Fungal genus Hypocrea/Trichoderma:from barcodes to biodiversity

Hypocrea/Trichoderma is a genus of soil-borne or wood-decaying fungi containing members important to mankind as producers of industrial enzymes and biocontrol agents against plant pathogens, but also as opportunistic pathogens of immuno- compromised humans and animals, while others can cause damage to cultivated mushroom. With the recent advent of a reliable, BarCode-aided identification system for all known taxa of Trichoderma and Hypocrea, it became now possible to study some of the biological fundamentals of the diversity in this fungal genus in more detail. In this article, we will therefore review recent progress in (1) the understanding of the geographic distribution of individual taxa; (2) mechanisms of speciation leading to development of mushroom diseases and facultative human mycoses; and (3) the possible correlation of specific traits of secondary metabolism and molecular phylogeny.

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 standard-ized principles of species recognition,at least in a given taxonomic group.However,in fungi,species delimitation is fre-quently 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 Tricho-derma(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 Interna-tional Subcommission on Taxonomy of Trichoderma www.trich oderm a.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.trich okey.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 short-comings,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 implementa-tion 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.

Review:Global nutrient profiling by Phenotype MicroArrays:a tool complementing genomic and proteomic studies in conidial fungi

Conidial fungi or molds and mildews are widely used in modern biotechnology as producers of antibiotics and other secondary metabolites,industrially important enzymes,chemicals and food.They are also important pathogens of animals including humans and agricultural crops.These various applications and extremely versatile natural phenotypes have led to the constantly growing list of complete genomes which are now available.Functional genomics and proteomics widely exploit the genomic information to study the cell-wide impact of altered genes on the phenotype of an organism and its function.This allows for global analysis of the information flow from DNA to RNA to protein,but it is usually not sufficient for the description of the global phenotype of an organism.More recently,Phenotype MicroArray (PM) technology has been introduced as a tool to characterize the metabolism of a (wild) fungal strain or a mutant.In this article,we review the background of PM applications for fungi and the methodic requirements to obtain reliable results.We also report examples of the versatility of this tool.

The Longibrachiatum Clade of Trichoderma:a revision with new species

The Longibrachiatum Clade of Trichoderma is revised.Eight new species are described(T.aethiopicum,T.capillare,T.flagellatum,T.gillesii,T.gracile,T.pinnatum,T.saturnisporopsis,T.solani).The twenty-one species known to belong to the Longibrachiatum Clade are included in a synoptic key.Trichoderma parareesei and T.effusum are redescribed based on new collections or additional observations.Hypocrea teleomorphs are reported for T.gillesii and T.pinnatum.Previously described species are annotated.

Forecasting the number of species of asexually reproducing fungi(Ascomycota and Basidiomycota)

Asexually reproducing fungi play a significant role in essential processes in managed and wild ecosystems such as nutrients cycling and multitrophic interactions.A large number of such taxa are among the most notorious plant and animal pathogens.In addition,they have a key role in food production,biotechnology and medicine.Taxa without or rare sexual reproduction are distinguished based on their sporulating structures and conidiomata in traditional morphology-based taxonomy.The number,variation and diversity of asexually reproducing taxa are insufficiently known,even though fungi capable of asexual reproduction may provide an untapped,rich biological resource for future exploitation.Currently,ca.30,000 asexual species belonging to ca.3800 genera have been reported(including 1388 coelomycetous and 2265 hyphomycetous genera).Recent reports(2017–2020)reiterate that the number of asexually producing fungi is higher than the number of frequently sexually-reproducing fungi.With the advent of molecular tools and the abandonment of the dual nomenclature system for pleomorphic fungi,priority criteria were established and revisited in the latest outline of fungi and fungus-like taxa.However,species numbers and taxonomic boundaries of pleomorphic taxa and their synanamorphs or synasexual morphs have yet to be addressed.The number of species of speciose genera(e.g.Alternaria,Aspergillus,Cercospora,Fusarium,Phoma and Pseudocercospora),cryptic species,species of pleomorphic genera,less studied life modes(such as lichenicolous taxa,taxa from extreme environments)and species from biodiversity-rich areas still need evaluation to achieve more reliable estimates of their diversity.This paper discusses the current knowledge on the matter,with diversity estimates,and potential obstacles in several chapters on(1)speciose genera;(2)pleomorphic genera;(3)cryptic species;(4)well-studied but insufficiently resolved taxa,e.g.leaf inhabiting species,marine fungi,(5)less studied life modes,e.g.lichenicolous,rock-inhabiting fungi,insect-associated and yeast-forming taxa and(6)species from biodiversity-rich areas.