acer pseudoplatanus in Austria and Fraxinus excelsior in the Czech Republic, T. sinopica on Hedera colchica in the Czech Republic and Bupleurum fruticosum in Spain, and T. zanthoxyli on Sorbus aucuparia in Belgium and Ulmus sp. in the USA. Thyronectria cucurbitula is confirmed by sequence data from Pinus strobus collected in the Czech Republic, challenging the host ranges given for T. cucurbitula (Pinus subgen. Pinus) and T. strobi (Pinus subgen. Strobus), and questioning the European and Chinese records of T. strobi.

Five new species of Trichoderma from moist soils in China

Trichoderma isolates were collected from moist soils near a water source in different areas of China. ITS sequences were submitted to MIST (Multiloci Identification System for Trichoderma) and meets the Trichoderma [ITS76] standard. Combined analyses of phylogenetic analyses of both phylograms (tef1-α and rpb2) and morphological characteristics, revealed five new species of Trichoderma, namely Trichoderma hailarense, T. macrofasciculatum, T. nordicum, T. shangrilaense and T. vadicola. Phylogenetic analyses showed T. macrofasciculatum and T. shangrilaense belong to the Polysporum clade, T. hailarense, while T. nordicum and T. vadicola belong to the Viride clade. Each new taxon formed a distinct clade in phylogenetic analysis and have unique sequences of tef1-α and rpb2 that meet the Trichoderma new species standard. The conidiation of T. macrofasciculatum typically appeared in white pustules in concentric rings on PDA or MEA and its conidia had one or few distinctly verrucose. Conidiophores of T. shangrilaense are short and rarely branched, phialides usually curved and irregularly disposed. The aerial mycelium of T. hailarense and T. vadicola formed strands to floccose mat, conidiation tardy and scattered in tufts, conidiophores repeatedly rebranching in dendriform structure. The phialides of T. nordicum lageniform are curved on PDA and its conidia are globose to obovoidal and large.

The pleiotropic functions of intracellular hydrophobins in aerial hyphae and fungal spores

Higher fungi can rapidly produce large numbers of spores suitable for aerial dispersal. The efficiency of the dispersal and spore resilience to abiotic stresses correlate with their hydrophobicity provided by the unique amphiphilic and superior surface-active proteins-hydrophobins (HFBs)-that self-assemble at hydrophobic/hydrophilic interfaces and thus modulate surface properties. Using the HFB-enriched mold Trichoderma (Hypocreales, Ascomycota) and the HFB-free yeast Pichia pastoris (Saccharomycetales, Ascomycota), we revealed that the rapid release of HFBs by aerial hyphae shortly prior to conidiation is associated with their intracellular accumulation in vacuoles and/or lipid-enriched organelles. The occasional internalization of the latter organelles in vacuoles can provide the hydrophobic/hydrophilic interface for the assembly of HFB layers and thus result in the formation of HFB-enriched vesicles and vacuolar multicisternal structures (VMSs) putatively lined up by HFBs. These HFB-enriched vesicles and VMSs can become fused in large tonoplast-like organelles or move to the periplasm for secretion. The tonoplast-like structures can contribute to the maintenance of turgor pressure in aerial hyphae supporting the erection of sporogenic structures (e.g., conidiophores) and provide intracellular force to squeeze out HFB-enriched vesicles and VMSs from the periplasm through the cell wall. We also show that the secretion of HFBs occurs prior to the conidiation and reveal that the even spore coating of HFBs deposited in the extracellular matrix requires microscopic water droplets that can be either guttated by the hyphae or obtained from the environment. Furthermore, we demonstrate that at least one HFB, HFB4 in T. guizhouense, is produced and secreted by wetted spores. We show that this protein possibly controls spore dormancy and contributes to the water sensing mechanism required for the detection of germination conditions. Thus, intracellular HFBs have a range of pleiotropic functions in aerial hyphae and spores and are essential for fungal development and fitness.

Expanding the Trichoderma harzianum species complex: Three new species from Argentine natural and cultivated ecosystems

A study was performed on a collection of 84 isolates from decaying plant tissues and soils in Argentina previously identified as Trichoderma harzianum. Based on multiple phenotypic characters and multilocus phylogenetic analyses, 10 species were distinguished, three of which are described as new species: T. austroindianum, T. hortense, and T. syagri. Among the remaining seven identified species, the following five can be added to the Argentine mycobiota: T. afarasin, T. afroharzianum, T. endophyticum, T. guizhouense, and T. neotropicale. Trichoderma afroharzianum and T. endophyticum were the most frequent species found in the samples. In addition, a collection of isolates previously identified as T. harzianum with antagonistic abilities were reidentified as T. afroharzianum, thus highlighting the importance of correct identification of biocontrol species.

Fungi inhabiting attine ant colonies: reassessment of the genus Escovopsis and description of Luteomyces and Sympodiorosea gens. nov

Escovopsis is a diverse group of fungi, which are considered specialized parasites of the fungal cultivars of fungus-growing ants. The lack of a suitable taxonomic framework and phylogenetic inconsistencies have long hampered Escovopsis research. The aim of this study is to reassess the genus Escovopsis using a taxonomic approach and a comprehensive multilocus phylogenetic analysis, in order to set the basis of the genus systematics and the stage for future Escovopsis research. Our results support the separation of Escovopsis into three distinct genera. In light of this, we redefine Escovopsis as a monophyletic clade whose main feature is to form terminal vesicles on conidiophores. Consequently, E. kreiselii and E. trichodermoides were recombined into two new genera, Sympodiorosea and Luteomyces, as S. kreiselii and L. trichodermoides, respectively. This study expands our understanding of the systematics of Escovopsis and related genera, thereby facilitating future research on the evolutionary history, taxonomic diversity, and ecological roles of these inhabitants of the attine ant colonies.

Antagonistic Potential of Native Trichoderma spp. against Phytophthora cinnamomi in the Control of Holm Oak Decline in Dehesas Ecosystems

Phytophthora root rot caused by the pathogen Phytophthora cinnamomi is one of the main causes of oak mortality in Mediterranean open woodlands, the so-called dehesas. Disease control is challenging; therefore, new alternative measures are needed. This study focused on searching for natural biocontrol agents with the aim of developing integrated pest management (IPM) strategies in dehesas as a part of adaptive forest management (AFM) strategies. Native Trichoderma spp. were selectively isolated from healthy trees growing in damaged areas by P. cinnamomi root rot, using Rose Bengal selective medium. All Trichoderma (n = 95) isolates were evaluated against P. cinnamomi by mycelial growth inhibition (MGI). Forty-three isolates presented an MGI higher than 60%. Twenty-one isolates belonging to the highest categories of MGI were molecularly identified as T. gamsii, T. viridarium, T. hamatum, T. olivascens, T. virens, T. paraviridescens, T. linzhiense, T. hirsutum, T. samuelsii, and T. harzianum. Amongst the identified strains, 10 outstanding Trichoderma isolates were tested for mycoparasitism, showing values on a scale ranging from 3 to 4. As far as we know, this is the first report referring to the antagonistic activity of native Trichoderma spp. over P. cinnamomi strains cohabiting in the same infected dehesas. The analysis of the tree health status and MGI suggest that the presence of Trichoderma spp. might diminish or even avoid the development of P. cinnamomi, protecting trees from the worst effects of P. cinnamomi root rot.

Three new species of Trichoderma in the Harzianum and Longibrachiatum lineages from Peruvian cacao crop soils based on an integrative approach

The hyperdiverse genus Trichoderma is one of most useful groups of microbes for a number of human activities, and their accurate identification is crucial. The structural simplicity and lack of distinctive phenotypic variation in this group enable the use of DNA-based species delimitation methods in combination with phylogenies (and morphology when feasible) to establish well-supported boundaries among species. Our study employed a multilocus phylogeny and four DNA-based methods (automated barcode gap discovery [ABGD], statistical parsimony [SPN], generalized mixed Yule coalescent [GMYC], and Bayesian phylogenetics and phylogeography [BPP]) for four molecular markers (acl1, act, rpb2, and tef1) to delimit species of two lineages of Trichoderma. Although incongruence among these methods was observed in our analyses, the genetic distance (ABGD) and coalescence (BPP) methods and the multilocus phylogeny strongly supported and confirmed recognition of 108 and 39 different species in the Harzianum and Longibrachiatum lineages, including three new species associated with cacao farms in northern Peru, namely, T.awajun, sp. nov., T. jaklitschii, sp. nov., and T. peruvianum, sp. nov. Morphological distinctions between the new species and their close relatives are primarily related to growth rates, colony appearance, and size of phialides and conidia. This study confirmed that an integrative approach (DNA-based methods, multilocus phylogeny, and phenotype) is more likely to reliably verify supported species boundaries in Trichoderma.

New Species of Trichoderma Isolated as Endophytes and Saprobes from Southwest China

During the investigation of endophytic fungi diversity in aquatic plants and the fungal diversity in soil in southwest China, we obtained 208 isolates belonging to Trichoderma, including 28 isolates as endophytes from aquatic plants and 180 isolates as saprobes from soil, respectively. Finally, 23 new species of Trichoderma are recognized by further studies. Their phylogenetic positions are determined by sequence analyses of the combined partial sequences of translation elongation factor 1-alpha (tef1) and gene encoding of the second largest nuclear RNA polymerase subunit (rpb2). The results revealed that the 23 new species are distributed in nine known clades. The morphology and culture characteristics are observed, described and illustrated in detail. Distinctions between the new species and their close relatives were compared and discussed. These include: Trichoderma achlamydosporum, T. amoenum, T. anaharzianum, T. anisohamatum, T. aquatica, T. asiaticum, T. asymmetricum, T. inaequilaterale, T. inconspicuum, T. insigne, T. obovatum, T. paraviride, T. pluripenicillatum, T. propepolypori, T. pseudoasiaticum, T. pseudoasperelloides, T. scorpioideum, T. simile, T. subazureum, T. subuliforme, T. supraverticillatum, T. tibetica, and T. uncinatum.

Evaluation of a Newly Identified Endophytic Fungus, Trichoderma phayaoense for Plant Growth Promotion and Biological Control of Gummy Stem Blight and Wilt of Muskmelon

Gummy stem blight and wilt are known to cause enormous losses to the global production of muskmelon (Cucumis melo). In this study, the potential of endophytic fungi isolated from leaves of Siam weed (Chromolaena odorata) was investigated for the inhibition of mycelial growth of Stagonosporopsis cucurbitacearum and Fusarium equiseti. Twenty-one fungal isolates were obtained. The results indicated that a fungal isolate UP-L1I3 displayed the highest percentage in terms of inhibition of the mycelial growth of F. equiseti and S. cucurbitacearum at 90.80 and 81.60%, respectively. Consequently, this isolate was selected for its potential ability to promote plant growth and control gummy stem blight and wilt in muskmelon seedlings. Morphological and multilocus phylogenetic analyses revealed that the isolate UP-L1I3 was a new species that has been described herein as Trichoderma phayaoense. Pathogenicity test confirmed that F. equiseti and S. cucurbitacearum were the cause of gummy stem blight and wilt disease in muskmelon seedlings, respectively. However, no disease symptoms were observed in seedlings inoculated with T. phayaoense. It was found that T. phayaoense could be used preventively in muskmelon seedlings that were inoculated with F. equiseti and S. cucurbitacearum, which could then reduce the impact on the disease severity index. T. phayaoense was also effective in improving plant development by increasing plant height, as well as shoot and root dry weight values. Moreover, T. phayaoense could effectively increase weight, diameter, and the circumference and total soluble solid of fruit without having a negative effect on fruit quality parameters. Additionally, T. phayaoense was able to tolerate a commonly applied fungicide (metalaxyl) in recommended dosages for field applications.

In honor of John Bissett: authoritative guidelines on molecular identification of Trichoderma

Modern taxonomy has developed towards the establishment of global authoritative lists of species that assume the standardized principles of species recognition, at least in a given taxonomic group. However, in fungi, species delimitation is frequently subjective because it depends on the choice of a species concept and the criteria selected by a taxonomist. Contrary to it, identification of fungal species is expected to be accurate and precise because it should predict the properties that are required for applications or that are relevant in pathology. The industrial and plant-beneficial fungi from the genus Trichoderma (Hypocreales) offer a suitable model to address this collision between species delimitation and species identification. A few decades ago, Trichoderma diversity was limited to a few dozen species. The introduction of molecular evolutionary methods resulted in the exponential expansion of Trichoderma taxonomy, with up to 50 new species recognized per year. Here, we have reviewed the genus-wide taxonomy of Trichoderma and compiled a complete inventory of all Trichoderma species and DNA barcoding material deposited in public databases (the inventory is available at the website of the International Subcommission on Taxonomy of Trichodermawww.trichoderma.info). Among the 375 species with valid names as of July 2020, 361 (96%) have been cultivated in vitro and DNA barcoded. Thus, we have developed a protocol for molecular identification of Trichoderma that requires analysis of the three DNA barcodes (ITS, tef1, and rpb2), and it is supported by online tools that are available on www.trichokey.info. We then used all the whole-genome sequenced (WGS) Trichoderma strains that are available in public databases to provide versatile practical examples of molecular identification, reveal shortcomings, and discuss possible ambiguities. Based on the Trichoderma example, this study shows why the identification of a fungal species is an intricate and laborious task that requires a background in mycology, molecular biological skills, training in molecular evolutionary analysis, and knowledge of taxonomic literature. We provide an in-depth discussion of species concepts that are applied in Trichoderma taxonomy, and conclude that these fungi are particularly suitable for the implementation of a polyphasic approach that was first introduced in Trichoderma taxonomy by John Bissett (1948–2020), whose work inspired the current study. We also propose a regulatory and unifying role of international commissions on the taxonomy of particular fungal groups. An important outcome of this work is the demonstration of an urgent need for cooperation between Trichoderma researchers to get prepared to the efficient use of the upcoming wave of Trichoderma genomic data.

Trichoderma reesei Isolated From Austrian Soil With High Potential for Biotechnological Application

Fungi of the genus Trichoderma are of high importance for biotechnological applications, in biocontrol and for production of homologous and heterologous proteins. However, sexual crossing under laboratory conditions has so far only been achieved with the species Trichoderma reesei, which was so far only isolated from tropical regions. Our isolation efforts aimed at the collection of Trichoderma strains from Austrian soils surprisingly also yielded 12 strains of the species T. reesei, which was previously not known to occur in Europe. Their identity was confirmed with tef1- and rpb2-sequencing and phylogenetic analysis. They could clearly be distinguished from tropical strains including the common laboratory wildtypes by UP-PCR and genetic variations adjacent to the mating type locus. The strains readily mated with reference strains derived from CBS999.97. Secreted cellulase and xylanase levels of these isolates were up to six-fold higher than those of QM6a indicating a high potential for strain improvement. The strains showed different responses to injury in terms of induction of sporulation, but a correlation to alterations in the nox1-gene sequence was not detected. Several synonymous SNPs were found in the sequence of the regulator gene noxR of the soil isolates compared to QM6a. Only in one strain, non-synonymous SNPs were found which impact a PEST sequence of NoxR, suggesting altered protein stability. The availability of sexually fertile strains from middle Europe naturally producing decent amounts of plant cell wall degrading enzymes opens up novel perspectives for non-GMO strain improvement and biological pretreatment of plant biomass for bioethanol production. Moreover, the varied response of these strains to injury in terms of sporulation, which is independent of Nox1 and NoxR suggests that additional regulators impact this phenomenon in T. reesei.

Emerging salt marshes as a source of Trichoderma arenarium sp. nov. and other fungal bioeffectors for biosaline agriculture

AIMS

Sustainable agriculture requires effective and safe biofertilizers and biofungicides with low environmental impact. Natural ecosystems that closely resemble the conditions of biosaline agriculture may present a reservoir for fungal strains that can be used as novel bioeffectors.

METHODS AND RESULTS

We isolated a library of fungi from the rhizosphere of three natural halotolerant plants grown in the emerging tidal salt marshes on the south-east coast of China. DNA barcoding of 116 isolates based on the rRNA ITS1 and 2 and other markers (tef1 or rpb2) revealed 38 fungal species, including plant pathogenic (41%), saprotrophic (24%) and mycoparasitic (28%) taxa. The mycoparasitic fungi were mainly species from the hypocrealean genus Trichoderma, including at least four novel phylotypes. Two of them, representing the taxa Trichoderma arenarium sp. nov. (described here) and T. asperelloides, showed antagonistic activity against five phytopathogenic fungi, and significant growth promotion on tomato seedlings under the conditions of saline agriculture.

CONCLUSIONS

Trichoderma spp. of salt marshes play the role of natural biological control in young soil ecosystems with a putatively premature microbiome.

SIGNIFICANCE AND IMPACT OF THE STUDY

The saline soil microbiome is a rich source of halotolerant bioeffectors that can be used in biosaline agriculture.

Ecological Genomics and Evolution of Trichoderma reesei

The filamentous fungus Trichoderma reesei (Hypocreales, Ascomycota) is an efficient industrial cell factory for the production of cellulolytic enzymes used for biofuel and other applications. Therefore, researches addressing T. reesei are relatively advanced compared to other Trichoderma spp. because of the significant bulk of available knowledge, multiple genomic data, and gene manipulation techniques. However, the established role of T. reesei in industry has resulted in a frequently biased understanding of the biology of this fungus. Thus, the recent studies unexpectedly show that the superior cellulolytic activity of T. reesei and other Trichoderma species evolved due to multiple lateral gene transfer events, while the innate ability to parasitize other fungi (mycoparasitism) was maintained in the genus, including T. reesei. In this chapter, we will follow the concept of ecological genomics and describe the ecology, distribution, and evolution of T. reesei, as well as critically discuss several common misconceptions that originate from the success of this species in applied sciences and industry.

Mycosphaerangium and Neomelanconium (Cenangiaceae) are closest relatives: phylogenetic relationships, morphology and a new species

Based on molecular phylogenetic analyses of a multigene matrix of partial nuSSU-ITS-LSU rDNA, RPB1, RPB2 and TEF1 sequences and by morphological evidence, the genus Mycosphaerangium is shown to be the closest relative of Neomelanconium, and confirmed to be a member of the Cenangiaceae (Leotiomycetes). While Mycosphaerangium and Neomelanconium share many traits like similar conidia, conidiogenesis, asci and ascospores, their apothecia differ particularly in excipular features and are therefore recognized as distinct genera. Mycosphaerangium tiliae, described from North America, is excluded from the genus but shown to represent the sexual morph of the European Neomelanconium gelatosporum, and it is therefore synonymized with the latter. Based on morphology, Neomelanconium deightonii is assumed to be congeneric with Neomelanconium gelatosporum, and it is lectotypified. Dermatea tetraspora and Phaeangium magnisporum, the basionyms of Mycosphaerangium tetrasporum and M. magnisporum, respectively, are lectotypified as well, and for M. tetrasporum, the asexual morph is recorded for the first time. Mycosphaerangium quercinum sp. nov. is described as a new species from various Quercus hosts in Europe, where it is shown to be widely distributed. It morphologically and ecologically closely resembles the North American M. tetrasporum, but differs in paraphysis and ascospore morphology and by croziers at its ascus base. The three accepted species of Mycosphaerangium and the two of Neomelanconium are described and illustrated. Mycosphaerangium magnisporum, M. quercinum and M. tetrasporum are recorded to be constantly associated with species of Coryneum, indicating a fungicolous habit, but no evidence for fungal associations has been found in Neomelanconium deightonii and N. gelatosporum.

Evolutionary compromises in fungal fitness: hydrophobins can hinder the adverse dispersal of conidiospores and challenge their survival

Fungal evolutionary biology is impeded by the scarcity of fossils, irregular life cycles, immortality, and frequent asexual reproduction. Simple and diminutive bodies of fungi develop inside a substrate and have exceptional metabolic and ecological plasticity, which hinders species delimitation. However, the unique fungal traits can shed light on evolutionary forces that shape the environmental adaptations of these taxa. Higher filamentous fungi that disperse through aerial spores produce amphiphilic and highly surface-active proteins called hydrophobins (HFBs), which coat spores and mediate environmental interactions. We exploited a library of HFB-deficient mutants for two cryptic species of mycoparasitic and saprotrophic fungi from the genus Trichoderma (Hypocreales) and estimated fungal development, reproductive potential, and stress resistance. HFB4 and HFB10 were found to be relevant for Trichoderma fitness because they could impact the spore-mediated dispersal processes and control other fitness traits. An analysis in silico revealed purifying selection for all cases except for HFB4 from T. harzianum, which evolved under strong positive selection pressure. Interestingly, the deletion of the hfb4 gene in T. harzianum considerably increased its fitness-related traits. Conversely, the deletion of hfb4 in T. guizhouense led to the characteristic phenotypes associated with relatively low fitness. The net contribution of the hfb4 gene to fitness was found to result from evolutionary tradeoffs between individual traits. Our analysis of HFB-dependent fitness traits has provided an evolutionary snapshot of the selective pressures and speciation process in closely related fungal species.

MIST: a Multilocus Identification System for Trichoderma

Due to the rapid expansion in microbial taxonomy, precise identification of common industrially and agriculturally relevant fungi such as Trichoderma species is challenging. In this study, we introduce the online multilocus identification system (MIST) for automated detection of 349 Trichoderma species based on a set of three DNA barcodes. MIST is based on the reference databases of validated sequences of three commonly used phylogenetic markers collected from public databases. The databases consist of 414 complete sequences of the nuclear rRNA internal transcribed spacers (ITS) 1 and 2, 583 sequence fragments of the gene encoding translation elongation factor 1-alpha (tef1), and 534 sequence fragments of the gene encoding RNA polymerase subunit 2 (rpb2). Through MIST, information from different DNA barcodes can be combined and the identification of Trichoderma species can be achieved based on the integrated parametric sequence similarity search (blastn) performed in the manner of a decision tree classifier. In the verification process, MIST provided correct identification for 44 Trichoderma species based on DNA barcodes consisting of tef1 and rpb2 markers. Thus, MIST can be used to obtain an automated species identification as well as to retrieve sequences required for manual identification by means of phylogenetic analysis.IMPORTANCE The genus Trichoderma is important to humankind, with a wide range of applications in industry, agriculture, and bioremediation. Thus, quick and accurate identification of Trichoderma species is paramount, since it is usually the first step in Trichoderma-based research. However, it frequently becomes a limitation, especially for researchers who lack taxonomic knowledge of fungi. Moreover, as the number of Trichoderma-based studies has increased, a growing number of unidentified sequences have been stored in public databases, which has made the species identification more ambiguous. In this study, we provide an easy-to-use tool, MIST, for automated species identification, a list of Trichoderma species, and corresponding sequences of reference DNA barcodes. Therefore, this study will facilitate the research on the biodiversity and applications of the genus Trichoderma.

Biodiversity of Trichoderma from grassland and forest ecosystems in Northern Xinjiang, China

Trichoderma spp., a cosmopolitan fungal genus, has remarkable economic value in industry and agriculture. The resources of Trichoderma spp. in the grassland and forest ecosystems of northern Xinjiang were explored in this study. A total of 634 soil samples was collected, and 312 strains assigned to 23 species of Trichoderma spp. were identified. T. harzianum was the dominant species with 28.2% from all isolates. The principal components analysis indicated that ecosystem was the most dominant impact factor among longitude, latitude, altitude and ecosystems for the species diversities of Trichoderma spp. with the decreasing trend from the north to the south of northern Xinjiang (e.g., from Altay, followed by Yili, Changji, Bayingolin and finally Urumqi). Overall, Trichoderma spp. were more frequently encountered in forest ecosystems (coniferous forest and coniferous and broadleaf mixed forest) than in grassland ecosystems (desert steppe and temperate steppe). Frequency of Trichoderma spp. was significantly decreased along with increased altitude and only a few strains were isolated from altitudes above 3000 m. The results provided essential information on Trichoderma occurrence and distribution, which should benefit the application of Trichoderma in agriculture.

Contribution to the Knowledge of Mycobiota of the Wielkopolski National Park (W Poland)

The Wielkopolski National Park is located in western Poland, near Poznań City. Its unique postglacial landforms are covered with various (semi)natural and anthropogenic ecosystems. The mycobiota of this Park has been studied for 90 years; however, current state knowledge is still insufficient. In 2018, a few-year- long project on the chorology, richness, and diversity of fungal biota of this area was started. In the first year, 312 taxa of macromycetes were found. Among them, 140 taxa were new for the biota of the Wielkopolski National Park. Five species (<em>Botryobasidium robustius</em>, <em>Hebeloma subtortum</em>, <em>Leccinum brunneogriseolum</em>, <em>Pachyella violaceonigra</em>, and <em>Sistotrema athelioides</em>) were new for Poland, and 26 taxa were new for the Wielkopolska region.

Problems, Limitations, and Challenges in Species Identification of Ascomycota Members on the Basis of ITS Regions

The internal transcribed spacer (ITS) region is regarded as a formal fungal primary barcode with a high probability of the correct identification for a broad group of fungi. ITS sequences have been widely used to determine many fungal species and analysis of rDNA ITS is still one of the most popular tools used in mycology. However, this region is not equally variable in all groups of fungi; therefore, identification may be problematic and result in ambiguous data, especially in some species-rich genera of Ascomycota. For these reasons, identification based on rDNA ITS is usually complemented by morphological observations and analysis of additional genes. Reliable species identification of Ascomycota members is essential in diagnosing plant diseases, verifying air quality and the effectiveness of agronomic practices, or analyzing relationships between microorganisms. Therefore, the present study aimed to verify, using specific examples, the extent to which ITS sequence analysis is useful in species identification of pathogens and saprobionts from Ascomycota and demonstrate problems related to such identification in practice. We analyzed 105 ITS sequences of isolates originating from air and plant material. Basic local alignment search tool (BLASTn) significantly contributed to the reliable species identification of nearly 80% of isolates such as <em>Arthrinium arundinis</em>, <em>Beauveria bassiana</em>, <em>Boeremia exigua</em>, <em>Cladosporium cladosporioides</em>, <em>Epicoccum nigrum</em>, <em>Nigrospora oryzae</em>, <em>Sclerotinia sclerotiorum</em>, or <em>Sordaria fimicola </em>and members of the genera <em>Alternaria </em>and <em>Trichoderma</em>. However, for most isolates, additional morphological observations, information regarding the isolate origin and, where possible, a PCR with species-specific primers were helpful and complementary. Using our practical approach, we determined that ITS-based species identification and comparative analysis with GenBank sequences significantly helps identifying Ascomycota members. However, in many cases, this should be regarded as suggestive of a taxon because the data usually require the use of additional tools to verify the results of such analysis.

Ochraceocephala foeniculi gen. et sp. nov., a new pathogen causing crown rot of fennel in Italy

A new disease of fennel is described from Sicily (southern Italy). Surveys of the disease and sampling were conducted during spring 2017 and 2018 in Adrano and Bronte municipalities (Catania province) where this crop is widely cultivated. Isolations from the margin of symptomatic tissues resulted in fungal colonies with the same morphology. Pathogenicity tests with one isolate of the fungus on 6-month-old plants of fennel reproduced similar symptoms to those observed in nature. Inoculation experiments to assess the susceptibility of six different fennel cultivars to infection by the pathogen showed that the cultivars 'Narciso', 'Apollo', and 'Pompeo' were more susceptible than 'Aurelio', 'Archimede', and 'Pegaso'. Phylogenetic analyses based on a matrix of the internal transcribed spacer (ITS), the large subunit (LSU), and the small subunit (SSU) rDNA regions revealed that the isolates represent a new genus and species within the Leptosphaeriaceae, which is here described as Ochraceocephala foeniculi gen. et sp. nov. This study improves the understanding of this new fennel disease, but further studies are needed for planning effective disease management strategies. According to the results of the phylogenetic analyses, Subplenodomus iridicola is transferred to the genus Alloleptosphaeria and Acicuseptoria rumicis to Paraleptosphaeria.

The genus Melanconis (Diaporthales)

The genus Melanconis (Melanconidaceae, Diaporthales) in the strict sense is here re-evaluated regarding phylogenetic structure, taxonomy, distribution and ecology. Using a matrix of sequences from ITS, LSU, ms204, rpb2, tef1 and tub2, eight species are recognised and their phylogenetic positions are determined. Based on phylogenetic, morphological and geographical differentiation, Melanconis marginalis is subdivided into four subspecies. Melanconis italica is reduced to a subspecies of Melanconis marginalis. The two species Melanconis larissae from Betula sp. and M. pacifica from Alnus rubra are described as new. Melanconis alni and M. stilbostoma are lectotypified and M. alni, M. marginalis and M. stilbostoma are epitypified. All GenBank sequences deposited as Melanconis alni are shown to actually represent M. marginalis and those as M. marginalis belong to the newly described M. pacifica. Currently, Alnus and Betula are the sole host genera of Melanconis. All species and subspecies are (re-)described and illustrated. In addition, the neotypification of Melanconium pterocaryae is here validated.

Linosporopsis, a new leaf-inhabiting scolecosporous genus in Xylariaceae

Based on molecular phylogenetic and morphological evidence, the new genus Linosporopsis (Xylariales) is established for several species previously classified within Linospora (Diaporthales). Fresh collections of Linospora ischnotheca from dead overwintered leaves of Fagus sylvatica and of L. ochracea from dead overwintered leaves of Malus domestica, Pyrus communis, and Sorbus intermedia were isolated in pure culture, and molecular phylogenetic analyses of a multi-locus matrix of partial nuITS-LSU rDNA, RPB2 and TUB2 sequences as well as morphological investigations revealed that both species are unrelated to the diaporthalean genus Linospora, but belong to Xylariaceae sensu stricto. The new combinations Linosporopsis ischnotheca and L. ochracea are proposed, the species are described and illustrated, and their basionyms lecto- and epitypified. Linospora faginea is synonymized with L. ischnotheca. Based on similar morphology and ecology, Linospora carpini and Linospora magnagutiana from dead leaves of Carpinus betulus and Sorbus torminalis, respectively, are also combined in Linosporopsis. The four accepted species of Linosporopsis are illustrated, a key to species is provided and their ecology is discussed.

Isolation and Characterization of Airborne Mushroom Damaging Trichoderma spp. from Indoor Air of Cultivation Houses Used for Oak Wood Mushroom Production Using Sawdust Media

Some species of the Trichoderma genus are reported as the major problem in oak wood mushroom production in Korea. In spite of economic loss by the fungi, scientific information on airborne Trichoderma species is not much available. To generate information for disease management development we analyzed airborne Trichoderma. A total of 1,063 fungal isolates were purely obtained from indoor air sampling of cultivation houses used for oak wood mushroom using sawdust media. Among the obtained isolates, 248 isolates were identified as Trichoderma fungi including T. harzianum, T. atroviride, T. citrinoviride, and T. pseudokoningii, by morphological and molecular analysis. T. harzianum was dominant among the four identified species. All the four Trichoderma species grew fast on solid nutrient media tested (potato dextrose agar [PDA], malt extract agar [MEA], Czapek's Dox + yeast extract agar [CYA] and cornmeal dextrose agar). Compact mycelia growth and mass spore production were better on PDA and CYA. In addition, T. harzianum and T. citrinoviride formed greenish and yellowish mycelium and spores on PDA and CYA. Greenish and yellowish pigment was saturated into PDA only by T. pseudokoningii. These four Trichoderma species could produce extracellular enzymes of sawdust substrate degradation such as β-glucosidase, avicelase, CM-cellulase, amylase, pectinase, xylanase, and protease. Their mycelia inhibited the growth of oak wood mushroom mycelia of two tested cultivars on dual culture assay. Among of eleven antifungal agents tested, benomyl was the best to inhibit the growth of the four Trichoderma species. Our results demonstrate that the airborne Trichoderma fungi need to be properly managed in the cultivation houses for safe mushroom production.

Fungal Systematics and Evolution: FUSE 5

Thirteen new species are formally described: Cortinarius brunneocarpus from Pakistan, C. lilacinoarmillatus from India, Curvularia khuzestanica on Atriplex lentiformis from Iran, Gloeocantharellus neoechinosporus from China, Laboulbenia bernaliana on species of Apenes, Apristus, and Philophuga (Coleoptera, Carabidae) from Nicaragua and Panama, L. oioveliicola on Oiovelia machadoi (Hemiptera, Veliidae) from Brazil, L. termiticola on Macrotermes subhyalinus (Blattodea, Termitidae) from the DR Congo, Pluteus cutefractus from Slovenia, Rhizoglomus variabile from Peru, Russula phloginea from China, Stagonosporopsis flacciduvarum on Vitis vinifera from Italy, Strobilomyces huangshanensis from China, Uromyces klotzschianus on Rumex dentatus subsp. klotzschianus from Pakistan. The following new records are reported: Alternaria calendulae on Calendula officinalis from India; A. tenuissima on apple and quince fruits from Iran; Candelariella oleaginescens from Turkey; Didymella americana and D. calidophila on Vitis vinifera from Italy; Lasiodiplodia theobromae causing tip blight of Dianella tasmanica 'variegata' from India; Marasmiellus subpruinosus from Madeira, Portugal, new for Macaronesia and Africa; Mycena albidolilacea, M. tenuispinosa, and M. xantholeuca from Russia; Neonectria neomacrospora on Madhuca longifolia from India; Nothophoma quercina on Vitis vinifera from Italy; Plagiosphaera immersa on Urtica dioica from Austria; Rinodina sicula from Turkey; Sphaerosporium lignatile from Wisconsin, USA; and Verrucaria murina from Turkey. Multi-locus analysis of ITS, LSU, rpb1, tef1 sequences revealed that P. immersa, commonly classified within Gnomoniaceae (Diaporthales) or as Sordariomycetes incertae sedis, belongs to Magnaporthaceae (Magnaporthales). Analysis of a six-locus Ascomycota-wide dataset including SSU and LSU sequences of S. lignatile revealed that this species, currently in Ascomycota incertae sedis, belongs to Pyronemataceae (Pezizomycetes, Pezizales).