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

Abstract

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.

At least three families of hyphosphere small secreted cysteine‐rich proteins can optimize surface properties to a moderately hydrophilic state suitable for fungal attachment

“…2A), including T. simmonsii, T. afroharzianum, T. harzianum and the putatively new species T. sp. M10 (Cai and Druzhinina, 2021). We did not detect any hfb11 sequences in Harzianum clade species such as T. pleuroti and T. pleuroticola or in the sister clade Virens.…”

Temperature Differentially Influences the Capacity of Trichoderma Species to Induce Plant Defense Responses in Tomato Against Insect Pests

“…Some of these antagonists of phytopathogens, not only contribute to biocontrol, but also provide well-recognized positive effects to the plant, such as improved vegetative-root growth, development, and yield; they also enhance nutrient availability and uptake by the plant (Vinale et al, 2008 ). For example, T. afroharzianum (ex-T. harzianum ; Cai and Druzhinina, 2021 ) strain T22, the active component of a commercial biofungicide product, was also found to improve the plant growth of important horticultural crops, such as lettuce, tomatoes, peppers, ornamentals, and woody crops, and to prevent diseases, both under greenhouse and field conditions (Harman et al, 2004 ; Lorito et al, 2010 ; Woo et al, 2014 ).…”

“…Numerous Trichoderma strains are the key components of commercially available microbial biofungicides (Harman et al, 2004;Woo et al, 2014;Alfiky and Weisskopf, 2021;Ferreira and Musumeci, 2021;Poveda, 2021). Among the 377 Trichoderma species identified, only 20-30 species are found in soils as ecological opportunists saprophytes, associated with the rhizosphere, avirulent to plants, that may be useful in agriculture (Druzhinina et al, 2011;Cai and Druzhinina, 2021). It cannot be generalized that all Trichoderma are extensive root colonizers or that they are endophytes (Howell, 2003;Harman et al, 2004).…”

Bioformulations with Beneficial Microbial Consortia, a Bioactive Compound and Plant Biopolymers Modulate Sweet Basil Productivity, Photosynthetic Activity and Metabolites

“…The microbial biostimulant treatments involved the use of different microorganisms, their components and natural molecules. Nine biostimulant treatments were adopted: (i) Trichoderma afroharzianum strain T22 (ex- Trichoderma harzianum [ 71 ]) commercial formulation of Trianum-P (Koppert Biological Systems, Rotterdam, the Netherlands) implemented at a final concentration of 10 7 spore mL −1 , (ii) Azotobacter chroococcum strain 76A ([ 72 ]; freeze-dried bacterial cells in a final concentration of 10 7 CFU mL −1 ), (iii) 6 pentyl-α-pyrone (6PP) concentration of 10 −6 M (Sigma-Aldrich, Milan, Italy), (iv) biopolymer (BP; diluted in water) composed of carboxymethyl cellulose (CMC), a polyanion derived from cellulose used as a thickener, emulsifier and nutrient carrier in agriculture with the addition of Pluronic F-127 (PF-127), as reported in [ 43 ], (v) T22 (10 6 spores mL −1 ) + 76A (10 7 CFU mL −1 ), (vi) BP + T22 (10 7 spores mL −1 ), (vii) BP + 76A (10 7 CFU mL −1 ), (viii) BP + T22 (10 6 spores mL −1 ) + 76A (10 7 CFU mL −1 ) and (ix) BP + 6PP (10 −6 M); additionally, (x), a control treatment, only water, was administrated at the same volume as the other treatments. The liquid bioformulations with the microorganisms and the metabolite were prepared in water throughout the experiment.…”