Hypocrea/Trichodermaspecies with pachybasium-like conidiophores: teleomorphs forT. minutisporumandT. polysporumand their newly discovered relatives

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.

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.

Molecular Identification of Trichoderma reesei

Fungi comprise one of the most diverse groups of eukaryotes with many cryptic species that are difficult to identify. In this chapter, we detail a protocol for the molecular identification of the most industrially relevant species of Trichoderma-T. reesei. We first describe how a single spore culture should be isolated and used for the sequencing of the diagnostic fragment of the tef1 gene. Then, we provide two alternative methods that can be used for molecular identification and offer the diagnostic oligonucleotide hallmark of the tef1 sequence that is present in sequences of all T. reesei strains known to date and that is therefore suitable for reliable and straightforward identification.

Trichoderma cyanodichotomus sp. nov., a new soil-inhabiting species with a potential for biological control

During a biodiversity survey of Trichoderma (Ascomycota, Hypocreales, Hypocreaceae) in coastal and lake wetlands of China, a new species, Trichoderma cyanodichotomus, was isolated from Dongting Lake wetland of Hunan province. The strain TW21990-1 was characterized as having two types of conidia and producing a distinct blue–green pigment on potato dextrose agar and cornmeal dextrose agar. The taxonomic position was analyzed using three molecular markers, internal transcribed spacer rDNA, translation elongation factor 1-alpha, and RNA polymerase II subunit B, revealing less than 95.0% homology with all known Trichoderma species. The combined phylogenetic tree further identified T. cyanodichotomus as an independent subgroup belonging to Section Pachybasium, with no close relatives. In vitro antagonistic activity by dual-culture assay exhibited broad inhibition against various plant pathogens, including Botryosphaeria dothidea, Pythium aphanidermatum, Rhizoctonia solani, and Verticillium dahliae. In addition, TW21990-1 demonstrated moderate hydrolase activity of cellulase, chitinase, β-1,3-glucanase, and protease, which might be involved in mycoparasitism. Greenhouse experiments showed strong biocontrol effects against tomato damping-off incited by P. aphanidermatum, together with increased seedling height and weight gain. The identification of T. cyanodichotomus will provide useful information for sufficient utilization of fungal resources.

Accepted Trichoderma names in the year 2015

A list of 254 names of species and two names of varieties in Trichoderma with name or names against which they are to be protected, following the ICN (Melbourne Code, Art. 14.13), is presented for consideration by the General Committee established by the Congress, which then will refer them to the Nomenclature Committee for Fungi (NCF). This list includes 252 species, one variety and one form. Two new names are proposed: T. neocrassum Samuel (syn. Hypocrea crassa P. Chaverri & Samuels), T. patellotropicum Samuels (syn. Hypocrea patella f. tropica Yoshim. Doi). The following new combinations in Trichoderma are proposed: T. brevipes (Mont.) Samuels, T. cerebriforme (Berk.) Samuels, T. latizonatum (Peck) Samuels, and T. poronioideum (A. Möller) Samuels.

The following species are lectotypified: T. americanum (Canham) Jaklitsch & Voglmayr, Gliocladium flavofuscum J.H. Miller, Giddens & A.A. Foster, T. inhamatum Veerkamp & W. Gams, T. konilangbra Samuels, O. Petrini & C.P. Kubicek, T. koningii Oudem., T. pezizoides (Berk. & Broome) Jaklitsch & Voglmayr, T. sulphureum (Schwein.) Jaklitsch & Voglmayr and T. virens (J.H. Miller, Giddens & A.A. Foster) Arx. Epitypes are proposed for the following species: T. albocorneum (Yoshim. Doi) Jaklitsch & Voglmayr, T. albofulvum (Berk. & Broome) Jaklitsch & Voglmayr, T. atrogelatinosum (Dingley) Jaklitsch & Voglmayr, T. corneum (Pat.) Jaklitsch & Voglmayr, T. cornu-damae (Pat.) Z.X. Zhu & W.Y. Zhuang, T. flaviconidium (P. Chaverri, Druzhinina & Samuels) Jaklitsch & Voglmayr, T. hamatum (Bonord.) Bain., T. hunua (Dingley) Jaklitsch & Voglmayr, T. patella (Cooke & Peck) Jaklitsch & Voglmayr, Hypocrea patella f. tropica Yoshim. Doi, T. polysporum (Link) Rifai, T. poronioideum (A. Möller) Samuels T. semiorbis (Berk.) Jaklitsch & Voglmayr, T. sulphureum (Schwein.) Jaklitsch & Voglmayr, and T. tropicosinense (P.G. Liu) P.G. Liu, Z.X. Zhu & W.Y. Zhuang.

Intact-cell MALDI-TOF mass spectrometry analysis of peptaibol formation by the genus Trichoderma/Hypocrea: can molecular phylogeny of species predict peptaibol structures?

Peptaibols are characteristic linear alpha-aminoisobutyrate-containing peptides produced by certain Ascomycetes, especially of the genus Hypocrea/Trichoderma [Hypocrea and Trichoderma are the names for the teleo- and anamorph forms of the same taxon; where known to occur in nature, the teleomorph is used to name the species. To aid the inexperienced reader, both names (the less well known one in parentheses) are given at the first mention of each species.] Here we have investigated whether phylogenetic relationships within Trichoderma permit a prediction of the peptaibol production profiles. To this end, representative strains from a third (28) of the known species of Trichoderma, identified by the sequences of diagnostic genes and covering most clades of the established multilocus phylogeny of Trichoderma/Hypocrea, were investigated by intact-cell MALDI-TOF mass spectrometry. Peptaibols were detected in all strains, and some strains were found to produce up to five peptide families of different sizes. Comparison of the data with phylogenies derived from rRNA spacer regions (ITS1 and 2) and RNA polymerase subunit B (rpb2) gene sequences did not show a strict correlation with the types and sequences of the peptaibols produced, but the production of some groups of peptaibols appears to be found only in some clades or sections of the genus, which could be used for more targeted screening of novel compounds of this type. In an analysis of peptaibol structures, we have defined conserved key positions and have further identified and compared sequences of the corresponding adenylate domains within non-ribosomal peptide synthetases producing trichovirins, paracelsins and atroviridins. These phylogenies are not concordant with those of their producers Hypocrea virens, Hypocrea jecorina and Hypocrea atroviridis as obtained from ITS1 and 2, and rpb2, respectively, and therefore hint at a complex history of peptaibol diversity.

Characterization of AfpA, an alkaline foam protein from cultures of Fusarium culmorum and its identification in infected malt

AIMS

The objective of this study was to evaluate the capability of Fusarium culmorum to produce non-hydrophobin surface-active proteins in vitro, to isolate and characterize such proteins from liquid cultures, to analyse their effect on overfoaming (gushing) of beer and to elucidate their prevalence in pure cultures and infected malt.

METHODS AND RESULTS

A 20 kDa protein was isolated from liquid cultures of F. culmorum BBA 62182 upon enrichment by foaming. BLAST search with N-terminal and internal sequences of the protein revealed high homology with a hypothetical protein predicted within the F. graminearum PH1 genome sequence. Oligonucleotide primers designed to bind 30 nt upstream and downstream of the predicted gene were used to amplify a 695 nt PCR fragment from genomic DNA of F. culmorum BBA 62182. Cloning and sequencing of the product revealed a 635 nt open reading frame which had 98% homology to the predicted F. graminearium PH1 gene code. Removal of a 59 nt intron and translation resulted in a 191 amino acid protein of 20.754 kDa with a calculated pI of 9.1. Amino acids obtained by Edman sequencing of fragments within the 20 kDa protein were 100% homologous with the sequence deduced from the DNA sequence. According to its properties, the new protein was termed alkaline foam protein A (AfpA). Sequence comparison revealed some homologies with proteins in Emericella nidulans, which are involved in phialide development and response to antifungal agents. Homologies with other hypothetical fungal proteins suggest a new group of proteins, for which we suggest the name fungispumins. Addition of AfpA to beer showed that overfoaming (gushing) is not induced in stable beer but can significantly enhance this effect in beer showing moderate gushing. Use of a polyclonal anti-AfpA antibody in a Western blot revealed that the protein is produced by various F. culmorum strains and also by F. graminearum, but not by other Fusarium spp. tested. PCR testing of 69 species of Fusarium and Trichoderma reesei with a gene specific primer pair revealed that the gene may be present exclusively in F. culmorum, F. graminearum, F. cerealis, F. lunulosporum and F. oxysporum f. sp . dianthi. Immunochemical detection of AfpA in malts artificially inoculated with F. culmorum and F. graminearum showed that the protein was present in gushing inducing malts (gushing test) but absent in malts which were negative in a gushing test.

CONCLUSIONS

AfpA is a member of a new protein class, fugispumins, and can be isolated from pure liquid cultures of F. culmorum. A homologous protein is synthesised by F. graminearum. The protein is produced in contaminated malt and enhances gushing of beer. The gene coding for AfpA is restricted to Fusarium species presumably involved in the induction of beer gushing.

SIGNIFICANCE AND IMPACT OF THE STUDY

We describe a new class of proteins, fungispumins, the natural function of which remains to be elucidated. Findings add useful information to research on the mechanisms involved in foam stability of beer. AfpA may be useful as a marker for gushing in future quality control applications for the brewing industry.

Two new species of Trichoderma from Yunnan, China

Two new species of the fungal genus Trichoderma, Trichoderma compactum and Trichoderma yunnanense, isolated from rhizosphere of tobacco in Yunnan Province, China are described based on morphological characters and phylogenetic analyses of nucleotide sequences. Our DNA sequences included the internal transcribed spacer (ITS) regions of the rDNA cluster (ITS1 and ITS2), and partial sequences of the translation elongation factor 1-alpha (tef1) and a fragment of the gene coding for endochitinase 42 (ech42). The analyses show that T. compactum belongs to the Harzianum clade, and T. yunnanense belongs to the Hamatum clade.

Rapid identification of clinical Trichoderma longibrachiatum isolates by cellulose-acetate electrophoresis-mediated isoenzyme analysis

Cellulose-acetate electrophoresis was used to investigate isoenzyme polymorphism among ten clinical and 11 non-clinical isolates of Trichoderma. Initial testing of 13 enzyme systems for activity and resolution of bands showed that seven were appropriate for identifying the different species. Each of the enzyme systems investigated (glucose-6-phosphate dehydrogenase, glucose-6-phosphate isomerase, 6-phosphogluconate dehydrogenase, peptidases A, B and D, and phosphoglucomutase) was diagnostic for at least one species. On the basis of the results of isoenzyme analysis, several isolates identified originally as Trichoderma pseudokoningii, T. koningii or T. citrinoviride were re-identified as T. longibrachiatum, in agreement with sequence analysis data for the internal transcribed spacer region of the isolates. The availability of a quick, inexpensive and reliable diagnostic tool for the identification of T. longibrachiatum isolates is important, as most clinical Trichoderma isolates belong to T. longibrachiatum. Furthermore, as many different enzyme systems are available, the method may also be suitable for the identification of other clinically relevant fungal species.

An oligonucleotide barcode for species identification in Trichoderma and Hypocrea

One of the biggest obstructions to studies on Trichoderma has been the incorrect and confused application of species names to isolates used in industry, biocontrol of plant pathogens and ecological surveys, thereby making the comparison of results questionable. Here we provide a convenient, on-line method for the quick molecular identification of Hypocrea/Trichoderma at the genus and species levels based on an oligonucleotide barcode: a diagnostic combination of several oligonucleotides (hallmarks) specifically allocated within the internal transcribed spacer 1 and 2 (ITS1 and 2) sequences of the rDNA repeat. The barcode was developed on the basis of 979 sequences of 88 vouchered species which displayed in total 135 ITS1 and 2 haplotypes. Oligonucleotide sequences which are constant in all known ITS1 and 2 of Hypocrea/Trichoderma but different in closely related fungal genera, were used to define genus-specific hallmarks. The library of species-, clade- and genus-specific hallmarks is stored in the MySQL database and integrated in the TrichOKey v. 1.0 - barcode sequence identification program with the web interface located on . TrichOKey v. 1.0 identifies 75 single species, 5 species pairs and 1 species triplet. Verification of the DNA-barcode was done by a blind test on 53 unknown isolates of Trichoderma, collected in Central and South America. The obtained results were in a total agreement with phylogenetic identification based on tef1 (large intron), NCBI BLAST of vouchered records and postum morphological analysis. We conclude that oligonucleotide barcode is a powerful tool for the routine identification of Hypocrea/Trichoderma species and should be useful as a complement to traditional methods.

Species concepts and biodiversity in Trichoderma and Hypocrea: from aggregate species to species clusters?

Trichoderma/Hypocrea 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 immunocompromised humans. Species identification, while essential in view of the controversial properties of taxa of this genus, has been problematic by traditional methods. Here we will present a critical survey of the various identification methods in use. In addition, we will present an update on the taxonomy and phylogeny of the 88 taxa (which occur as 14 holomorphs, 49 teleomorphs and 25 anamorphs in nature) of Trichoderma/Hypocrea that have been confirmed by a combination of morphological, physiological and genetic approaches.