Soil health, and the closely related terms of soil quality and fertility, is considered as one of the most important characteristics of soil ecosystems. The integrated approach to soil health assumes that soil is a living system and soil health results from the interaction between different processes and properties, with a strong effect on the activity of soil microbiota. All soils can be described using physical, chemical, and biological properties, but adaptation to environmental changes, driven by the processes of natural selection, are unique to the latter one. This mini review focuses on fungal biodiversity and its role in the health of managed soils as well as on the current methods used in soil mycobiome identification and utilization next generation sequencing (NGS) approaches. The authors separately focus on agriculture and horticulture as well as grassland and forest ecosystems. Moreover, this mini review describes the effect of land-use on the biodiversity and succession of fungi. In conclusion, the authors recommend a shift from cataloging fungal species in different soil ecosystems toward a more global analysis based on functions and interactions between organisms.

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Fungal Biodiversity and Their Role in Soil Health.

The plant-Trichoderma-pathogen triangle is a complicated web of numerous processes Trichoderma spp are avirulent opportunistic plant symbionts In addition to being successful plant symbiotic organisms, Trichoderma spp also behave as a low cost, effective and ecofriendly biocontrol agent They can set themselves up in various patho-systems, have minimal impact on the soil equilibrium and do not impair useful organisms that contribute to the control of pathogens This symbiotic association in plants leads to the acquisition of plant resistance to pathogens, improves developmental processes and yields and promotes absorption of nutrient and fertilizer use efficiency Among other biocontrol mechanisms, antibiosis, competition and mycoparasitism are among the main features through which microorganisms, including Thrichoderma, react to the presence of other competitive pathogenic organisms, thereby preventing or obstructing their development Stimulation of every process involves the biosynthesis of targeted metabolites like plant growth regulators, enzymes, siderophores, antibiotics, etc This review summarizes the biological control activity exerted by Trichoderma spp and sheds light on the recent progress in pinpointing the ecological significance of Trichoderma at the biochemical and molecular level in the rhizosphere as well as the benefits of symbiosis to the plant host in terms of physiological and biochemical mechanisms From an applicative point of view, the evidence provided herein strongly supports the possibility to use Trichoderma as a safe, ecofriendly and effective biocontrol agent for different crop species

https://www.mdpi.com/2223-7747/9/6/762/pdf

Trichoderma: The “Secrets” of a Multitalented Biocontrol Agent

Plants interact with root microbes via chemical signaling, which modulates competence or symbiosis. Although several volatile organic compounds (VOCs) from fungi may affect plant growth and development, the signal transduction pathways mediating VOC sensing are not fully understood. 6-pentyl-2H-pyran-2-one (6-PP) is a major VOC biosynthesized by Trichoderma spp. which is probably involved in plant-fungus cross-kingdom signaling. Using microscopy and confocal imaging, the effects of 6-PP on root morphogenesis were found to be correlated with DR5:GFP, DR5:VENUS, H2B::GFP, PIN1::PIN1::GFP, PIN2::PIN2::GFP, PIN3::PIN3::GFP and PIN7::PIN7::GFP gene expression. A genetic screen for primary root growth resistance to 6-PP in wild-type seedlings and auxin- and ethylene-related mutants allowed identification of genes controlling root architectural responses to this metabolite. Trichoderma atroviride produced 6-PP, which promoted plant growth and regulated root architecture, inhibiting primary root growth and inducing lateral root formation. 6-PP modulated expression of PIN auxin-transport proteins in a specific and dose-dependent manner in primary roots. TIR1, AFB2 and AFB3 auxin receptors and ARF7 and ARF19 transcription factors influenced the lateral root response to 6-PP, whereas EIN2 modulated 6-PP sensing in primary roots. These results indicate that root responses to 6-PP involve components of auxin transport and signaling and the ethylene-response modulator EIN2.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.13725

The volatile 6-pentyl-2H-pyran-2-one from Trichoderma atroviride regulates Arabidopsis thaliana root morphogenesis via auxin signaling and ETHYLENE INSENSITIVE 2 functioning.

Trichoderma species are soil-borne filamentous fungi widely utilized for their many plant health benefits, such as conferring improved growth, disease resistance and abiotic stress tolerance to their hosts. Many Trichoderma species are able to produce the auxin phytohormone indole-3-acetic acid (IAA), and its production has been suggested to promote root growth. Here we show that the production of IAA is strain dependent and diverse external stimuli are associated with its production. In in vitro assays, Arabidopsis primary root length was negatively affected by the interaction with some Trichoderma strains. In soil experiments, a continuum effect on plant growth was shown and this was also strain dependent. In plate assays, some strains of Trichoderma spp. inhibited the expression of the auxin reporter gene DR5 in Arabidopsis primary roots but not secondary roots. When Trichoderma spp. and A. thaliana were physically separated, enhancement of both shoot and root biomass, increased root production and chlorophyll content were observed, which strongly suggested that volatile production by the fungus influenced the parameters analyzed. Trichoderma strains T. virens Gv29.8, T. atroviride IMI206040, T. sp. "atroviride B" LU132, and T. asperellum LU1370 were demonstrated to promote plant growth through volatile production. However, contrasting differences were observed with LU1370 which had a negative effect on plant growth in soil but a positive effect in plate assays. Altogether our results suggest that the mechanisms and molecules involved in plant growth promotion by Trichoderma spp. are multivariable and are affected by the environmental conditions.

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Environmental growth conditions of Trichoderma spp. affects indole acetic acid derivatives, volatile organic compounds, and plant growth promotion

Mechanisms underlying the protective effects of beneficial fungi against plant diseases

Seventy-seven headspaceTrichoderma isolates belonging to eight species—T. atroviride, T. citrinoviride, T. hamatum, T. harzianum, T. koningii, T. viride, T. viridescens, and T. virens—were screened for their ability to produce 6-n-pentyl-2H-pyran-2-one (6-PAP) and other volatiles using solid phase microextraction (SPME) coupled to gas chromatography–mass spectrometry (GC-MS). Intra- and interspecies variability was demonstrated in the 6-PAP synthesis. The most efficient producer of 6-PAP on potato dextrose agar (PDA) was T. atroviride. However, the variation in 6-PAP synthesis differed significantly among strains of this species, the lowest value being 33.4 μg (strain AN212), whereas the highest reached 1,426 μg per culture for strain AN35. Also, T. viridescens produced significant amounts of 6-PAP (200.1–526.3 μg for 11 out of 12 strains). Moderate producers were isolates belonging to T. hamatum (up to 155 μg) and T. citrinoviride (up to 200 μg). Trichoderma viride isolates showed very little production of 6-PP on PDA. No 6-PAP formation was detected in cultures of 25 isolates belonging to three species, T. koningii, T. harzianum, and T. virens. Trichoderma atroviride AN35, as the most efficient producer of 6-PAP, was selected to observe the dynamics of 6-PAP formation during growth on PDA at 20 °C for 6 days. A radical increase in 6-PAP production started after the fourth day of incubation, and the maximum expression was achieved in the final phase of the experiments, 6 days after inoculation. Apart from 6-PAP, over 40 other volatile compounds were detected in the survey of Trichoderma species. Among them, the most commonly produced substrates were 1-octene-3-ol, isoamyl alcohol, 3-octanone, cyclohept-3-en-1-one, 2-pentylfuran, linalol isobutyrate, toluene, D-limonene, and α-bergamotene. Seventeen of the detected compounds have never previously been reported as a secondary metabolite of Trichoderma.

https://link.springer.com/content/pdf/10.1007%2Fs11557-013-0942-2.pdf

Formation of 6-n-pentyl-2H-pyran-2-one (6-PAP) and other volatiles by different Trichoderma species

The degradation of native cellulose to glucose monomers is a complex process, which requires the synergistic action of the extracellular enzymes produced by cellulolytic microorganisms. Among fungi, the enzymatic systems that can degrade native cellulose have been extensively studied for species belonging to the genera of Trichoderma. The majority of the cellulolytic enzymes described so far have been examples of Trichoderma reesei, extremely specialized in the efficient degradation of plant cell wall cellulose. Other Trichoderma species, such as T. harzianum, T. koningii, T. longibrachiatum, and T. viride, known for their capacity to produce cellulolytic enzymes, have been isolated from various ecological niches, where they have proved successful in various heterotrophic interactions. As saprotrophs, these species are considered to make a contribution to the degradation of lignocellulosic plant material. Their cellulolytic potential is also used in interactions with plants, especially in plant root colonization. However, the role of cellulolytic enzymes in species forming endophytic associations with plants or in those existing in the substratum for mushroom cultivation remains unknown. The present review discusses the current state of knowledge about cellulolytic enzymes production by Trichoderma species and the encoding genes, as well as the involvement of these proteins in the lifestyle of Trichoderma.

The significance of cellulolytic enzymes produced by Trichoderma in opportunistic lifestyle of this fungus.

Cremenolide, a new antifungal, 10-member lactone from Trichoderma cremeum with plant growth promotion activity.

The aim of this study was to explore the species diversity of Trichoderma obtained from samples of wood collected in the forests of the Gorce Mountains (location A), Karkonosze Mountains (location B) and Tatra Mountains (location C) in Central Europe and to examine the cellulolytic and xylanolytic activity of these species as an expression of their probable role in wood decay processes. The present study has led to the identification of the following species and species complex: Trichoderma atroviride P. Karst., Trichoderma citrinoviride Bissett, Trichoderma cremeum P. Chaverri & Samuels, Trichoderma gamsii Samuels & Druzhin., Trichoderma harzianum complex, Trichoderma koningii Oudem., Trichoderma koningiopsis Samuels, C. Suarez & H.C. Evans, Trichoderma longibrachiatum Rifai, Trichoderma longipile Bissett, Trichoderma sp. (Hypocrea parapilulifera B.S. Lu, Druzhin. & Samuels), Trichoderma viride Schumach. and Trichoderma viridescens complex. Among them, T. viride was observed as the most abundant species (53 % of all isolates) in all the investigated locations. The Shannon's biodiversity index (H), evenness (E), and the Simpson's biodiversity index (D) calculations for each location showed that the highest species diversity and evenness were recorded for location A-Gorce Mountains (H' = 1.71, E = 0.82, D = 0.79). The preliminary screening of 119 Trichoderma strains for cellulolytic and xylanolytic activity showed the real potential of all Trichoderma species originating from wood with decay symptoms to produce cellulases and xylanases-the key enzymes in plant cell wall degradation.

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Trichoderma species occurring on wood with decay symptoms in mountain forests in Central Europe: genetic and enzymatic characterization

Genus Trichoderma contains the most powerful agents used in biocontrol. Our study demonstrated that T. harzianum, T. hamatum and T. longibrachiatum can effectively control phytopathogenic fungi Leptosphaeria maculans and L. biglobosa. The effects of Trichoderma on pathogens’ growth (in dual cultures on agar media) and on disease severity (on seedlings in controlled conditions) were also confirmed by field experiments. Additionally, spraying with conidiospores in the autumn was helpful in reducing the incidence and severity of phoma leaf spots. It has also accelerated the degradation of plant stubble and the decomposition of pathogens’ fruiting bodies. Furthermore, all Trichoderma isolates showed higher cellulolytic activity and enhanced resistance to flusilazole treatments as compared to Leptosphaeria spp., which coincided with upregulation of 14α-sterol demethylases and an AbcG5 transporter. The effects we observed justify the use of Trichoderma to enhance the resistance of oilseed rape against pathogens, which in turn may lead to a decrease in the use of pesticides.

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Judyta Strakowska

Papers

Formation of 6-n-pentyl-2H-pyran-2-one (6-PAP) and other volatiles by different Trichoderma species

The significance of cellulolytic enzymes produced by Trichoderma in opportunistic lifestyle of this fungus.

Cremenolide, a new antifungal, 10-member lactone from Trichoderma cremeum with plant growth promotion activity.

Trichoderma species occurring on wood with decay symptoms in mountain forests in Central Europe: genetic and enzymatic characterization

Optimal Trichoderma strains for control of stem canker of brassicas: molecular basis of biocontrol properties and azole resistance