Trichoderma : the genomics of opportunistic success

TL;DR: Recent advances in molecular ecology and genomics indicate that the interactions of Trichoderma spp.

Abstract: Trichoderma is a genus of common filamentous fungi that display a remarkable range of lifestyles and interactions with other fungi, animals and plants. Because of their ability to antagonize plant-pathogenic fungi and to stimulate plant growth and defence responses, some Trichoderma strains are used for biological control of plant diseases. In this Review, we discuss recent advances in molecular ecology and genomics which indicate that the interactions of Trichoderma spp. with animals and plants may have evolved as a result of saprotrophy on fungal biomass (mycotrophy) and various forms of parasitism on other fungi (mycoparasitism), combined with broad environmental opportunism.

Summary

1 Introduction

• Flow control of separated and complex flows is a challenge in both academic and industrial research.
• As it is difficult to deal with all the complexity of the flow over a real vehicle, it is important to define a simple 3D geometry to study the relation between the structures of the near-wake and the aerodynamic forces.
• Control the flow using actuation in the volume down- stream the separation.
• In the following sections, the vortex generators geometry and the corresponding parameters are presented before turning to the results of a detailed parametric study.

2 Experimental set-up and reference flow

• In order to deal with a 3D separated flow with a free separation line, the rear of the original Ahmed bluff-body (Ahmed et al. 1984), as shown on Fig. 1a, has been modified.
• Its origin s = 0 is located at the beginning of the rounded wall and it is positive toward the rear of the model (Fig. 2a).
• One should notice here that the dimensions are different from the original Ahmed body.
• As can be seen in Fig. 3, a fixed raised floor was used for the measurements.

2.3.1 Aerodynamic balance

• To evaluate the efficiency of the VGs on the aerodynamic forces, a six-components aerodynamic balance is used.
• Only the results on the drag and lift forces will be discussed.
• Cd and Cl are respectively the global drag and lift coefficients, while ClRear is the lift coefficient applied on the rear-axle.
• FzRear is the lift force on the rear axle of the model.

2.3.2 Wall pressure measurements

• The static wall pressure coefficients Cp are defined by Eq. 2: Cp ¼ P& P0 1 2qU 2 0 ð2Þ where U0 and P0 are respectively the free-stream velocity and pressure measured upstream of the model, and q is the density of the fluid.
• The pressure coefficients are measured on the vehicle body with 8 9 10-4 m diameter pressure taps (Drück!).
• 62 sensors are located on the left half of the rear part of the model as shown in Fig. 4 (open circles over the curved wall), while the 6 remaining sensors are located on the other half in order to check the symmetry of the timeaveraged flow.
• Since the plane y = 0 is actually a symmetry plane for themean flow, the pressure coefficients distribution will be shown only on the left part.
• The data are recorded as long as necessary to reach a well converged mean value.

2.3.3 Particle image velocimetry set-up and base flow

• Thanks to these different PIV measurements, one can identify the 3D structures of the flow.
• During the data acquisition, both laser source and camera are placed outside the test-section and the measurements are performed through transparent walls or sufficiently small holes to avoid perturbations (Fig. 5).
• The air-flow is seeded 12 L upstream from the model using a grid injection device, which is far enough not to perturb the incoming flow.
• Two Nd:Yag laser sources (120 mJ during a 10 ns pulse) provide double-pulsed light.

2.3.4 Hot wire measurements

• A standard one component boundary-layer hot-wire probe (Dantec! boundary layer probe 55p15) is used to investigate the boundary layer profile over the bluff-body.
• The single wire probe is moved over the bluff-body using a motorized device.
• Each velocity measurements is the average of 1.31 9 105 data with a 1 kHz sampling frequency.

3 Vortex generators for flow control

• The vortex generators used in this study are trapezoidal blades as shown in Fig.
• The results are detailed in a companion paper (Aider et al. 2009a), where it is shown that the vorticity is induced by the horseshoe vortex created around the base of the VG through a junction flow mechanism (Simpson 2001).
• As will be shown in the following, one can design a motorized device where the input parameter I could be the freestream velocity.
• In the following, the influence of the four parameters will be studied.

4 Parametric study of the influence of the vortex generators on the aerodynamic forces

• 1 Influence of the longitudinal position and angle of the vortex generators Since it is not possible to predict numerically or through a stability analysis the right perturbation, it is necessary to investigate the receptivity of the flow through a parametric study.
• The second observation is the evolution of the drag reduction as a function of the longitudinal position of the VGs: in both cases, one can see a clear single minimum, and a relatively large longitudinal region where the VGs are efficient.
• 2 Influence of the spacing between the vortex generators.
• The optimal longitudinal position for the lift reduction is different than the one for the drag reduction in the a = 120" case.
• These results are more interesting when plotted as contours of drag and lift modification (in percentage compared to the reference case) as a function of the longitudinal position versus the angle a for the three freestream velocities (Fig. 15).

5 Investigation of the near-wake of the bluff-body

• The previous sections illustrate the high dependance of the aerodynamic forces on the VGs and also the difficulty in understanding the way the VGs interact with the boundary layer.
• But whatever the preferred terminology, it is important to underline the fact that the drag experienced by a 3D bluff-body includes contributions from the separation bubbles and from the trailing vortices, which both contribute to the total drag through the momentum and the pressure deficits.

6 Conclusion

• An extensive parametric study of the influence of a vortex generators line on the aerodynamic coefficients of a 3D bluff-body has been carried out.
• For some configurations, the lift on the rear axle can even be cancelled out (more than -100%).
• Thanks to these mechanical vortex generators, the optimal configurations for both drag and lift can be found more easily in the space parameter (s, a).
• The importance of both the location of the VGs and of the angle between the blade and the wall is clearly confirmed for both drag and lift.
• It is then demonstrated that triggering early separation can be a very efficient way to reduce the total drag of a bluff-body, specifically when the trailing vortices and the recirculation bubble interact in the near-wake.

Figures

Figure 1.

Figure 4

Figure 3

Figure 2

Table 1. Endophytic Hypocrea/Trichoderma spp.

Frequently asked questions

Q1. What are the contributions mentioned in the paper "Trichoderma: the genomics of opportunistic success" ?

For example, in this paper, the authors identify the most commonly isolated species of the filamentous ascomycete Trichoderma, which are known as Hypocrea/Trichoderm spp. The sexual ( teleomorphic ) stage is known by the generic nameHypocrea, while the asexual ( anamorphic or mitosporic ) stage was called Trichodorma. 

Q2. What future works have the authors mentioned in the paper "Trichoderma: the genomics of opportunistic success" ?

Further studies of the interactions between plants, mycorrhizae and Hypocrea/Trichoderma strains are needed for a better understanding of these processes. They act synergistically with cell wall hydrolases to antagonize other fungi by preventing cell-wall resynthesis, and thus 20 potentially have a role in mycotrophy 105. • Isoprenoid derived metabolites H. virens produces the fungistatic and anti-cancer steroid viridin, which can be reduced to viridiol, which has herbicidal properties 111. 

Q3. What is the effect of T. longibrachiatum on human cells?

When T. longibrachiatum is confronted with lung cell cultures,the human cells rapidly start to sediment and lose their adhesive properties, suggesting the12action of proteases and/or secondary metabolites. 

Q4. What is the role of XYN2 in eliciting the plant response?

In fact, to elicit the plant response, XYN2 binds to the plant LeEix receptor,a member of a superfamily of leucine-rich repeat receptor-like proteins of plants that also carrya signal for receptor-mediated endocytosis that is essential for proper induction of defenseresponses 80, 81. 

Q5. Why are some Trichoderma strains used for biological control of plant diseases?

Because of their ability to stimulateplant growth and defense, some Trichoderma strains are used for biological control of plantdiseases. 

Q6. What are some of the traits that appear to have evolved in Hypocrea/Trichoderma?

Some of the traits that seem to have evolved in Hypocrea/Trichoderma in relation tomycotrophy may have functioned as preadaptations to allow parasitism or predation onanimals. 

Q7. What is the role of the fungi in the biocontrol of plants?

In thecourse of these studies, it was observed that Hypocrea/Trichoderma biocontrol strains can 20establish themselves in the plant rhizosphere, stimulate plant growth and elicit plant defensereactions against pathogens. 

Q8. What is the mechanism of the GPCRs in H. atroviridis?

It has been suggested that class IV G-protein coupled receptors (GPCRs) present in H.atroviridis20 could act as sensors for these oligopeptides13. 

Q9. What is the role of nitrilases in plant growth?

These nitrilases may have a role either inhydrolysing ß-cyano-L-alanin, a metabolite which is formed from cyanide released during thefinal step of ethylene biosynthesis, or in conversion of the plant metabolite indole-3-acetonitrile to indole-3-acetic acid (IAA), a plant root growth-promoting hormone 96.10Endophytic biotrophy (i.e. symptom-less growth inside plant tissue) is very common amongbacteria and fungi. 

Q10. What is the role of the ABC transporter in the death of the prey?

The final death of the prey results from the synergistic action of antifungal secondarymetabolites (Box 2) and cell-wall hydrolytic enzymes that are secreted byHypocrea/Trichoderma. 

Q11. What is the role of the carbohydrate binding module in chitinases?

Enhancingchitinase activity by addition of a carbohydrate binding module (CBM) to the chitinases CHIT33and CHIT42 increased the mycoparasitic ability of T. harzianum47. 

Q12. What is the mechanism of the signaling cascade?

Further signaltransduction from any of these receptors occurs via a conserved G-protein signaling cascade(Figure 2) that comprises three Gα subunits, one Gβ subunit and one Gγ subunit. 

Q13. What is the importance of these molecules to the life style of the mycoparasiteis?

The importance of these molecules to the life style of the mycoparasiteis reflected in the great number of genes encoding enzymes for their synthesis in 5Hypocrea/Trichoderma genomes13. 

Q14. What is the way to induce ISR in plants?

Blocking the synthesis of peptaibols (a group of non-ribosomal peptides, Box 2) in H.virens by disrupting the gene encoding the peptaibol synthase TEX1 results in strains that do not induce ISR in cucumber, although this can be overcome by addition of peptaibol mixtures 83. 

Q15. What is the role of the fungi in the establishment of the tomato rhizo?

In summary, the presence of fungal preys and the availability of root-derived 15nutrients may have been major attractors for Hypocrea/Trichoderma ancestors to establishthemselves in the rhizosphere and to develop interactions with plant roots. 

Q16. What is the main fraction of Hypocrea/Trichoderma species?

Theseconclusions are also reflected in the results from biodiversity surveys on Hypocrea/Trichodermathat led to the summary that of about 150 Hypocrea/Trichoderma species currently known andcharacterized by genetic markers, the main fraction comprises holomorphic species that growon decaying wood or on basidiomycetes3,4. 

Q17. What is the role of sucrose in the establishment of H. virens?

5Monosaccharides and disaccharides excreted by plant roots into the rhizosphere providean important carbon substrate for mycorrhizae 69, and sucrose has a similar role for the establishment of H. virens in the rhizosphere 70.