This article provides an outline of the classification of the kingdom Fungi (including fossil fungi. i.e. dispersed spores, mycelia, sporophores, mycorrhizas). We treat 19 phyla of fungi. These are Aphelidiomycota, Ascomycota, Basidiobolomycota, Basidiomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Entorrhizomycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota. The placement of all fungal genera is provided at the class-, order- and family-level. The described number of species per genus is also given. Notes are provided of taxa for which recent changes or disagreements have been presented. Fungus-like taxa that were traditionally treated as fungi are also incorporated in this outline (i.e. Eumycetozoa, Dictyosteliomycetes, Ceratiomyxomycetes and Myxomycetes). Four new taxa are introduced: Amblyosporida ord. nov. Neopereziida ord. nov. and Ovavesiculida ord. nov. in Rozellomycota, and Protosporangiaceae fam. nov. in Dictyosteliomycetes. Two different classifications (in outline section and in discussion) are provided for Glomeromycota and Leotiomycetes based on recent studies. The phylogenetic reconstruction of a four-gene dataset (18S and 28S rRNA, RPB1, RPB2) of 433 taxa is presented, including all currently described orders of fungi.

https://biblio.ugent.be/publication/8660838/file/8660843.pdf

Outline of Fungi and fungus-like taxa

The Colletotrichum boninense species complex

The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for "hot topic" research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei, T. atroviride, and T. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N-linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma, and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway.

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

Control plant-parasitic nematodes with Trichoderma species and nematode-trapping fungi: The role of chi18-5 and chi18-12 genes in nematode egg-parasitism

The use of Trichoderma isolates with efficient antagonistic activity represents a potentially effective and alternative disease management strategy to replace health hazardous chemical control. In this context, twenty isolates were obtained from tomato rhizosphere and evaluated by their antagonistic activity against four fungal pathogens (Fusarium oxysporum f. sp. lycopersici, Alternaria alternata, Colletotrichum gloeosporoides and Rhizoctonia solani). The production of extracellular cell wall degrading enzymes of tested isolates was also measured. All the isolates significantly reduced the mycelial growth of tested pathogens but the amount of growth reduction varied significantly as well. There was a positive correlation between the antagonistic capacity of Trichoderma isolates towards fungal pathogens and their lytic enzyme production. The Trichoderma isolates were initially sorted according to morphology and based on the translation elongation factor 1-α gene sequence similarity, the isolates were designated as Trichoderma harzianum, T. koningii, T. asperellum, T. virens and T. viride. PCA analysis explained 31.53, 61.95, 62.22 and 60.25% genetic variation among Trichoderma isolates based on RAPD, REP-, ERIC- and BOX element analysis, respectively. ERG-1 gene, encoding a squalene epoxidase has been used for the first time for diversity analysis of antagonistic Trichoderma from tomato rhizosphere. Phylogenetic analysis of ERG-1 gene sequences revealed close relatedness of ERG-1sequences with earlier reported sequences of Hypocrea lixii, T. arundinaceum and T. reesei. However, ERG-1 gene also showed heterogeneity among some antagonistic isolates and indicated the possibility of occurrence of squalene epoxidase driven triterpene biosynthesis as an alternative biocontrol mechanism in Trichoderma species.

https://link.springer.com/content/pdf/10.1186%2Fs40064-016-3657-4.pdf

Identification, characterization and phylogenetic analysis of antifungal Trichoderma from tomato rhizosphere.

This chapter attempts to summarize the recently available and rapidly increasing amount of information in the literature about the occurrence and biodiversity of Trichoderma species in different ecological habitats. Members of the genus are common in soil and rhizosphere of plants in natural and agricultural fields and forests and on decaying wood. They are also occurring in the air, settled dust and different water-related habitats including marine environments and drinking water. Furthermore, certain species are known as endophytes of plants, colonizers of mushroom-related natural and artificial substrata and facultative pathogens of humans, demonstrating a high adaptability to various ecological niches.

Biodiversity of the Genus Hypocrea/Trichoderma in Different Habitats

The orchid collection of the ELTE Botanical Garden, Budapest, Hungary was monitored for airborne fungi using viable and non-viable air-sampling methods (Hirst-type and a 3-stage Andersen sampler) with three different culture media. A new culture method was also applied to identify fungal spores from Hirst-type samples. The aim of this study was to determine the diversity, human- and phytopathological potential of the air spora. To find out sources of airborne fungi, samples were collected from the air in an adjacent greenhouse and outdoors, and from necrotic plants. A total of 58 genera were found in the air samples. Cladosporium and Penicillium spp. were common members of the airborne biota. A high proportion (27.5%) of identified genera may be presented as a member of microbial consortium associated with the orchids. Airborne fungi potentially pathogenic to humans were also detected. One species, Zygosporium masonii, was new to Hungary. Statistical analysis indicated that conditions of sampling had significant effects. The principal component analysis elucidated the three principal components representing 75.34% of the total variance; the clusters of variables were related to the three types of culture media. Relative abundance of small-sized spores was high, presumably because of the fungal species composition and accelerated sedimentation of large spores in still air. Apparently, in the studied orchid greenhouse, a specific mycobiota developed due to the climate and hosts (Orchideaceae) grown there.

The air spora of an orchid greenhouse

One hundred and sixteen Trichoderma isolates were collected from chopped roots of winter wheat of five agricultural fields in the Great Hungarian Plain. The isolates were identified by the sequence analysis of the internal transcribed spacer (ITS) region with TrichOKEY 2.0 and BLAST similarity searches. The Trichoderma species detected in the samples were T. atroviride, T. brevicompactum, T. gamsii, T. harzianum, T. koningiopsis/T. ovalisporum, T. longibrachiatum/H. orientalis, T. pleuroticola, T. rossicum, T. spirale, T. tomentosum/T. cerinum and T. virens. Benefi- cial taxa widely used as biocontrol agents against plant pathogenic fungi (e.g. T. harzianum, T. virens, T. atroviride) could be isolated from the samples examined during this study, indicating that the winter wheat rhizosphere may be a rich source of potential biocontrol isolates. Several species could be characterized with well-defined isoenzyme patterns during cellulose-acetate electrophoresis, suggesting that this method can be used for the analysis of biochemical diversity between and within particular species of the genus Trichoderma.

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Genetic and biochemical diversity among Trichoderma isolates in soil samples from winter wheat fields of the great Hungarian plain

A composite soil bioinoculant containing beneficial bacteria and fungi was developed for biocontrol of plant pathogens, phosphorous mobilization, stem degradation, humification, and nitrogen fixation. A Trichoderma asperellum isolate with outstanding in vitro antagonistic abilities toward a series of plant pathogenic fungi was included as a potential biocontrol component. The selected strain was also shown to promote growth and increase photosynthetic activity of tomato plants. For phosphorous mobilization and stem degradation, a Trichoderma atrobrunneum strain was selected, which produced cellulose-degrading enzymes even in the absence of stem residues, while this ability increased 10–15-fold in the presence of ground maize stem. The strain was also shown to produce large amounts of enzymes liberating organically bound phosphorous, as well as cellulase and xylanase activities in solid-state fermentation on various plant residues. A Streptomyces albus strain with excellent peroxidase-producing abilities was selected as a potential humus-producing component, while an Azotobacter vinelandii strain with the potential to provide excess nitrogen for crops was included for nitrogen fixation. The assembled soil bioinoculant had positive effect on the uptake of certain important macro- and microelements (potassium, sodium, and manganese) from the soil by field-grown tomato plants. The applied screening strategy proved to be applicable for the assembly of a composite soil bioinoculant with notable application potentials.

https://www.mdpi.com/2073-4395/10/2/220/pdf

A composite bioinoculant based on the combined application of beneficial bacteria and fungi

Mycoceros antennatissimus gen. et sp. nov. is described and illustrated from pollen grains deposited on the bark of Elaeagnus angustifolia and Platanus × acerifolia in Hungary. This fungus is shown to capture pollen grains by its three-dimensional shape. It clearly shows seasonality and appears to be rare. The following factors determine its ecological niche: (1) the availability of fresh Pinaceae pollen grains deposited from the air on the bark of a nearby standing angiosperm tree with (2) water-retaining spongious bark, and (3) rainy weather. Conidia are mainly dispersed by stemflow rainwater, while they hardly become airborne. Direct polymerase chain reaction (PCR) from single conidia made it possible to perform molecular phylogenetic investigation in order to clarify its taxonomic relationship within the Ascomycota.

/pdf/mycoceros-antennatissimus-gen-et-sp-nov-a-mitosporic-fungus-gdooj6xr0a.pdf

Péter Körmöczi

Papers

Biodiversity of the Genus Hypocrea/Trichoderma in Different Habitats

The air spora of an orchid greenhouse

Genetic and biochemical diversity among Trichoderma isolates in soil samples from winter wheat fields of the great Hungarian plain

A composite bioinoculant based on the combined application of beneficial bacteria and fungi

Mycoceros antennatissimus gen. et sp. nov.: a mitosporic fungus capturing pollen grains