Trichoderma spp, Allelopathies in the Rhizosphere of Plants: For the Management of Soil Borne Pathogen, Rhizoctonia solani

Abstract

Among the many plant diseases, those brought on by soil-borne pathogens are the ones that result in significant losses. Rhizoctonia solani, one of many soil-borne pathogens, has been identified as a potential culprit for yield loss due to its broad host range. Prior to the development of extremely potent and selective fungicides, chemical treatment is not a practical option. However, the dangers associated with agrochemicals are reducing their use. Scientists are becoming more interested in biological management in this situation because it is an environmentally beneficial method. Biological control is the process through which one organism controls another. Trichoderma has become one of the most important biocontrol agents currently available due to its extensive antagonistic pathways. There are 89 species in this genus, and numerous strains have been discovered to be powerful biocontrol agents for plant diseases. The species T. viride, T. hamantum, T. koningii, and others make up the majority of the Trichoderma biocontrol agents. Direct and indirect antagonistic mechanisms are the two categories. Mycoparasitism, antibiosis, and pathogen enzyme inactivation are examples of direct methods. Indirect mechanisms include competition for nutrients and space, the activation of plant defensive systems (such as induced systemic resistance), and others. Their antagonistic characteristics are affected by a number of variables, including pH and temperature.

1. Introduction

Both prices are rising as a result of major losses in both quality and quantity caused by plant diseases. Since the beginning of the green revolution, controlling plant diseases and pests has become more and more dependent on the extensive use of dangerous chemicals. The cost of attaining the green revolution, however, was incalculable since agrochemicals damaged the ecosystem and upset the delicate balance between its various components. Recent research revealing that the widespread use of pesticides in the previous 10 to 15 years has had little effect in lowering the losses due to pests and diseases demonstrate that chemical use has reached a saturation point. As a result, we now need to decide whether or not supporting the use of these substances is a wise course of action. According to this viewpoint, environmentally friendly crop pest and disease management has been recognised as a substitute and essential element of sustainable agriculture. In the natural environment, microorganisms have been parasitizing both uncultivated and domesticated plants for millions of years. However, scientists have recently become interested in the phenomenon of employing bacteria for disease management, also referred to as biological control. As a biological control agent for soil-found plant pathogenic fungus, Trichoderma species have been investigated [1]. Several strains of Trichoderma considerably lessened the severity of plant diseases caused by pathogens such Gaeumannomycesgraminis var. tritici, Sclerotium rolfsii, Phythiumaphanidermatium, Fusarium oxysporum, and Rhizoctonia solani in greenhouse and field conditions. Based on findings from several studies [1, 2, 3, 4]. Trichoderma strains have the capacity to either directly or indirectly inhibit fungal phytopathogens. Mycoparasitism, antibiosis, and pathogen enzyme inactivation are examples of direct techniques. Examples of indirect pathways include competition for resources and space, environmental changes, and the activation of plant defence mechanisms [5]. Salinity, alkalinity, nutritional insufficiency, drought, and other environmental factors all allow Trichodema to survive [6, 7]. This chapter will clearly explain the many mechanisms involved in Trichoderma’s antagonistic behaviour.

Trichoderma interact with pathogenic fungi to advantageously reduce the growth of pathogens. In the past, Howell et al. [8] demonstrated that, in the presence of favourable growth conditions, Trichoderma rapidly filled the culture space and gradually covered the agar plate’s surface, preventing the growth of the pathogenic fungus R. solani. Infections with hyperparasites are one of the key ways that Trichoderma species eliminate infections [9, 10, 11]. The identification of pathogens and hyperparasite signalling were greatly aided by the markedly increased gene expression of proteases linked to host recognition, oligopeptide transporters, and GPCRs during hyperparasite infection [12, 13, 14]. During the hyperparasite infection of Trichoderma in hosts, there was a considerable upregulation of the expression of genes associated with hydrolase secretion. Trichoderma’s capacity to become hyperparasitic in hosts was decreased by deleting these genes.

2. Role of Rhizoctonia solani in causing plant diseases

Soil-borne fungus is the primary reason for the fall in crop productivity. Currently, R. solani is one of 1258 different fungus species that have been identified as potential crop diseases [15, 16, 17]. Plant roots and lower stems can become infected by the fungus pathogen R. solani. There are few options for controlling R. solani infections because of the variety of hosts and lack of resistant plant species. The majority of researchers are more interested in biological control among the several methods for preventing soil-borne diseases that have been suggested (Tables 1 and 2) [15, 23, 24, 25].

Trichoderma spp.	Metabolites	Disease control
T. lignorum, T. virens, T. hamatum, T. harzianum and T. pseudokoningii (Rifai)	Unknown inhibitory substances; Extracellular metabolites or antibiotics, or lytic enzyme action	Damping-off of bean
T. virens isolates GL3 and GL21	Antibiotics gliovirin and gliotoxin	Damping-off of cucumber

Table 1.

Trichoderma spp. antagonism against diseases caused by R. solani.

Trichoderma spp.	Reference
T. viride, T. harzianum	[18]
T. viride	[19]
T. harzianum, T. virens and T. atroviride	[20]
Trichoderma spp. Isolates	[21]
T. asperellum	[22]

Table 2.

Uses of various Trichoderma spp. for the control of sheath blight of rice.

3. Different mechanisms involved in the antagonism of Trichoderma

There are broadly two different mechanisms in which Trichoderma inhibits the growth of phytopathogenic fungus.

1. Direct mechanism

2. In direct mechanism

3.1 Direct mechanism

In this approach, the biocontrol agent uses many mechanisms, such as mycoparasitism, antibiosis, pathogen enzyme inactivation, etc. to directly impede the growth of the phytopathogenic fungus.

3.1.1 Mycoparasitism

Mycoparasitism is another name for this biocontrol mechanism. This is an instance of another fungus parasitizing a harmful fungus. Fungi are recognised to cause the bulk of plant diseases, and it is well-known that many fungi can parasitize other fungi. The phenomenon of one fungus parasitizing another is referred to as mycoparasitism, hyperparasitism, direct parasitism, and interfungal parasitism. Coiling (Figure 1), hooks, and appressorium-like structures are used by Trichoderma species to adhere to host hyphae before secreting lytic enzymes to compromise the host cell wall [27]. Mycoparasites are fungi that may infiltrate other fungi and scavenge nutrients for their own growth by generating enzymes that breakdown cell walls. The majority of phytopathogenic fungi have an amorphous arrangement of the structural component chitin and the filler substance b-1,3-glucan in their cell walls. B-1,3-glucanases and chitinases have been discovered to directly affect how Trichoderma species interact with their hosts during mycoparasitism [27]. The Trichodermaschitinolytic system (NAGase) is composed of two different types of enzymes: chitinases and N acetyl-b-D-glucosaminidase. Despite multiple studies, it is still unclear how Trichoderma produces and controls chitinolytic and glucanolytic enzymes [23, 27].

Figure 1.

Transmission electron microscopy of T. Harzianum mycelium growing on R. solani. The arrow indicates the T. Harzianum coiling. Bar = 10 mm (source: Ref. [26]).

3.1.2 Antibiosis

The biological control agent’s capacity to suppress pathogenic organisms by secreting toxic or inhibitory substances is known as antibiosis. This occurs when a biocontrol agent and a pathogenic fungus interact, and some strains of Trichoderma produce low molecular weight diffusible compounds or antibiotics that inhibit the growth of other bacteria. The majority of Trichoderma strains release toxic compounds, both volatile and nonvolatile, that prevent fungus they have antagonised from colonising. Heptelidic acid, alamethicins, tricholin, peptaibols, 6-penthyl-pyrone, massoilactone, viridin, gliovirin, and glisoprenins are a few of the metabolites created [28]. Gliovirin can be produced by the strains of T. virens that are most effective for biocontrol [29]. Furthermore, the strains’ performance was undoubtedly correlated with the pyrone antibiotics they produced, which are produced by the most effective isolates of T. harzianum against Gaeumannomycesgraminis var. tritici. Combining hydrolytic enzymes and antibiotics results in greater antagonism than using each strategy separately (Table 3) [29, 32].

Proteins	Encodinggene	Accession number (Gene Bank)	Trichoderma spp.
Peptaibol	N.A.	N.A.	Trichoderma spp.
Lipoxygenase	N.A.	N.A.	T. atroviride
Polyketide synthases (PKS)	pks4	N.A.	T. atroviride
	pks4	N.A.	T. reesei
	pks4	N.A.	T. virens
GliCCytochromeP450	gliC	N.A.	T. virens
	gliF	N.A.	T. virens
ɣ-glutamylcyclotransferase-likeprotein	gliK	N.A.	T. virens
Glutathione S-transferase	gliG	N.A.	T. virens
NRPSmodules	gliP	N.A.	T. virens
O-methyltransferase	gliM	N.A.	T. virens
Cytochrome P450 monooxygenases	tri4	FN394496	T. arundinaceum
Major facilitator super family transporter	Thmfs1	JN689385	T. harzianum
L-amino acidoxidase	Th-LAAO	GU902953	T. harzianum
ABC transporters	Taabc2	AY911669	T. atroviride

Table 3.

Trichoderma spp. proteins associated with antagonism and involved in the synthesis of secondary metabolites deleterious to R. solani [30, 31].

N.A.: Not available.

3.1.3 Pathogen enzyme inactivation

Trichoderma degrades the toxic compounds that pathogenic bacteria secrete, which reduces their capacity to inhibit Trichoderma growth through the utilisation of heat shock proteins, ABC transporter proteins, and other mechanisms [33, 34, 35]. In order to prevent Trichoderma from growing and to offset the host’s inhibition during contact between the two organisms, the host pathogen secretes several toxic substances. Transmembrane proteins with specific roles include ABC Transporter proteins. These proteins have two ends, one of which is referred to as a ligand binding domain and the other as an ATP binding domain. The ligand binding domain only permits a limited number of molecules to enter the cells, but the ATP binding domain eliminates any harmful substances that enter the cell. These ABC transporter proteins are triggered when some inhibitors of the host enter the cell of the biocontrol agent, and they force the toxins out of the cell before they can harm the cells [33, 34, 35].

3.2 In direct mechanism

By competing for nutrients and available space, the biocontrol agent indirectly prevents the growth of pathogenic fungus, a process known as induced systemic resistance (ISR).

3.2.1 Competition for nutrients and space

One of the most frequent causes of death for microorganisms is starvation, and fungal phytopathogens are biologically controlled by competition for few resources [36]. The majority of filamentous fungus need iron to survive, and when iron is scarce, the majority of fungi produce siderophores, low molecular weight chelators that are specific to ferric iron, to mobilise ambient iron [37]. The iron is then taken out of the ferri-siderophore complexes using specialised uptake processes. According to studies by [1], some Trichoderma isolates produce potent siderophores that chelate iron and inhibit the growth of other fungi (Table 4). Pythium is affected by the soil’s composition and iron availability as well as Trichoderma’s capacity to biocontrol it. Furthermore, T. harzianum competes with Fusarium oxysporum for nutrients and rhizosphere colonisation, preventing it from growing and boosting the efficiency of biocontrol when nutrient concentrations fall [38]. It has been discovered that Botrytis cinerea, the pathogenic agent that is most common throughout the pre- and post-harvest period in many countries, is particularly significant for the biocontrol of phytopathogens [39]. Because of its enormous genetic variability, the fungus can develop resistance to new chemical fungicides almost immediately after exposure [39]. The advantage of using Trichoderma to manage B. cinerea is that it allows multiple mechanisms to function at once, virtually preventing the generation of resistant strains. The most crucial of these mechanisms is nutritional competition since B. cinerea is so susceptible to food shortages. Trichoderma has a greater ability than other species to move and absorb soil nutrients (Figure 2).

Proteins	Encodinggene	Accession number (Gene Bank)	Trichoderma spp.
High-affinity glucosetransporterGtt1	Gtt1	AJ269534	T. harzianum
EndopolygalacturonaseThpg1	Thpg1	AM421521	T. harzianum
Harzianic acid	N.A.	N.A.	T. harzianum
Proteases	TaPapA	AAT09023	T. asperellum
	TaPapB	AAU11329	T. asperellum

Table 4.

Trichoderma spp. associated with antagonism with R. solani and involved in the competition [30, 31].

N.A.: Not available.

Figure 2.

Activities of Trichoderma spp. in rhizosphere against R. solani (source: Ref. [40]).

3.2.1.1 Stimulation of plant defence mechanism induced systemic resistance (ISR)

When plants are exposed to specific signal molecules made by PGPR or other non-pathogenic fungus biocontrol agents, a phenomena known as ISR occurs. These signal molecules are circulated throughout the plant’s entire system, activating its defences. Trichoderma strains added to the rhizosphere shield plants from a range of diseases, including viral, bacterial, and fungal pathogens, by inducing resistance mechanisms similar to the hypersensitive response (HR), systemic acquired resistance (SAR), and insensitive shock response (ISR) in plants [41, 42]. Resistance causes an increase in the concentration of metabolites and protective enzymes including phenylalanine ammoniolyase (PAL) and chalcone synthase (CHS), which are responsible for the formation of phytoalexins (HR response), chitinases, and glucanases. These comprise pathogenesis-related proteins (PR) (SAR response) and oxidative stress-responsive enzymes [43]. A range of chemicals that bacteria (elicitors) emit cause plant genes to respond. As a result, a pathogen is not necessarily necessary to initiate a plant’s defence systems. Adding Trichoderma metabolites, which could trigger plant resistance. If added, Trichoderma elicitors, which are crucial for preventing infections in fruits after harvest, could have a similar result. When a plant is exposed to pathogens (fungi, bacteria, viruses, or nematodes), phytoalexins, antimicrobial peptides, and tiny proteins (such as thionins, defensins, hevein-like proteins, and knottin-like peptides) are created, and a number of antimicrobial proteins are upregulated [44, 45]. When Trichoderma, a plant pathogen, interacts with biocontrol agents, elicitors are produced. These elicitors cause plants to release something akin to PR proteins. These proteins prevent or eliminate the infection (Tables 5 and 6).

Proteins	Encodinggene	Accession number (Gene Bank)	Trichoderma spp.
Seven-transmembrane receptorGpr1	gpr1	N.A.	Trichodermaatroviride
G-proteinone	N.A.	FD484960	T. asperellum
G-protein ypt3	N.A.	FD486508	T. asperellum
G-protein rab2	N.A.	FD485766	T. asperellum
α-subunit of G protein1	tga1	AY036905	T. atroviride
α-subunit of G protein3	tga3	AF452097	T. atroviride
Mitogen-activatedprotein kinases (MAPK)	tmkA	AY141978	T. virens
	tvk1	AY162318	T. virens
Adenylate cyclase Tac1	tac1	EF189190	T. virens
pHregulator PacC	pacC	N.A.	T. virens
pHregulator Pac1	pac1	EF094462	T. harzianum
Transcription factorThCtf1	ctf1	EU551672	T. harzianum
VELVETProteinVel1	vel1	N.A.	T. virens
XylanasetranscriptionalregulatorXyr1	xyr1	N.A.	T. atrovide

Table 5.

Trichoderma spp. proteins associated with antagonism and involved in R. solani recognitions, signal transduction and genetic reprogramming of gene expression [30, 31].

N.A.: Not available.

Proteins	Encoding gene	Accession number (Gene Bank)	Trichoderma spp.
41-KDachitinase	chit41	N.A.	T. flavus
Chitinase1	N.A.	FD484447	T. asperellum
33-KDa Endochitinases	chit33	JK840912	T. harzianum
	Tv-cht1	AF395753	T. virens
	Tv-cht2	AF395754	T. virens
36-KDa Endochitinases	chit36Y	AF406791	T. asperellum
42-KDa Endochitinases	chit42	N.A.	T. atroviride
	echi42	FD485995	T. asperellum
	chit42	S78423	T. harzianum
	Tv-ech1	AF050098	T. virens
	Tv-ech2	AF395760	T. virens
46-KDa Endochitinase	chit46	N.A.	T. asperellum
Endochitinases (GH18)	crchi1	X80006	T. harzianum
N-acetyl-β-Glucosaminidases	exc1Y	AJ314642	T. asperellum
	nag1	N.A.	T. atroviride
	eng18B	N.A.	T. atroviride
	nag1	N.A.	T. harzianum
	Tvnag1	AF395761	T. virens
	Tvnag2	AF395762	T. virens
b-1,3-glucanases	tag83	EU314718	T. asperellum
	lam1.3	AJ002397	T. harzianum
29-KDab-1,3-Glucanase	N.A.	N.A.	T. harzianum
36-KDab-1,3-Glucanase	N.A.	N.A.	T. harzianum
78-KDab-1,3-Glucanase	bgn13.1	X84085	T. harzianum
b-1,6-glucanase	bgn16.2	N.A.	T. harzianum
	Tvbgn3	AF395757	T. virens
b-1,3-glucanase	N.A.	N.A.	T. koningii
	Tvbgn1	AF395755	T. virens
	Tvbgn2	AF395756	T. virens
Endo-1,3(4)-b-Glucanase	N.A.	FD486867	T. asperellum
Asparticproteases	TaAsp	EU816200	T. asperellum
	TaPAPA	AAT09023	T. asperellum
	Sa76	EF063645	T. harzianum
	P6281	AJ967001	T. harzianum
	N.A.	FD485588	T. asperellum
Serineproteases	Spm1	FD486577	T. asperellum
	prb1	AAA34209	T. harzianum
	tvsp1	AY242844	T. virens
	prb1	AAA34209	T. harzianum

Table 6.

Trichoderma proteins associated with mycoparasitism of R. solani [30, 31].

N.A.: Not available.

3.2.1.2 Factors influencing antagonistic activity of Trichoderma species against pathogens

The two elements that affect the antagonistic property are temperature and pH [22]; they have carried out an in vitro experiment to test the biocontrol performance of various Trichoderma isolates on R. solani at various temperatures and pH levels. At 25°C and 30°C, the three Trichoderma species (T. asperellum, T. harzianum, and Trichoderma spp.) showed their maximum mycelial development, however at 20°C, the growth rate was noticeably slower and they hardly colonised 1/4th of the medium surface. The pH range of 5 to 6 was the most acidic, while 6.5 to 7.0 is where mycelium grows at the slowest rate. Above these pH limits, there was either no or very little growth (0.9–1.2 cm).

4. Role of Trichoderma for management of abiotic stress

In the short term, using biological agents such as water deficit-tolerant Trichoderma may be an affordable, sustainable, and eco-friendly way to lessen the effects of drought [46, 47]. However, the interactions between particular fungal isolates and plant cultivars are complicated, and our understanding of the mechanisms behind the drought tolerance that Trichoderma colonisation induces in plants is lacking. According to Hoeksema [48] coevolution involving heritable genetic variation in both plants and microbes that promote colonisation as well as abiotic stress responses may be the basis for adaptation to mutualism as a strategy of survival under harsh environmental conditions. According to Kubicek et al. [49], Trichoderma is a “environmental opportunist and generalist” that can quickly adapt to flourish as a free-living organism or a plant symbiont in novel or challenging situations. The asexual conidiospores and chlamydospores that the fungi can produce are resistant to harsh environmental conditions. Stress caused by a water scarcity considerably reduces crop quality and output. Trichoderma inoculation may help promote plant growth and lessen the harmful effects of water deficiency stress [50, 51]. It has been shown by Mastouri et al. [52, 53] that Trichoderma inoculation affects plant performance, but only in stressed conditions. According to their research, when tomato seeds were cultivated in conditions of water deprivation, the T22 inoculation enhanced germination and other growth metrics. According to Bashyal et al. [51], plants inoculated with Trichoderma showed higher expression levels of genes linked to photosynthesis, including those encoding for photosystem I subunits, photosystem II core complex proteins, osmotin-like proteins, and stomatal development, in comparison to non-inoculated controls. Improved physiological health is shown by plants infected with Trichoderma during water scarcity [46, 54, 55] According to reports, plants injected with Trichoderma species accumulate more metabolites, such as proline, flavonoids, and phenolics. These metabolites boost antioxidant activity and guard against photooxidative damage to photosynthetic pigments and pathways [56, 57, 58]. It is thought that plants respond to droughts by increasing the amount of abscisic acid in their tissues, which controls stomatal motions and aids in maintaining water balance. According to Martinez-Medina et al. [59], compared to non-inoculated control plants, Trichoderma harzianum colonised plants showed greater expression levels of the ABA-responsive marker gene involved in various defence-related pathways.

5. Benefits and limitations

5.1 Benefits

1. Trichomonia is widely used to treat post-harvest infections. Phytophthora, Sclerotium, Fusarium, and other fungal infections are said to respond favourably to it.

2. Trichoderma strains may solubilise phosphates, which really aids in plant growth in general.

3. Trichoderma strains are essential for bioremediation of pesticide and herbicide-contaminated soil. They are able to degrade pesticide residues made of organochlorines, organophosphates, and carbonates.

4. Trichoderma contains a large number of biocontrol genes. The endochitinase gene from Trichoderma has been introduced in plants, including tobacco and potato plants. These plants demonstrated enhanced infection resistance.

5. Rhizobium, Azospirilium, Bacillus subtilis, and other biofertilizers are compatible with Trichoderma as are organic manures. It works well on the seeds treated with metalaxyl and thiram, but not on seeds treated with mercurials.

5.2 Limitations

1. For up to 4 to 5 days after using Trichoderma, no chemical fungicides should be used.

2. Trichoderma needs adequate moisture to flourish, thus the field should not be dry.

3. Trichoderma-treated seeds should be dried in the shade, away from direct sunshine.

6. Conclusion

Global population pressures are increasing on scarce agricultural areas, calling for an increase in productivity. On the other hand, risky pesticide effects are restricting their use, which could temporarily lower production levels. It has been determined that using environmentally friendly pest and disease management techniques is pertinent in this situation as a component of sustainable agriculture. Because most biocontrol agents are part of natural biodiversity and are safe for the environment, biological control has therefore become increasingly important. Trichoderma has become quite important since it is an excellent biocontrol agent that can work against a variety of pathogenic soil fungus. Scientists are attempting to discover the genes that are responsible for its biocontrol activity in the hope of creating transgenic plants that are similar to Bt cotton using the data from recent investigations, which have yielded many hints for future research.