Trichoderma: a multifunctional agent in plant health and microbiome interactions

Abstract

The beneficial fungus Trichoderma is a key component of agricultural soils, contributing to sustainable crop production through multiple mechanisms. Among its major roles are the suppression of plant pathogens, promotion of plant growth, and activation of plant immune responses. This study reviews recent advances in understanding the modes of action of Trichoderma spp. related to pathogen control and plant growth promotion, using comparative analysis of its interactions across different plant-associated habitats. In recent years, considerable progress has been made in elucidating how Trichoderma interacts with plants in the rhizosphere, endosphere, and phyllosphere, where it exhibits distinct colonization patterns and functional traits. Additionally, this review explores emerging but less-studied topics, such as the involvement of Trichoderma in the pathobiome concept. Finally, we discuss the synergistic interactions between Trichoderma and other plant-associated microorganisms, highlighting their importance in shaping complex microbial networks within agroecosystems.

Introduction

Plants worldwide continuously face biotic and abiotic stressors such as pathogens, drought, nutrient deficiencies, and extreme environmental conditions [19, 79]. As sessile organisms, plants rely heavily on beneficial interactions with microorganisms to enhance nutrient uptake and strengthen their defense against these challenges [146]. In return, plants support soil microbial communities by secreting a portion of their fixed carbon and nitrogen [117] and providing habitats, such as the rhizosphere, plant endosphere, and phyllosphere [92]. This unique microbial community, or microbiota, inhabits the plant in a well-defined niche with specific physiochemical properties, collectively forming what is known as the plant microbiome [18].

The plant microbiome plays a crucial role in helping plants cope with abiotic stresses, such as drought, salinity, heavy metal exposure, and nutrient acquisition, while also enhancing overall health, pathogen resistance, and productivity [82]. This concept underpins efforts to manipulate or engineer the plant microbiome as a potential biotechnological tool for sustainable agriculture aimed at boosting crop productivity and reducing plant disease [139]. For example, in a study conducted by Liu et al. [74], more than 1,900 fungal operational taxonomic units (OTUs) and another 2,600 bacterial OTUs were identified within the endosphere of banana plants. The authors compared the diversity and abundance of these bacterial and fungal OTUs in root tissues and shoot tips, both in healthy plants and in those affected by wilting disease caused by Fusarium oxysporum f. sp. cubense. The most abundant bacterial genera were Caulobacter and Paracoccus, while Cladosporium and Eurotium were predominant among the fungi. Interestingly, three endophytic strains were isolated and engineered to express 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity on their cell walls: Enterobacter sp. E5, Kosakonia sp. S1, and Klebsiella sp. Kb. Inoculation of banana plants with these bacteria enhanced resistance to wilting and promoted plant growth compared to non-inoculated plants, highlighting the importance of ACC deaminase activity.

Diversity within plant microbiomes is substantial, encompassing hundreds to thousands of bacterial and fungal species [62, 88]. For example, the rhizosphere microbiome of avocado plants contains 3411 bacterial OTUs and 1184 fungal OTUs [129], while 306 bacterial isolates from the endosphere microbiome of saffron (Crocus sativus) have been identified, with Bacillus being the most abundant genus, exhibiting biocontrol and growth-promoting traits [5]. The rhizosphere microbiome of the five coffee tree species was similarly diverse, predominantly comprising Proteobacteria, Actinobacteria, Ascomycota, and Mucoromycota [34].

Among these beneficial microorganisms, such as bacteria and fungi, Trichoderma spp. have emerged as both valuable microbiome components and microbiome modulators [34, 50, 62, 148]. Trichoderma has been widely recognized as a plant growth promoter and an effective biocontrol agent, benefiting crops such as maize [134], beans [53], wheat [150], and cotton [126].

Efforts to manipulate or modify the plant microbiome have enabled researchers to increase the prevalence of beneficial microorganisms and decrease that of pathogens in agriculturally important plants, with Trichoderma playing an important role [148, 152]. Given the critical role that Trichoderma plays in enhancing plant health and productivity, understanding its interactions with the plant microbiome is essential for developing sustainable agricultural practices. This review aims to summarize recent findings on the mechanisms by which Trichoderma interacts with plants and their associated microbiomes, highlighting its multifaceted contributions to plant growth promotion, pathogen suppression, and modulation of microbial communities. By elucidating these interactions, we sought to provide insights that can inform future research and practical applications, ultimately contributing to the advancement of agroecosystem resilience and sustainability.

Trichoderma as a plant growth promoter

Trichoderma spp. are soil-borne fungi belonging to the phylum Ascomycota and family Hypocreaceae. The Trichoderma genus comprises over 500 species commonly found in soil, surrounding plant roots, and decayed organic matter as saprophytes [58]. Trichoderma species are fast-growing fungi with hyaline phialides, septate hyphae, and conidiophores that often form tree-like shapes; their mature conidia are typically yellow to green in color [21, 59]. Many Trichoderma species are widely used in agriculture because of their beneficial interactions with plants and ability to antagonize various plant pathogens [35, 85, 135], making these fungi valuable biotechnological tools for sustainable agriculture.

One of key contributions of Trichoderma in agriculture is its ability to enhance plant growth and productivity through beneficial plant interactions. Trichoderma promotes plant growth through mechanisms that include root colonization [134], nutrient solubilization and bioavailability in the soil [133, 138], abiotic stress tolerance [30, 121], secondary metabolite production [140], and the synthesis of plant hormones such as auxins, gibberellins, and cytokinins [57]. Once Trichoderma colonizes the root, it establishes a mutualistic interaction, exchanging secondary metabolites and nutrients with the plant in return for carbon sources, such as sugars.

For instance, T. viride Tv-1511 colonizes peppermint roots, promotes growth, and enhances essential oil production [44]. Similarly, T. atroviride colonization in wheat, mediated by the glycosyltransferase Taugt17b1, enhances plant growth and defense against Rhizoctonia cerealis [26].

Trichoderma also facilitates the availability of mineral nutrients in the soil by solubilizing them, thereby improving the soil quality and enhancing plant nutrition, growth, and productivity. For example, Trichoderma koningiopsis can solubilize phosphate under alkaline and drought conditions, and antagonize Rhizoctonia solani [133]. T. harzianum SQR-T037 solubilizes minerals, such as phosphorus, iron, manganese, copper, and zinc, promoting the growth and development of tomato plants under nutrient-limited conditions [68]. Different Trichoderma spp. also confer resistance to abiotic stresses. T. longibrachiatum TG1 and T. harzianum mitigate salt stress in wheat and cucumber plants, respectively, whereas T. asperellum helps Solanum lycopersicum (tomato) resist drought and cold stress [30].

In addition, Trichoderma can produce plant hormone-like compounds, which may explain its plant growth-promoting traits. Illescas et al. [57] found that T. virens T49 and T. harzianum T115, which produce gibberellins, auxins, and cytokinins, promote growth and reduce drought stress in wheat. However, T. longibrachiatum T68 and T. spirale T75, which produce these hormones to a lesser extent, were less effective in promoting growth. Trichoderma is a prolific producer of secondary metabolites. These metabolites serve multiple functions, including helping Trichoderma compete for nutrients and space to inhibit the growth of other microorganisms harmful to plants, facilitating colonization by modulating plant defense responses, and promoting plant productivity. A notable example is the secondary metabolite 6-pentyl-α-pyrone (6PP), which enhances plant growth and productivity [23, 33, 61]. Therefore, Trichoderma species are well-suited for enhancing sustainable agriculture by promoting plant growth and yield and establishing beneficial interactions with plant hosts (Fig. 1).

Fig. 1.

Interactions between Trichoderma and the plant, highlighting the services it provides in conjunction with the host-associated microbiome

Trichoderma as a biocontrol agent

Another important and widely recognized trait of Trichoderma in agriculture is its ability to antagonize plant pathogens through direct and indirect mechanisms, collectively known as its biocontrol capacity [130]. Direct biocontrol mechanisms include antibiosis and mycoparasitism, whereas indirect methods involve competition for nutrients and space, as well as activation of plant immune defense systems [46, 86].

Trichoderma spp. are often used as biocontrol agents because of their mycoparasitic abilities. Mycoparasitism involves a series of steps that allow Trichoderma to attack its fungal prey. First, the mycoparasite grows toward its prey, secreting chitinolytic enzymes to degrade the prey’s cell wall. Upon reaching its target, Trichoderma attaches to and coils around the hyphae of prey and begins to degrade [35]. This process inhibits the growth of pathogens and prevents them from causing plant diseases.

Studies have shown that Trichoderma is effective against several fungal pathogens such as Botrytis cinerea [51], Rhizoctonia solani [48], Fusarium oxysporum [14], Alternaria alternata, Aspergillus flavus [22], and Fusarium pseudograminearum [52]. This mycoparasitic activity in the rhizosphere is crucial because its presence can directly help manage plant diseases.

Another important biocontrol trait of Trichoderma spp. is antibiosis. During antibiosis, Trichoderma produce secondary metabolites that inhibit or limit the growth of plant pathogens [7, 86]. These compounds include gliotoxins from T. virens Q strains, which inhibit Pythium aphanidermatum and prevent damping-off disease in tomato plants [60]. Gliotoxins also damage the hyphal cells of Sclerotium rolfsii, antagonizing this pathogen [54]. Another example is the 6-Pentyl-2H-pyran-2-one (6PP) from T. atroviride, which inhibits Cylindrocarpon destructans [61].

Trichoderma’s antibiotic secondary metabolites also inhibit bacterial pathogens such as Xanthomonas oryzae pv. oryzae, a rice pathogen, is strongly inhibited by Trichokonins A and peptaibols from T. longibrachiatum SMF2, which damages bacterial cells [154]. Additionally, T. hamatum FB10 produces secondary metabolites with antibacterial effects against Erwinia carotovora and Acidovorax avenae, antifungal activity against S. sclerotiorum, R. solani, Alternaria radicina, A. citri, and A. dauci, and nematicidal effects against M. incognita [12].

A significant feature of Trichoderma as a biocontrol agent is its capacity to induce systemic resistance in plants. When a plant encounters a pathogen, Systemic Acquired Resistance is triggered (SAR), involving salicylic acid– mediated signaling, leading to plant protection against pathogens; however, when the plant encounters beneficial microbes, such as Trichoderma, Induced Systemic Resistance is triggered (ISR), which involves jasmonic acid-and ethylene– mediated signaling [113]. Induced Systemic Resistance (ISR) primes plants to respond more quickly and strongly to pathogen attacks, and beneficial microorganisms such as Trichoderma and plant growth-promoting bacteria (PGPB) can trigger ISR [90]. For example, T. pubescens Tp21 increases the expression of defense-related genes PAL (Phenylalanine Ammonia-Lyase, an enzyme that initiates the phenylpropanoid pathway and contributes to the production of antimicrobial compounds), CHS (Chalcone Synthase, a key enzyme in flavonoid biosynthesis involved in antioxidant and antimicrobial defenses), and HQT (Hydroxycinnamoyl-CoA Quinate Hydroxycinnamoyl Transferase, responsible for the synthesis of chlorogenic acid, a phenolic compound with protective functions) in tomatoes. Additionally, strain Tp21 reduces oxidative stress during R. solani infection, and enhances antioxidant enzyme activity such as superoxide dismutase (SOD), catalase (CAT), polyphenol oxidase (PPO), and peroxidase (POX) production, thereby conferring resistance against R. solani [17].

Similarly, T. hamatum Th23 protects tomatoes from Tobacco Mosaic Virus (TMV) by reducing oxidative stress, increasing the activities of antioxidant enzymes such as CAT, SOD, and PPO, and upregulating genes involved in the polyphenolic biosynthetic pathway (HQT and CHS) as well as pathogenesis-related proteins (PR-1, PR-2, and PR-7), thereby enhancing resistance against TMV [1]. Trichoderma spp. can also induce resistance against other plant pests, such as insects. When applied to the roots of Lansium domesticum plants, Trichoderma spp. increase salicylic and jasmonic acid concentrations, protecting against infestation by the scale insect Unaspis mabilis and activating plant defenses [125]. These biocontrol mechanisms enable Trichoderma to antagonize a wide range of plant pathogens and protect agriculturally significant crops. Thus, Trichoderma is a valuable tool for sustainable agriculture, serving as an effective alternative to chemical fertilizers and pesticides [2, 11]. While much of the research has focused on using single or multiple Trichoderma species, there is a growing interest in combining Trichoderma with other beneficial microorganisms, suggesting that it may play a vital role as part of the plant microbiome.

Critical roles of Trichoderma in diverse plant-associated zones

Plants can interact with their associated microbiota through three main zones: the rhizosphere (the soil zone surrounding and influenced by the roots) [25], the endosphere (the interior of plant tissues) [28], and the phyllosphere (the surface of leaves and other aerial parts of the plant) [155]. Other zones can also be colonized by endophytic microorganisms, such as the caulosphere (stem), anthosphere (flowers), carposphere (fruits), and spermosphere (seeds) [73, 87]. By colonizing seeds, microbial endophytes —including Trichoderma species— can be vertically transmitted to the next plant generation [43]. In addition, the rhizosphere can be subdivided into the ecto-rhizosphere (rhizospheric soil), the rhizoplane (root surface), and the endo-rhizosphere (inner root tissue), where plant-Trichoderma interactions can influence plant and fruit growth, development, and health [55, 64, 71, 84]. In this review, we focus on analyzing studies of Trichoderma-plant interactions within these closely connected regions (rhizosphere, endosphere, and phyllosphere).

Trichoderma in the rhizosphere

The rhizosphere is a narrow soil region directly surrounding plant roots, affected by root exudates, and inhabited by a diverse array of microorganisms associated with plants, known as the “rhizobiome” or “rhizosphere microbiome.” [91]. Plant growth-promoting fungi (PGPF) in the rhizosphere, such as Gliocladium spp., arbuscular mycorrhizal fungi, and Trichoderma spp., also contribute to increased crop production and plant resistance to both abiotic and biotic stress by improving plant development and defense systems, mineral solubilization, and pathogen inhibition [4]. Thus, the rhizosphere microbiome plays a crucial role in plant growth, productivity, nutrient acquisition, overall plant health, and soil quality, thereby enhancing plant resistance to both biotic and abiotic stresses.

The composition of the rhizosphere is determined by various factors, including soil properties, plant root exudates, plant age or developmental stage, environmental conditions, chemical compounds, and the microorganisms themselves [129, 151]. Pear fruits treated with 1-methylcyclopropene (1-MCP) to prevent post-harvest decay caused by pathogenic fungi changed the bacterial and fungal microbiota, decreasing the presence of infecting fungi and improving resistance to post-harvest decay [151]. During flooding stress and elevated CO₂ (eCO₂) conditions, bacterial and fungal communities associated with soybean plants increased compared to non-stressed plants, with Trichoderma being among the most abundant fungal genera in the eCO₂ and eCO₂ + flooding treatments [27], indicating that abiotic stress factors can induce significant shifts in plant microbiome structure.

Root exudates from stressed tomato plants exposed to either the foliar pathogen B. cinerea or abiotic stress, such as salinity or wounding, attracted T. harzianum more strongly than non-stressed plants. Furthermore, tomato and cucumber plants infected with B. cinerea exhibited increased T. harzianum growth when inoculated near the roots [77], showing that changes in root exudates due to plant stress can attract beneficial soil microbes, such as Trichoderma. Therefore, any change in rhizobiome composition can potentially alter its ecological functions, affecting the overall health of the plant and rhizosphere [129].

Trichoderma is present in the root microbiome of various agriculturally important plants. For instance, Trichoderma has been found in the rhizosphere of cotton plants that are resistant to Verticillium wilt [146]. de Sousa et al. [34] analyzed the microbiome of five coffee species (Coffea arabica, C. canephora, C. stenophylla, C. racemosa, and C. liberica) and found several bacterial genera, including Streptomyces, Bradyrhizobium, and Mycobacterium, as well as fungal species, such as Rhizophagus, Fusarium, and Trichoderma among the most abundant. Olowe et al. [89] isolated seven Trichoderma strains from the rhizospheres of maize, banana, and cassava plants. All isolates showed antagonistic capacity against two Fusarium isolates, suggesting the potential of rhizospheric Trichoderma as a biocontrol agent and its presence in maize rhizosphere. Microorganisms in the plant rhizosphere mediate nutrient acquisition under stressful conditions. Under nutrient deprivation, plants secrete secondary metabolites into the soil, signaling rhizospheric microorganisms to make nutrients available to the plant and thereby indirectly promoting growth [93]. Trichoderma was no exception: co-inoculation of four T. asperellum isolates and B. subtilis in the rhizosphere of Marandu grass (Urochloa brizantha cv. Marandu) improved nitrogen, potassium, and phosphorus uptake and promoted plant growth [32]. Inoculation with T. viride alone or with Azotobacter chroococcum increased soil micro- and macronutrients, enhancing the growth of cotton and wheat [138]. As a rhizosphere inhabitant, Trichoderma uses biocontrol and plant growth-promoting traits to support plant health. For example, seven rhizospheric Trichoderma isolates, including T. virens, T. harzianum, T. erinaceum, and T. koningiopsis, inhibit the growth of Fusarium proliferatum, a plant pathogen [89]. A microbial consortium of T. harzianum and B. subtilis (a commercial product called Micro-ecological Agents for Controlling Continuous Crop Diseases; Sino Green Agri-Biotech Co. Ltd., Beijing, China) helped reduce the disease index of potato common scab in potato plants, thereby increasing tuber yield [143].

Adedayo and Babalola [4] reviewed the plant growth-promoting mechanisms of PGPF, including Trichoderma spp., highlighting their significance as bioagents to enhance crop yields and resistance to abiotic and biotic stress, and demonstrating the key role of PGPF, such as Trichoderma in maintaining healthy plant environments. Table 1 presents some of the most recent studies involving Trichoderma strains isolated from, or associated with, the rhizosphere.

Table 1.

Example studies on rhizospheric Trichoderma species with biological control action against various pathogens and benefited crop plants

Trichoderma species/strain	Origin	Biocontrolled pathogen(s)/Disease	Beneficiated crop	Mechanisms of action	References
T. harzianum MC2 and NBG	Rhizosphere of tomato, brinjal, and chili	Suppressed bacterial wilt caused by Ralstonia solanacearum	Tomato (Solanum lycopersicum)	Antagonistic activity, promotion of plant growth, production of secondary metabolites	[104]
T. asperellum TaspHu1	Rhizosphere soil of Juglans mandshurica	Enhanced growth, resistance to Alternaria alternata	Tomato (Solanum lycopersicum)	Stress tolerance, increased enzyme activity, enhanced nitrogen absorption	[149]
T. atroviride C52	Soil with Sclerotium cepivorum	Controlled onion root rot	Onion (Allium cepa)	Rhizosphere competence, formulation-dependent effectiveness	[80]
T. virens	Tomato plant rhizosphere	Inhibited growth of rhizosphere bacteria	Tomato (Solanum lycopersicum)	Secreted proteins and metabolites inhibit bacteria, volatile compounds affect interactions	[69]
T. pseudoharzianum T1	Rhizosphere soil of Syringa oblata	Biocontrol of Microsphaera syringejaponicae	Syringa oblata	Induction of ABA production, increase in catalase activity	[76]
T. viride	Soybean rhizosphere	Reduced disease index in soybean root rot	Soybean (Glycine max)	Altered microbial community, increased diversity, and reduced relative abundance of pathogenic fungi	[39]
T. asperellum 7316	Castor plant roots	Limiting Fusarium oxysporum infection	Castor (Ricinus communis L.)	High rhizosphere competence, mycoparasitic ability, enhanced plant growth	[100]
T. asperelloides, T. koningiopsis	Rhizosphere of Ilex paraguariensis	Controlled Fusarium oxysporum and Fusarium solani	Ilex paraguariensis	Inhibited mycelial growth, increased oxidative enzymes	[103]
T. virens T1-02	Rhizosphere of flamingo flower	Controlled flower blight caused by Neopestalotiopsis clavispora	Anthurium andraeanum	Production of volatile antifungal compounds, direct parasitism	[10]
Trichoderma asperellum (TR1, TR2, TR3, TR6) Trichoderma hamatum (TR4, TR5)	Subabul rhizospheric soil	Effective against Fusarium equiseti (70–90% inhibition)	Subabul (Leucaena leucocephala)	Production of volatile metabolites, siderophores, nutrient solubilization (P and K)	[95]
Trichoderma atroviride (ATR697) Trichoderma longibrachiatum (LON701)	Red pepper rhizosphere	Effective against Colletotrichum acutatum	Red pepper (Capsicum annuum)	Production of volatile organic compounds (VOCs), inhibiting mycelial growth, resistance to chemical fungicides	[63]
Trichoderma gamsii (RH4)	Rhizosphere of black gram (Vigna mungo)	Protective against Fusarium oxysporum	Black gram (Vigna mungo)	Lytic properties, enzyme production, growth promotion	[137]
Trichoderma virens	Tomato rhizosphere	Enhanced growth, suppresses Fusarium oxysporum	Tomato (Solanum lycopersicum)	Volatile compounds affecting pathogen growth	[14]
Trichoderma harzianum (TBR-7)	Rhizosphere of Egyptian clover (Trifolium alexandrinum)	Antagonistic against crown rot pathogens	Egyptian clover	Upregulation of defense enzymes, seed treatment, foliar spray	[20]
Trichoderma asperellum, Trichoderma spirale	Rubber tree rhizosphere	Inhibitory against Rigidoporus microporus	Rubber tree (Hevea brasiliensis)	Production of antifungal metabolites, hydrolytic enzymes	[41]
Trichoderma spp.	Soil from diverse regions of Lorestan Province, Iran	Control of Rhizoctonia solani	Strawberry (Fragaria × ananassa)	Production of volatile metabolites, enhancing plant defense mechanisms	[81]
Trichoderma virens, Trichoderma harzianum	Rhizospheric of banana in Tenerife	Biocontrol against Fusarium oxysporum f. sp. cubense	Banana (Musa acuminata)	Diversity in Trichoderma species correlates with soil chemistry	[31]
Trichoderma spp. (PBT3, PBT4, PBT9, PBT13)	Various rhizospheric soils	Antagonistic against Fusarium oxysporum f.sp. ciceri and Sclerotium rolfsii	Chickpea (Cicer arietinum)	Production of antifungal metabolites, cell-wall degrading enzymes	[66]

Trichoderma in the endosphere

Endophytic microorganisms inhabit plant tissues such as roots, stems, leaves, flowers, fruits, and seeds without causing apparent damage. In this hidden world, they can interact with their plant hosts, aiding in their defense against pathogens, stimulating growth, and increasing production. Among these endophytic microorganisms, we found various fungal species belonging to the genera Piriformospora, Penicillium, Beauveria, Serendipita, and Glomus. Additionally, nonpathogenic strains have been reported as endophytes from genera such as Colletotrichum, Phoma, Fusarium, and Alternaria [15, 98]. In the case of Trichoderma, species have also been reported living as endophytes in crops, such as T. harzianum, T. viride, T. asperellum, to name a few [114].

A recent example of the beneficial effects of endophytic strains of Trichoderma was recently published Hasan et al. [49]. In this study, two strains of Trichoderma spp., ReTk1 and ReTv2 were isolated, and their potential for promoting plant growth and biocontrol of clubroot disease caused by the pathogen Plasmodiophora brassicae in rapeseed plants (Brassica napus L.) was evaluated. Rapeseed is one of the most important vegetable oil crops in the world. These two endophytic strains promoted plant growth by increasing parameters such as shoot and root length, leaf diameter, and total biomass production. Furthermore, both the ReTk1 and ReTv2 strains showed relevant results in inhibiting the germination of resting spores of P. brassicae in root exudate experiments, indicating a possible mechanism of action. Additionally, the authors reported that both endophytic strains stimulated the expression of defense-related markers involved in the jasmonate (BnOPR2), ethylene (BnACO and BnSAM3), auxin (BnAAO1), and salicylic acid (BnPR2) pathways, demonstrating the excellent potential of these strains with multiple benefits for their plant host, Brassica napus L.

Another study reported Rajani et al. [105] that endophytic strains of Trichoderma were able to restrict the growth of pathogens, such as Sclerotinia sclerotiorum, Sclerotium rolfsii, and Fusarium oxysporum, where mechanisms such as mycoparasitism and the production of volatile organic compounds are relevant in antagonism. Similarly, the volatiles produced by the endophyte T. asperelloides PSU-P1 demonstrated their function as antagonists of various pathogens, such as Colletotrichum sp., Corynespora cassiicola, Curvularia lunata, Ganoderma sp., Penicillium oxalicum, Neopestalotiopsis clavispora, S. rolfsii, and Stagonosporopsis cucurbitacearum. Additionally, volatiles such as 2-methyl-1-butanol, 2-pentylfuran, acetic acid, and 6-pentyl-2H-pyran-2-one (6-PP) stimulate growth and defense responses in Arabidopsis thaliana plants [97].

In recent years, there has been an effort to find genetic or genomic differences that result in intrinsic characteristics that differentiate Trichoderma strains capable of living as endophytes from those that do not. The rationale is based on studies showing that plants produce metabolites, such as flavonoids, phenolics, and terpenes, which have defensive functions, and that endophytes must have tolerance/resistance mechanisms against these plant compounds. Therefore, only those species of Trichoderma with these capabilities will be able to colonize the interior space of a plant, including vascular tissues, without causing damage or colonizing various aerial and root parts.

Thus Scott et al. [120], through a comparative genomic analysis of more than 38 genomes from the metabolic repertoire of endophytic and non-endophytic Trichoderma strains, we found greater diversity in biosynthetic gene clusters (BGC) and degradative gene clusters (DGC) in the endophytic strains. Although variations in BGCs and DGCs might be attributed to species differences rather than lifestyle, genome comparisons should be conducted within a single species using isolates with distinct lifestyles to confirm this. However, this is an effort to discern intrinsic differences between endophytic strains and those that are not, for example, may only colonize regions such as the rhizosphere or phyllosphere, where plant metabolites may not be “toxic or restrictive” for colonization by these Trichoderma strains. Years before, a similar study attempting to discern the genetic capabilities of endophytism, but in endophytic bacteria versus rhizospheric ones, was conducted by Ali et al. [8], comparing the genomes of nine plant growth-promoting endophytic bacteria (PGPB), including genera such as Azoarcus, Azospirillum, Burkholderia, Enterobacter, Klebsiella, Pseudomonas, and Serratia. From this comparative analysis, genes with potential roles in endophytic colonization were identified, such as transporter proteins, secretion and delivery systems, plant polymer degradation/modification, detoxification, and redox potential maintenance.

As can be seen in the studies mentioned above, some functions are related to resistance mechanisms to the endophytic environment, where the plant, either constitutively or induced, produces defense compounds against pathogens. However, these endophytes have tolerance mechanisms, either by degrading or modifying their structure to mitigate their “antimicrobial” effect [8, 120]. Table 2 shows recent studies involving endophytic Trichoderma strains, as well as some phyllospheric strains, and their biocontrol roles against multiple plant pathogens.

Table 2.

Key studies on endophytic and phyllospheric Trichoderma species with biocontrol activity against various pathogens

Trichoderma species/strain	Origin	Biocontrolled pathogen(s)/Disease	Beneficiated crop	Mechanisms of action	References
T. harzianum KUFA0436, KUFA0437	Endophytic	Phytophthora palmivora (Phytophthora leaf fall)	Rubber (Hevea brasiliensis)	Fast growth, competition for resources, antifungal crude extract production	[127]
T. longibrachiatum MD33	Endophytic	None (focus on enhancing dendrobine production)	Dendrobium nobile	Enhancement of secondary metabolite production (dendrobine)	[115]
T. asperellum KUFA0702, KUFA0703, T. harzianum KUFA0710, KUFA0713	Endophytic	Exserohilum turcicum (Northern leaf blight)	Corn (Zea mays)	Fast growth, nutrient competition, antifungal crude extract production	[75]
T. longibrachiatum WKA55	Endophytic	Mycotoxinogenic fungi	Peanut (Arachis hypogaea)	Enzymatic activity (cellulase, protease, polygalacturonase), citric acid production	[6]
T. erinaceum	Endophytic	Pythium ultimum	Common bean (Phaseolus vulgaris)	Mycelial growth inhibition through new alkene and known bioactive compounds	[124]
T. asperellum T-AS2, T-AS7, T. harzianum T-H5	Endophytic	Phytophthora cinnamomi (Avocado root rot)	Avocado (Persea americana)	Competition, resource exclusion, inhibition of pathogen spread	[9]
T. longibrachiatum MD33	Endophytic	None (focus on producing dendrobine)	Dendrobium nobile	Production of bioactive compounds, antibacterial activity	[116]
Trichoderma sp. T154	Endophytic	Phaeoacremonium minimum (Grapevine trunk disease, esca)	Grapevine (Vitis vinifera)	Spore adhesion, niche exclusion, hyphal coiling	[24]
Trichoderma gamsii T6085	Endophytic	Fusarium head blight (FHB)	Wheat (Triticum aestivum’Apogee’)	Induction of defense genes: pal1, pr1, pgip2 and lox1 genes	[108]
Trichoderma zelobreve T20	Endophytic	Cytospora cincta and Neoscytalidium dimidiatum (apple canker)	Apple trees	Not specified	[107]
Trichoderma asperellumstrain 6S-2	Endophytic	Fusarium proliferatum f. sp. malus domestica MR5	Apple replant disease (ARD)	Protease, amylase, cellulase, and laccase activities	[144]
T. asperelloides PSU-P1	Endophytic	Colletotrichum sp. (Leaf blight), Corynespora cassiicola (Leaf spot), Curvularia lunata (Leaf spot), Ganoderma sp. (Basal stem rot), Penicillium oxalicum(Blue mold), Neopestalotiopsis clavispora (Flower blight), Sclerotium rolfsii (Southern blight), Stagonosporopsis cucurbitacearum (Gummy stem blight)	A. thaliana	Volatiles: 2-methyl-1-butanol, 2-pentylfuran, acetic acid, and 6-pentyl-2H-pyran-2-one (6-PP)	[97]
Nineteen Trichoderma strains	Endophytic	Colletotrichum truncatum, Lasiodiplodia theobromae, Macrophomina phaseolina, and Sclerotium delphinii	Not specified	Antibiosis, together with multiple mechanisms	[83]
Trichoderma sp. strain BHUF4	Phyllospheric	Colletotrichum capsici	Chili (Capsicum annuum L.)	Stimulation of antioxidant enzymes; reduced anthracnose lesions in chili leaves	[119]
Trichoderma sp. strain BHUF4	Phyllospheric	Colletotrichum truncatum	Chili (Capsicum annuum L.)	Stimulation of the defense responses	[118]

Trichoderma in the phyllosphere

According to Vorholt [141], the surface area of the phyllosphere is approximately twice the size of the Earth’s surface, providing a vast habitat for a wide variety of microorganisms. Naturally, the conditions in the soil or within plant tissues differ greatly from those encountered by organisms living as epiphytes on plant surfaces; therefore, they must possess innate colonization abilities to adapt and survive in such environments [16]. In fact, the phyllosphere can be a hostile environment, subject to continuous environmental fluctuations and exposure to UV radiation, sunlight, rain, ice, and more. As a result, microbial densities are usually lower compared to other ecosystems such as the rhizosphere or bulk soil [65, 145]. The topology of plant leaves, as well as their age and leaf side (adaxial and abaxial), are important factors in establishing the structure and diversity of microbial communities in the phyllosphere [40, 70, 128]. In agroecosystems, the phyllosphere can also be sprayed with agrochemicals that may be bactericidal or fungicidal, thereby altering both pathogenic and beneficial microbial communities [147]. The same occurs with bioinoculants, which, when inoculated in the phyllosphere, can alter the microbiota residing there [102]. This is also the case when Trichoderma harzianum (strain T22) was inoculated in the strawberry phyllosphere, as fungal communities were altered but bacterial communities were not [132], suggesting some specific interactions between these fungal communities and Trichoderma that require further investigation.

In the case of Trichoderma, this mycoparasitic fungus has also been reported as a phyllosphere inhabitant, although the number of studies reporting its isolation, presence, or characterization in this habitat is lower compared to rhizospheric or endophytic isolates (Fig. 2). This research bias has contributed to a greater understanding of Trichoderma as a rhizospheric antagonist [37]. In contrast, studies on its interactions within other specific plant zones, such as the endosphere and phyllosphere, remain scarce and remain poorly understood and require more focused investigation [29].

Fig. 2.

Number of documents retrieved from the Scopus database using keywords such as “Trichoderma” AND either “rhizosphere,” “endosphere,” or “phyllosphere/epiphyte” (https://www.scopus.com). This illustrates the significant disparity in research attention, with phyllospheric Trichoderma being notably less studied compared to isolates from endosphere and rhizosphere ecosystems

To address this, Saxena et al. [119] we evaluated and compared the biocontrol capabilities of a phyllospheric Trichoderma strain (BHUF4) and a rhizospheric strain (T16A) against the pathogen Colletotrichum capsici, which causes anthracnose disease in chili (Capsicum annuum L.). The results showed that the phyllosphere isolate stimulated defense networks in plants, where enzymes such as phenylalanine ammonia-lyase (PAL), peroxidase (PO), polyphenol oxidase (PPO), superoxide dismutase (SOD), and total phenolic content (TPC) were significantly increased. It also significantly reduced anthracnose lesions in chili leaves compared to the rhizospheric strain, while promoting plant growth. Later studies by the same research group demonstrated that the phyllospheric Trichoderma strain BHUF4 stimulated the systemic acquired resistance (SAR) pathway, whereas the rhizospheric Trichoderma strain T16A used the induced systemic response (ISR) pathway to elicit defence responses in the host plant Capsicum annuum L. under C. truncatum inoculation [118].

Recently, the use and application of chlamydospores from T. asperellum T36 and T. harzianum Td50b were evaluated through foliar spraying to improve the physiology and yield of Momordica charantia. M. charantia is a plant from the Cucurbitaceae family, native to tropical and subtropical regions, with extensive culinary and medicinal uses owing to its production of secondary metabolites. The results showed that the chlamydospore suspension significantly improved physiological parameters, polyphenol and flavonoid content, and antioxidant activity in both leaves and fruits. An increase in yield from 25.33% to 53.07% was also observed [13]. These results suggest that the Trichoderma strains demonstrated good colonization and survival capacity in the phyllosphere of M. charantia plants, from which they showed a beneficial interaction with their host.

In another recent study, the influence of spore concentration on the phyllosphere colonization capacity of a Trichoderma consortium in Passiflora caerulea was evaluated. The authors reported that morphological, physiological, and ultrastructural characteristics, as well as fruit yield and quality, were improved by these Trichoderma strains [122]. The inoculated consortium consisted of the same two strains reported in previous studies: T. asperellum T36b and T. harzianum Td50b.

Due to their sessile nature, plants are subjected to interactions with microorganisms, including beneficial fungi such as Trichoderma, especially in environments such as the phyllosphere [16]. Therefore, it is advisable to further investigate the succession of phyllospheric Trichoderma communities and their influence on plant growth, development, and health. It is currently unknown whether there are specific interactions with certain plant hosts and whether these are of agro-food importance. Just as some interactions occur in the rhizosphere, where root exudates influence specific interactions to recruit a beneficial microbiome, it is unknown what type of compounds, whether diffusible or volatile organic compounds, attract Trichoderma strains and promote their recruitment.

Interplay between Trichoderma and plant-associated microorganisms

Microorganisms do not exist in isolation within their environments, and Trichoderma not only interacts with its plant or fungal hosts but also with other beneficial microorganisms such as plant growth-promoting bacteria (PGPB) or PGPF-like mycorrhiza [96]. This interplay, or crosstalk, between microbiome organisms and plants is complex, with Trichoderma engaging in interactions and communication with other plant-associated organisms. Microorganisms use various molecules for communication, including secondary metabolites and effector proteins [96]. This communication is essential among microorganisms within the plant microbiome, shaping their relationships with both plants and each other.

A study on metabolites, volatile compounds, and proteins produced by T. virens and T. harzianum Li et al. [69] demonstrated that these compounds mediate interactions with different rhizospheric bacteria, including phyla such as Firmicutes, Alpha-proteobacteria, and Gamma-proteobacteria, affecting bacterial growth to varying extents. Additionally, compounds secreted from T. atroviride were found to inhibit the growth of PGPB, such as Bacillus velezensis AF12 and Bacillus halotolerans AF23, but did not affect the growth of Pseudomonas fluorescens UM270 [47].

Effector molecules from Trichoderma have been studied as key communication molecules with their hosts that modulate the nature of these interactions [106, 112]. Trichoderma effectors are involved in mycoparasitic interactions with plant pathogens such as R. solani, B. cinerea, S. cepivorum, and C. lindemuthianum [45, 112], as well as in beneficial interactions with plants that induce resistance and promote growth [110]. Effector-coding genes from Trichoderma also respond to PGPBs, which are commonly found in the rhizosphere [47].

Thus, secondary metabolites and effector molecules of Trichoderma play a role in communicating with other beneficial microorganisms, potentially influencing their interactions. This suggests that as part of the plant microbiome, Trichoderma utilizes its molecular arsenal to communicate and interact with microbial communities associated with plants.

Trichoderma as a key player in plant microbiome dynamics

Plants exert strong modulatory effects on soil microbiomes [56]. Root exudates influence the assembly of microorganisms that are associated with the root microbiome. For example, coumarins in the root exudates of Arabidopsis thaliana shape the plant microbiota to promote health by activating the MYB72 transcription factor, which is induced in the presence of beneficial microorganisms, such as T. asperellum T-34 and T. harzianum T-78 [94, 131]. This suggests that beneficial microorganisms capable of inducing changes in root exudates may help plants to endure environmental stress. Because plants modulate their associated microbiomes, microorganisms can influence each other. Several studies have found that the presence of Trichoderma in the rhizosphere can alter microbiota composition, favoring the presence of plant-beneficial microorganisms.

The inoculation of T. harzianum LTR-2 in the cabbage rhizosphere increased the abundance of beneficial bacteria, such as Pseudomonas and Bacillus, conferring resistance to clubroot disease, compared to non-inoculated rhizospheres [72]. Seed coatings of T. guizhouense on watermelon and maize modified the microbial community of the rhizosphere, correlating with improved seed germination and plant growth and promoting beneficial microbes such as Trichoderma spp. and Mortierella [148].

The presence of T. viride affected microbial diversity in the soybean rhizosphere, with Planctomycetes, Patescibacteria, and Myxococcota being the most abundant bacterial phyla, whereas Ascomycota and Mortierellomycota were the predominant fungal phyla. These changes were correlated with a reduction in soybean root rot disease [39].

In tomato plants, inoculation with T. virens influenced the relative abundance of fungal and bacterial phyla and genera associated with the plant, promoting tomato growth, especially when applied at transplant, suggesting that inoculation methods can affect interactions with plants and other microorganisms [14]. The dual inoculation of T. viride and dark septate fungi effectively protected Astragalus mongholicus plants against drought, enriching rhizosphere soil fungi, including Stachybotrys and Trichoderma, with being Ascomycota the main fungal phylum, compared to non-inoculated plants [50]. In watermelon, inoculation with T. asperellum M45a reduced fungal diversity while increasing beneficial bacteria such as Pseudomonas, enhancing resistance to F. oxysporum f. sp. niveum wilt disease, and promoting plant growth [153]. Umadevi et al. [136] showed that the presence of T. harzianum in the rhizosphere of Piper nigrum plants altered the microbial community and its functional dynamics, selectively recruiting beneficial microbial communities, as indicated by a reduction in pathogenicity islands and an increase in plant growth-promoting fungi.

Trichoderma and the pathobiome concept

The term pathobiome was recently used to refer to a group of associated microorganisms, as well as their interactions with the plant causing an infection, and consequently, symptoms of a disease develop [78]. This concept of the pathobiome has previously been employed to define dysbiosis in human hosts and in studies on gut microbiota. In the case of plants, this concept has gained relevance because of its similarities to the human microbiome and its role in disease development. Therefore, it can be said that the pathobiome arises from the interactions generated between the plant, the associated microbiome, and potential pathogens [38]. Under this concept, what role does Trichoderma play? How can mycoparasitic fungi control the emergence of a pathobiome? These are questions that still lack clear answers, although Trichoderma has been widely studied as a biocontrol fungus of single-pathogen diseases, its role as a regulator of interactions within the pathobiome has not yet been clearly studied.

Within this concept, Trichoderma could play a significant role in reducing pathogen proliferation in ecosystems such as the rhizosphere, ultimately affecting the assembly of several pathogens that could lead to a state of infection in the plant host. The disease state caused by multiple species has been reviewed in Abdullah et al. [3], where they analyzed studies of co-infection in susceptible plant hosts and proposed some pathogen interactions that enable infection. Some of these include competition for physical space and resources, cooperation between pathogens, where they beneficially interact through chemical signals, and functional complementation via the exchange of resources necessary for survival in the environment. Finally, niche specialization allows the coexistence of pathogens, which can lead to greater infection and disease development.

Droby et al. [36] recently reported that the pathobiome concept can be applied to postharvest diseases, where changes in the microbiome of fruits and vegetables may also be responsible for the onset of diseases. In the case of fruits and vegetables, damage such as wounds could be a factor that creates a condition in which the pathobiome emerges, and multiple species of pathogens “take advantage” of the availability of resources. Through cooperation and colonization, they infect and damage produce. The authors mentioned some examples of postharvest diseases involving multispecies causal agents, such as banana crown rot, apple diseases originating from latent infections by fungal pathogens such as Colletotrichum spp. and Neofabraea spp., as well as stem-end rots in fruits such as mango and avocado.

In this context, Trichoderma has been applied as a biocontrol agent against postharvest diseases of various fruits and vegetables [71], and its role as a biocontrol agent for multiple species should continue to be investigated, especially as a regulator of interactions within the pathobiome, as previously mentioned. Figure 3 shows the pathobiome concept and how the microbiome, including Trichoderma (and other PGPB, beneficial fungi, etc.), could potentially regulate the proliferation of pathogens through different mechanisms of action. However, the role of Trichoderma in modulating microbiome interactions remains unknown. One possibility could be the production of effector-type proteins, which would not only regulate plant metabolism but also affect the effector proteins produced by pathogens to infect the plant host [45]. At the same time, it induces the plant’s immune system (ISR) and defense mechanisms, making it less susceptible to the pathogen. However, this hypothesis requires further investigation.

Fig. 3.

General overview of the pathobiome concept. Under optimal growth conditions, a healthy plant is associated with its beneficial microbiome, or symbiome—the latter referring to the total assemblage of associated organisms, excluding the plant itself. Over time, pathogen proliferation can disrupt this balance, leading to the formation of a pathobiome. In this state, interactions among the plant, its microbiome, and pathogens result in infection and disease. Such a disruption mirrors dysbiosis observed in the human gut microbiome [142]

Perspectives of Trichoderma research

The presence of beneficial microorganisms in the plant microbiome is crucial for the development of new biocontrol agents and promoters of plant growth. An emerging agricultural biotechnology is microbiome engineering, which involves the modulation or manipulation of the plant microbiome to harness its benefits in improving plant production and resistance to environmental stress factors [92, 109, 139]. Thus, manipulating the plant microbiome using plant-associated microorganisms such as Trichoderma spp. could be of great importance for enhancing sustainable agricultural techniques.

A four-species synthetic community (SynCom), Stenotrophomonas sp., Rhizobium sp., Advenella sp., and Ochrobactrum sp., selected from the rhizosphere of A. mongholicus plants infected with Fusarium oxysporum, was effective at reducing root rot disease [67]. Gonçalves et al. [42] designed a microbial community associated with Vellozia epidendroides and Barbacenia macrantha plants to fulfill specific microbiome functions, such as nitrogen fixation, phosphorus solubilization, and siderophore production, to better understand and enhance plant–microbe interactions. Shi et al. [123] constructed 18 SynComs based on their ability to antagonize Fusarium spp. that cause potato dry rot disease, showing promising results as biocontrol agents.

Synthetic communities designed to control Fusarium wilt in banana plants were effective against the pathogen using a combination of various beneficial microorganisms, including Trichoderma and plant growth-promoting bacteria (PGPB) [101]. This demonstrates the biocontrol potential of modulating the diversity of microorganisms associated with plants of interest. T. simmonsii, in combination with Serendipita indica, showed biocontrol capacity against Phytophthora capsici on bell pepper plants [111], whereas a consortium formed by T. harzianum and Bacillus subtilis improved potato yield and increased plant resistance against common scab disease [143].

Therefore, modulating microbial communities with Trichoderma could be a part of agricultural management techniques aiming to achieve optimal combinations of microorganisms to benefit the plant [47, 99]. The use of specific Trichoderma species according to particular agricultural needs aims to optimize beneficial interactions with plants [99] and/or develop more efficient inoculants.

The presence of different Trichoderma species in the rhizosphere appears to correlate with changes in microbial communities that are part of the plant microbiome. Its presence as part of plant-associated microbes is beneficial, demonstrating its potential as a biocontrol agent and biostimulant for improved and sustainable agriculture. In fact, there are studies in which Arabidopsis plants have been propagated under sterile conditions and inoculated with a synthetic microbiome, clearly showing the effects of such inoculation. These studies have revealed how complex the environment and the interactions between different players can be in a changing environment, but the mechanisms governing such dynamics are beginning to be uncovered [142]. Under these conditions, Trichoderma may play an important role in modulating the plant microbiome, recruiting beneficial microorganisms, and improving soil quality. Therefore, all these interactions are fundamental for achieving consistent and positive results under open-field conditions, which will help mitigate unpredictable abiotic factors.

Conclusions

In summary, Trichoderma spp. are pivotal components of the plant microbiome, significantly contributing to sustainable agricultural practices through their roles as plant growth promoters and biocontrol agents. Their multifaceted interactions with plants and associated microorganisms enhance nutrient uptake, improve resistance to abiotic stress, and suppress pathogen proliferation. The ability of Trichoderma to modulate the dynamics of the plant microbiome underscores its potential as a biotechnological tool to improve crop productivity and resilience. This review highlights the importance of understanding the mechanisms underlying Trichoderma interactions in various plant-associated environments, such as the rhizosphere, endosphere, and phyllosphere, as well as its role in the emerging concept of the pathobiome.

Despite progress made in understanding Trichoderma interactions within the plant microbiome, several research gaps remain. Future studies should focus on elucidating the molecular mechanisms underlying the beneficial effects of Trichoderma, particularly in relation to its interactions with diverse plant species under varying environmental conditions. Additionally, exploring the genetic and genomic differences between endophytic and non-endophytic Trichoderma strains could provide insight into their ecological roles and adaptability.

There is a pressing need for research on the synergistic effects of Trichoderma when combined with other beneficial microorganisms, as this could lead to the development of more effective microbial consortia for agricultural applications. Investigating the interactions of Trichoderma with the pathobiome is also crucial for understanding how to manage plant diseases in a holistic manner.

Furthermore, the integration of Trichoderma into microbiome engineering approaches holds promise in enhancing plant health and productivity. Future research should aim to optimize the application methods and formulations of Trichoderma inoculants to maximize their benefits under field conditions. By addressing these research gaps, we can unlock the full potential of Trichoderma as a cornerstone for sustainable agriculture, paving the way for innovative solutions to meet the challenges of food security and environmental sustainability.

Authors’ contributions

PG and GS drafted the first version of the work with significant input and revisions from HE. All authors have approved the final version.

Funding

G.S. thanks CONAHCYT-Mexico, CIC-UMSNH, and ICTI-Michoacan for their support of his research projects.

Data availability

No datasets were generated or analysed during the current study.

Declarations

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare no competing interests.