Various Trichoderma species possess significance in agricultural systems as biofertilizers or biocontrol agents (BCAs). Besides these beneficial features, certain Trichoderma species can also act as agricultural pests, causing the green mold disease of cultivated mushrooms. This double-faced nature of the genus in agricultural environments points at the importance of proper monitoring tools, which can be used to follow the presence and performance of candidate as well as patented and/or registered biocontrol strains, to assess the possible risks arising from their application, but also to track harmful, unwanted Trichoderma species like the green molds in mushroom growing facilities. The objective of this review is to discuss the molecular tools available for the species- and strain-specific monitoring of Trichoderma, ranging from immunological approaches and fingerprinting tools to exogenous markers, specific primers used in polymerase chain reaction (PCR) as well as “omics” approaches.

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.

Previously, severe green mould infections could be attributed mainly to Trichoderma aggressivum Samuels & W. Gams, as well as T. pleuroti S.H. Yu & M.S. Park and T. pleuroticola S.H. Yu & M.S. Park in the case of Agaricus bisporus (J.E. Lange) Imbach (button mushroom) and Pleurotus ostreatus (Jacq.) P. Kumm. (oyster mushroom), respectively. The purpose of our study was the examination of green mould agents deriving from the growing facilities of button mushroom, oyster mushroom and shiitake (Lentinula edodes (Berk.) Pegler) located in various countries of Europe, and initially classified into the Trichoderma harzianum Rifai species complex (THSC). Species identification was carried out using the multilocus sequence typing analysis of the internal transcribed spacer regions, as well as translation elongation factor 1-alpha, calmodulin and RNA polymerase B subunit II gene sequences. In vitro confrontation assays were applied to test the aggressiveness of the isolates towards mushrooms, while the effect of commercial fungicides on the growth of the strains was examined by the macrodilution method. Six Trichoderma species, namely T. afroharzianum P. Chaverri, F.B. Rocha, Degenkolb & Druzhin., T. atrobrunneum F.B. Rocha, P. Chaverri & Jaklitsch, T. guizhouense Q.R. Li, McKenzie & Yong Wang, T. harzianum sensu stricto, T. pollinicola F. Liu & L. Cai and T. simmonsii P. Chaverri, F.B. Rocha, Samuels, Degenkolb & Jaklitsch were detected in the different samples, with T. harzianum, T. pollinicola and T. simmonsii being the most aggressive. Prochloraz was found to have strong in vitro inhibitory effect on mycelial growth on most strains, however, T. simmonsii isolates showed remarkable tolerance to it. Our data suggest that T. harzianum and T. simmonsii may also be considered as potential causal agents of mushroom green mould.

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The phylogeny, identification, and characterization of 33 B. cereus sensu lato isolates originating from 17 agricultural soils from 11 countries were analyzed on the basis of whole genome sequencing. Phylogenetic analyses revealed all isolates are divided into six groups, which follows the generally accepted phylogenetic division of B. cereus sensu lato isolates. Four different identification methods resulted in a variation in the identity of the isolates, as none of the isolates were identified as the same species by all four methods—only the recent identification method proposed directly reflected the phylogeny of the isolates. This points to the importance of describing the basis and method used for the identification. The presence and percent identity of the protein product of 19 genes potentially involved in pathogenicity divided the 33 isolates into groups corresponding to phylogenetic division of the isolates. This suggests that different pathotypes exist and that it is possible to differentiate between them by comparing the percent identity of proteins potentially involved in pathogenicity. This also reveals that a basic link between phylogeny and pathogenicity is likely to exist. The geographical distribution of the isolates is not random: they are distributed in relation to their division into the six phylogenetic groups, which again relates to different ecotypes with different temperature growth ranges. This means that we find it easier to analyze and understand the results obtained from the 33 B. cereus sensu lato isolates in a phylogenetic, patho-type and ecotype-oriented context, than in a context based on uncertain identification at the species level.