Comparative transcriptomics reveals different strategies of Trichoderma mycoparasitism

Abstract

Background: Trichoderma is a genus of mycotrophic filamentous fungi (teleomorph Hypocrea) which possess a bright variety of biotrophic and saprotrophic lifestyles. The ability to parasitize and/or kill other fungi (mycoparasitism) is used in plant protection against soil-borne fungal diseases (biological control, or biocontrol). To investigate mechanisms of mycoparasitism, we compared the transcriptional responses of cosmopolitan opportunistic species and powerful biocontrol agents Trichoderma atroviride and T. virens with tropical ecologically restricted species T. reesei during confrontations with a plant pathogenic fungus Rhizoctonia solani.

Results: The three Trichoderma spp. exhibited a strikingly different transcriptomic response already before physical contact with alien hyphae. T. atroviride expressed an array of genes involved in production of secondary metabolites, GH16 ß-glucanases, various proteases and small secreted cysteine rich proteins. T. virens, on the other hand, expressed mainly the genes for biosynthesis of gliotoxin, respective precursors and also glutathione, which is necessary for gliotoxin biosynthesis. In contrast, T. reesei increased the expression of genes encoding cellulases and hemicellulases, and of the genes involved in solute transport. The majority of differentially regulated genes were orthologues present in all three species or both in T. atroviride and T. virens, indicating that the regulation of expression of these genes is different in the three Trichoderma spp. The genes expressed in all three fungi exhibited a nonrandom genomic distribution, indicating a possibility for their regulation via chromatin modification.

Conclusion: This genome-wide expression study demonstrates that the initial Trichoderma mycotrophy has differentiated into several alternative ecological strategies ranging from parasitism to predation and saprotrophy. It provides first insights into the mechanisms of interactions between Trichoderma and other fungi that may be exploited for further development of biofungicides.

Figure 1

Mycoparasitism of Trichoderma spp. in dual confrontations assays with Rhizoctonia solani. Fungi were incubated for 10 days on PDA at 25°C and 12 hours cyclic illumination. Arrows indicate overgrowth of R. solani by Trichoderma spp.

Figure 2

Development of mycoparasitic reaction of Trichoderma atroviride against Rhizoctonia solani. The mycelium was sampled before contact (BC), at the contact (C) and after the contact (=overgrowth, AC) with R. solani.

Figure 3

Averaged regulation of all genes (|log₂ (ratio)| > 1.5) involved in mycoparasitsm of T. reesei, T. atroviride and T. virens during the three confrontation stages with R. solani (BC, C and AC). Vertical bars denote 0.95 confidence intervals. The same letters above the bars indicate the statistical significance (ANOVA) between the stages of each species: for m–n–r p < 0.005; s–t p < 0.02; u–z p < 0.001. The plot shows different trends of gene expression kinetics between the species and does not reflect the gene regulation intensity differences among the species.

Figure 4

The Venn diagram showing the number of orthologous genes of T. reesei, T. atroviride and T. virens that are involved in mycoparasitic response against Rhizoctonia solani (at all stages of confrontation). The total number of orthologous genes per species is given below the respective species name.

Figure 5

Scatter plots of all regulated genes in each stage for (A) T. atroviride, (B) T. virens and (C) T. reesei, respectively. The log₂ (ratio) regulation for the genes at contact (C, circles) and after the contact (AC, squares) stages are plotted against the genes regulated prior the contact (BC). The genes, for which a stage-specific difference was found, are indicated by their functional names.

Figure 6

Gliotoxin and gliotoxin precursor biosynthesis in T. virens during mycoparasitism with R. solani. A) Only enzymes, whose genes are up-regulated are shown, marked as blue, yellow and green arrows for gene up-regulation before contact (BC), at the contact (C) and after the contact (AC), respectively. B) The arrows show the gliotoxin gene cluster including gene nomenclature, protein numbers and their regulation (blue, yellow and green arrows marking up-regulation BC, at C and AC, respectively) during mycoparasitic reaction with R. solani.