The Biocontrol and Growth-Promoting Potential of Penicillium spp. and Trichoderma spp. in Sustainable Agriculture

Abstract

Plant-growth-promoting fungi (PGPF) play a central role in promoting sustainable agriculture by improving plant growth and resilience. The aim of this literature review is to survey the impacts of Trichoderma spp. and Penicillium spp. on various agricultural and horticultural plants. The information provided in this manuscript was obtained from randomized control experiments, review articles, and analytical studies and observations gathered from numerous literature sources such as Scopus, Google Scholar, PubMed, and Science Direct. The keywords used were the common and Latin names of various agricultural and horticultural species, fungal endophytes, plant-growth-promoting fungi, Trichoderma, Penicillium, microbial biostimulants, and biotic and abiotic stresses. Endophytic fungi refer to fungi that live in plant tissues throughout part of or the entire life cycle by starting a mutually beneficial symbiotic relationship with its host without any negative effects. They are also capable of producing compounds and a variety of bioactive components such as terpenoids, steroids, flavonoids, alkaloids, and phenolic components. Penicillium is extensively known for its production of secondary metabolites, its impact as a bioinoculant to help with crop productivity, and its effectiveness in sustainable crop production. The plant-growth-promotion effects of Trichoderma spp. are related to better absorption of mineral nutrients, enhanced morphological growth, better reproductive potential and yield, and better induction of disease resistance. Both Penicillium spp. and Trichoderma spp. are effective, affordable, safe, and eco-friendly biocontrol agents for various plant species, and they can be considered economically important microorganisms for both agricultural and horticultural sciences. The present review article aims to present the most up-to-date results and findings regarding the practical applications of two important types of PGPF, namely Penicillium spp., and Trichoderma spp., in agricultural and horticultural species, considering the mechanisms of actions of these species of fungi.

1. Introduction

Plant-growth-promoting microorganisms (PGPM) include fungi, bacteria, and other microorganisms that improve the performance of plants as well as increase their nutrient absorption under both abiotic and biotic stress conditions, with notable potential advantages for the growth and development of seedlings [1,2,3]. Plant-growth-promoting fungi (PGPF) are a group of non-pathogenic soil-borne filamentous fungi that exert positive effects on plants; these can enhance plant growth both indirectly and directly by producing phytohormones, fixing nitrogen, and inducing systemic resistance [4,5,6]. Trichoderma and Penicillium are the most effectual organisms among the numerous phosphate-solubilizing fungi that can dissolve insoluble phosphate and improve its uptake by plant roots, which are the main reasons for the plant’s appropriate growth and development [7,8,9]. In many research studies, it has been reported that a combination of biologically active compounds of plant or microbial origin, or their synthesized analogues, together with fungicides is a promising and sustainable approach to controlling crop diseases [10]. Fungi show significant metabolic properties because of their sophisticated genomic network, and they have notable importance because of their different roles in our world, such as in their applications in agriculture, industry, and medicine. Filamentous fungi of the genera Trichoderma have been widely studied because they can interact with and colonize plant roots via different processes that can increase plant growth through phytohormone synthesis, nutrient absorption, tolerance to abiotic stress, and the induction of systemic resistance as well as by acting as biological control factors. Their applications and their wonderful roles in environmentally friendly agricultural practices for different crops such as lettuce, soybean, wheat, corn, tomato, beans, etc., have been mentioned in previous research studies [11,12,13,14].

Some species of Penicillium produce different biologically active compounds [15,16,17], some of them with an extensive range of fungicidal action [18,19] and plant growth-stimulating activity [20]. Different species of Penicillium can significantly improve the dry and fresh weight of shoots as well as enhance the chlorophyll content [21]; for example, P. pinophilum can form arbuscular mycorrhizae, which can enhance the nitrogen content, photosynthesis rate, P content, and plant dry weight of strawberry plants [22]. The free-living soil fungi Trichoderma spp. are potential biological control agents of plant-parasitic nematodes [23], and they can control a wide range of economically notable plant pathogenic fungi, nematodes, bacteria, and viruses [24,25]. Trichoderma is the asexual stage of the filamentous Hypocrea genus belonging to the Ascomycota fungi division [26], and it is considered the most frequently isolated soil microorganism [27]. As PGPF, Penicillium spp. are known to grown in extreme conditions such as areas with high salt concentrations, and their application has increased in recent years due to their noticeable ability to increase salt-stress tolerance in different plant species as well as increase the levels of chemical components and improve the antioxidative system through the production of organic acids. Penicillium species can inhibit pathogens in the soil, and they are also highly effective in fixing potassium, dissolving phosphorus, and solubilizing soil-bound phosphate. In fact, Penicillium species can increase the absorption of phosphorus, improve soil conditions, help plants defend against diseases, and improve seed protection in plants facing pathogens. There has not been enough research on the effects of Penicillium fungi on plants, and more research is needed to study the effects of Penicillium fungi on soil phosphorus cycling and phosphorus uptake in plants as well as their importance in increasing plant growth. P. citrinum has been found to be a common endophytic fungus in cereal plants and has been isolated from various environmental conditions, ranging from permafrost sediments to agricultural fields and forest soils [28].

Trichoderma species such as T. harzianum, T. viride, T. atrovitide, T. hamatum, T. virens, and T. longibrachiatum are common in root and soil ecosystems, where they can establish root colonization, enhance crop productivity, growth and development, increase the use and uptake of nutrients, and improve resistance to abiotic stresses [29,30,31]. Chinnaperumal et al. [32] reported that Trichoderma viride can be considered an important inhibitor of the development of Helicoverpa armigera, with no negative impacts on earthworms. Panchalingam et al. [33] showed the positive effects of the combined use of a Streptomycetes consortium and Trichoderma as a potential biocontrol agent against the brown root rot pathogen Pyrrhoderma noxium (Corner) L.W. Zhou and Y.C. Dai in soil. The volatile organic compounds (VOCs) emitted by Trichoderma spp. have various effects against plant pathogenic fungi such as Sclerotinia nivalis, Cylindrocarpon destructans, Botrytis cinerea, Alternaria panax, Stagonosporopsis cucurbitacearum, Penicillium oxalicum, Ganoderma sp., Fusarium oxysporum, Sclerotium rolfsii, and Sclerotinia sclerotiorum [34,35]. Trichoderma is highly known as a biostimulant because of its main effects on plants, such as stimulating higher nutrient uptake efficiency, improving the rate of photosynthesis and metabolism, and as a potential biocontrol agent. Its different types of products can increase productivity and plant growth, and it can be applied as a good biocontrol agent that does not negatively influence other microorganisms in the soil. Trichoderma-based products have been identified as appropriate biological control agents for different plant pathogens, and they increase resistance to biotic stresses; thus, its different species have gained importance as microbial plant biostimulants in both agricultural and horticultural sciences. They can also mitigate the detrimental effects of abiotic stresses, improve nutritional quality and yield, and enhance plant growth. As important endophytic fungi, Trichoderma spp. can interact with other strains of the microbial community in the rhizosphere, which shows the importance of evaluating the ecological effects of different soil management and microbial-based biostimulants on the soil ecosystem.

Endophytes are known as microorganisms that can be found inside plant tissue without triggering any adverse impacts; rather, they reveal a positive influence on crop yield and plant growth, showing a high capacity for decreasing the need for fertilizer and stimulating plant biochemical components by providing osmoregulation, antioxidative defenses, and affecting nutrient uptake effectiveness during various biotic and abiotic stresses [36,37,38,39,40]. Different endophytic bacteria and fungi, including Bacillus, Actinomycetes, Trichoderma, Pseudomonas, and Epicoccum, were reported to elicit plant disease tolerance in cacao, potato, chili, cotton, and tomato [41]. It is also very important to choose suitable fungal strains, as some strains of the genera Penicillium are pathogens of crops and animals; P. allii is a pathogen of garlic, Penicillium spp. is a pathogen of pear, apple, and citrus fruit [42,43], and P. glabrum is a pathogen of garlic and onion [44].

Plant–fungal interactions can be categorized as mutualistic, commensalistic, and pathogenic [45]. The most important mechanisms of PGPF involve the production of plant growth regulators such as abscisic acid, ethylene, gibberellins, cytokinins, and auxins; the production of organic acids and siderophores such as iron, zinc, potassium, phosphorus, and nitrogen; an increase in water uptake; the production of hydrolytic enzymes such as cellulases, pectinases, laccases, and xylanases; reductions in the amount of ethylene; relief from various abiotic stresses in harsh environments; and the induction of plant defense mechanisms against pathogens [46,47]. Trichoderma spp. and Penicillium spp. can be further studied to improve their ability as effective biocontrol agents; moreover, they show various antagonistic mechanisms against plant pathogens such as mycoparasitism, antibiosis, the promotion of plant growth, and competition for nutrients and space. They can be also considered important candidates for application in green technologies because of their great biostimulatory and biofertilization potential. The aim of this literature review is to survey the impacts of Trichoderma spp. and Penicillium spp. on various agricultural and horticultural plants, with the information provided in this manuscript obtained from randomized control experiments, review articles, and analytical studies and observations gathered from numerous literature sources such as Scopus, Google Scholar, PubMed, and Science Direct. The keywords used were the common and Latin names of various agricultural and horticultural species, fungal endophytes, plant-growth-promoting fungi, Trichoderma, Penicillium, microbial biostimulants, and biotic and abiotic stresses. The benefits and advantages of applications of both Penicillium spp. and Trichoderma spp. are presented in Figure 1.

2. Penicillium spp. as Plant-Growth-Promoting Fungi with Biocontrol Properties

Beneficial Penicillium spp. are used in the production of antibiotics, with the most famous advantage being the production of penicillin by P. chrysogenum, while some species produce griseofulvin, which is an antifungal drug. Other species are used in food and beverage production; in bioremediation, as some Penicillium species can break down different contaminants and pollutants in water and soil; and some species produce enzymes used in different industrial processes. They are also used to promote plant growth and stress tolerance, as certain species can help plants tolerate environmental stresses like drought, salinity, and heavy metals, and they can also increase the nutrient availability and promote root development in various plants. It is also reported that some species such as P. roqueforti and P. camemberti are important for cheese production. When using Penicillium for specific applications, it is essential to select the appropriate strain due to variations in their capabilities and properties.

Pencillium spp. are known to grow in extreme environments such as those with high salt concentrations, and some strains and species have been reported as PGPF with the ability to increase salt tolerance in different plant species [48,49,50,51,52]. Penicillium spp. colonize plant roots via several mechanisms, including endophytism, rhizosphere association, and mycorrhizal-like interactions [53,54,55]. They are often involved in a range of complex interactions with plants and use various strategies and develop distinct ways to mediate improvements in seed vigor, seed germination, plant growth, flowering, and productivity of host plants.

Root colonization by Penicillium spp. or its cell-free filtrate elicited an induced systemic resistance against infection by Pseudomonas syringae pv. Tomato DC3000 (Pst), leading to restricted pathogen growth and disease development [56]. Hossain et al. [56] showed that signal transduction leading to a GP16-2-mediated induced systemic resistance (ISR) requires responsiveness to JA and ET in an NPR1-dependent manner, while the cell-free filtrate (CF)-mediated ISR shows that salicylic acid (SA)-, JA-, ET-, and NPR1-dependent signaling is dispensable (at least individually). Moreover, root colonization by GP16-2 is not connected with a direct effect on the expression of known defense-related genes; however, it potentiates the activation of JA/ET-inducible basic chitinase (ChitB), which only becomes apparent after infection by Pst. But CF-mediated ISR is partly associated with the direct activation of marker genes responsive to both SA and JA/ET signaling pathways and partly associated with priming, leading to the activation of JA/ET-inducible ChitB and hevein-like protein (Hel) genes.

Species of Penicillium are ubiquitous fungi because of their ability to grow over a wide range of environments and conditions and their undemanding nutritional requirements; moreover, the genus is one of the largest groups of fungi. Its important species are P. chrysogenum, P. citreonigrum, P. citrinum, P. digitatum, and P. janthinellum [57,58,59]. Endophytic Penicillium species have different applications in (1) biotechnology—such as in the production of enzymes (such as lipase, inulinase, amylase, protease, cellulase, xylanase, β-glucosidase, etc. [60]), biotransformation [61,62], and the synthesis of nanoparticles like silver nanoparticles [63,64]; (2) agriculture—such as in phytoremediation, biocontrol, and insecticidal activities [65,66,67]; for example P. chrysogenum QEN-24S displayed potent activity against the pathogen Alternaria brassicae, which infects important crops such as oil seed rape, cabbage, and broccoli [67], while penicisteroids A and B, two new polyoxygenated steroids obtained from the culture extract of P. chrysogenum QEN-24S, revealed potent antifungal and cytotoxic activity in preliminary bioassays [65,66]; and (3) drug discovery—such as in immuno-suppressive [67], antifibrotic [68,69], neuroprotective [70], antidiabetic [70], anti-obesity [70,71,72], anti-inflammatory [22], antioxidative [22], anticancer, antiparasitic [73], antiviral [73,74], and antimicrobial [74] applications.

The species are also well-known for their unique potency in removing pollutants like heavy metals, such as mercury, lead, chromium, arsenic, and cadmium, from various ecosystems [75,76,77,78,79]. Sonderegger et al. [79] found that small, cysteine-rich, and cationic antifungal proteins (Aps) from filamentous ascomycetes, such as NFAP from Neosartorya fischeri and PAF from P. chrysogenum, are promising candidates for novel drug development. Garcia-Estrada et al. [80] showed that penicillin biosynthesis by P. chrysogenum is one of the best-characterized biological process from molecular, genetic, biochemical, and subcellular points of view, and omics studies have been conducted on this filamentous fungus over the last decade, which have contributed to gathering a deep knowledge about the molecular mechanisms underlying the improved productivity in industrial strains.

It has been reported that a halotolerant phenylacetate-degrading fungus P. chrysogenum CLONA2 strain can produce non-aromatic natural penicillin rather than benzylpenicillin, and it can be an appropriate option for aromatic compounds remediation in high-salinity regions [74]. Penicillium CLONA2, isolated from a salt mine at Algarve (Portugal), was identified as a variant of P. chrysogenum using ITS-5,85 rDNA and the D1/D2 domain of 28S rDNA sequences. Due to the ability of P. chrysogenum CLONA2 to degrade aromatic compounds, this strain can be considered an important organism for aromatic compound remediation in high-salinity environments. Garcia-Rico et al. [81] found that the heterotrimeric Gα protein, Pga1, of P. chrysogenum controls conidiation, vegetative growth, and secondary metabolite production. The secondary metabolites of P. chrysogenum are chrysogine, penicillins, sorrentanone, secalonic acids, and PR-toxins [82,83,84]. Guijarro et al. [85] reported that P. frequentans (Pf909) could decrease brown rot caused by Monilinia spp. in stone fruit, and that it could survive and establish actively in a broad range of climatic conditions. Arunthirumeni et al. [86] concluded that Penicillium spp. can produce secondary components that are effectual for the control of Spodoptera litura and Culex quinquefasciatus larvae. The combined application of a commercial azoxystrobin-based fungicide and the P. chrysogenum F-24-28 strain (DMP) induced to prolonged growth inhibition of F. culmorum, F. graminearum, and F. oxysporum at fungicide concentrations, which suggests that this approach can be used to control crop diseases [87]. Sikandar et al. [88] reported that P. chrysogenum Snef1216 has the potential to be used against Meloidogyne incognita, the main root-knot nematode, which is one of the most dangerous nematodes due to its high reproduction rate and extensive host range. P. citrinum has been found to be a common positive endophytic fungus of cereal plants like soybean and wheat [89]. Nguyen et al. [90] reported that P. citrinum can be used for the biological control of Plutella xylostella and Spodoptera litura in some crops. The non-volatile components produced by P. simplicissimum CEF-818, which is an endophyte from Gossypium hirsutum, were shown to strongly suppress the growth of the plant pathogen Verticillium dahliae isolate Vd080 [91,92,93]. It was shown that P. commune MC-9L could act as a biological agent against Sclerotinia sp. in fumigation assays [94,95]. It was also found that P. crustosum and P. chrysogenum isolated from Teucrium polium produced ammonia and IAA and showed a high phosphate solubilization capacity [96].

P. janthinellum can be used for the biological control of phytophthora root rot in azalea [97], while P. citrinum can noticeably enhance chemical metabolite production and yield [98]. Dry mycelium of P. chrysogenum is important in controlling fungal diseases in cotton [99], and it is also effective in increasing the germination index, germination rate, and seed germination rate in cucumber [100]. Moreover, P. chrysogenum can improve the flowering activity of jujube [101] and improve the yield and yield components of maize [102] and pearl millet [103]. Dry mycelium of P. chrysogenum can increase the resistance of seedlings against the root-knot nematode Meloidogyne javanica in tomato [104], and P. janthinellum LK5 can increase the resistance of plants against salinity stress [105] and increase metal phytoextraction while promoting crop physiological homeostasis [106]. The impacts of various species of Penicillium spp. on the yield and yield components of various plants are shown in

Table 1. The effects of different species of Penicillium spp. on the yield and yield components of plants.

Plant	Plant Family	Penicillium spp. Species	Key Point	References
Azalea	Ericaceae	P. janthinellum	It can be used as a biological control agent of phytophthora root rot in azalea.	[97]
Banana	Musaceae	P. citrinum BTF08	It has great potential against the pathogenic F. oxysporum f. sp. cubense race 4 (FocR4)	[107]
Choy sum (Brassica rapa var. parachinensis)	Brassicaceae	P. citrinum	It can significantly increase yield and chemical metabolites.	[98]
Cotton (Gossypium hirsutum L.)	Malvaceae	Dry mycelium of P. chrysogenum	It is effective in controlling fungal diseases. It can be used against soil-borne pathogens that may penetrate the cotton root. It is important against wilt diseases.	[99]
		Dry mycelium of P. chrysogenum	It is effective in controlling Verticillium dahliae Kleb (Vd) and F. oxysporum f. sp vasinfectum (Fov) as well as the accumulation of pathogenesis-related protein transcripts.	[108]
			It is important in increasing resistance against Verticillium dahliae in cotton, which is the main cause of wilt in cotton.	[109]
Cucumber (Cucumis sativus L.)	Cucurbitaceae	P. chrysogenum	It can enhance the germination rate, germination index, and seed germination as well as increase the potential biocontrol against the root-knot nematode (Meloidogyne incognita) in cucumber.	[88]
Ginseng (Panax ginseng L.)	Araliaceae	P. citrinum YW322	It has special potency in controlling ginseng root rot disease caused by F. oxysporum.	[110]
Jujube (Ziziphus jujuba L.)	Rhamnaceae	P. chrysogenum	The endophyte P. chrysogenum has shown plant-growth-promoting activity and flowering-promoting activity.	[111]
Lettuce (Lactuca sativa L.)	Asteraceae	P. pinophilum	Inoculation with it can increase plant tolerance to Rhizophagus intraradices and Penicillium pinophilum.	[112]
Maize (Zea mays L.)	Poaceae	P. chrysogenum strain 34-P	Inoculation with it can influence maize seedling growth with significantly higher fresh biomass, dry biomass, and total chlorophyll.	[102]
Melon (Cucumis melo L.)	Cucurbitaceae	The extract of dead P. chrysogenum	It can enhance resistance against Fusarium wilt in melon.	[113]
Pearl millet (Pennisetum glaucum L.)	Poaceae	P. chrysogenum (PenC-JSB9)	It can positively promote growth, increase seed germination and shoot and root length, and induce resistance to downy mildew disease caused by Sclerospora graminicola.	[103]
Pineapple (Ananas comosus (L.) Merr.)	Bromeliaceae	Penicillium sp.	It can control pineapple internal browning. It can change the endophyte fungi community structure and abundance during storage. Exogenous inoculation may control internal browning by increasing the plant’s antioxidative capacity.	[114]
Pomegranate (Punica granatum L.)	Punicaceae	P. pinophilum (NFCCI2498)	Its inoculation into soil was found to promote nutrient uptake and induce a higher photosynthetic rate and leaf area index.	[115]
Rice (Oryza sativa L.)	Poaceae	P. citreonigrum	It can improve the yield and reduce the risk of harmful toxins.	[116]
Tobacco (Nicotiana glutinosa L.) (Nicotiana benthamiana) (Nicotiana glutinosa)	Solanaceae	Dry mycelium of P. chrysogenum	The crude peptides derived from it can be used to protect Nicotiana glutinosa against tobacco mosaic virus (TMV) by accelerating a TMV-N gene-triggered hypersensitive response (HR) rather than by priming callose deposition.	[117,118]
		P. chrysogenum	It can be used to prevent TMV spread in N. benthamiana plants.	[119]
		Dry mycelium of P. chrysogenum	It can activate defense responses in tobacco BY-2 cell suspensions, including the expression of defense responses genes and the accumulation of secondary metabolites against TMV.	[120]
		P. chrysogenum	It can protect flue-cured tobacco against brown spot and wildfire disease.	[121]
		Dry mycelium of P. chrysogenum	The abscisic acid biosynthetic pathway and β-1,3-glucanase, a callose-degrading enzyme, have significant roles in enhancing the defense response against TMV.	[122]
		Dry mycelium of P. chrysogenum	A polypeptide and a polysaccharide extract of it can induce the production of hydrogen peroxide and nitric oxide and improve the resistance of Peruvian tobacco (Nicotiana glutinosa) to TMV.	[123]
Tomato (Solanum lycopersicum L.)	Solanaceae	Dry mycelium of P. chrysogenum	It can promote resistance in plants against the root-knot nematode Meloidogyne javanica.	[104]
		P. janthinellum LK5	It can modulate stress responses through a reduction in the level of jasmonic acid and the synthesis of ABA. It can increase the resistance of plants to salinity stress by activating defensive mechanisms and the production of gibberellins in the hosts.	[105]
		P. janthinellum LK5 (PjLK5)	Its application could enhance metal phytoextraction while promoting crop physiological homeostasis.	[106]
Wheat (Triticum aestivum L.)	Poaceae	P. chrysogenum #5TAKL-3a	It is an appropriate substitute that can be used to increase the adaptability of plants under drought stress. It can also increase the resistance of plants to drought stress by increasing the production of ammonia, gibberellic acid, and IAA.	[124]

.

3. Trichoderma spp. as Plant Growth-Promoting Fungi with Biocontrol Properties

The species of fungi belonging to Trichoderma genus are endophytic saprophytes, which can easily colonize the host root surface of plants, induce resistance, promote plant health as a biocontrol agent, and increase plant growth [125]. Trichoderma is highly known as a biostimulant because of its main impacts on plants, such as stimulating a higher nutrient uptake efficiency, improving the rate of metabolism and photosynthesis, and as a potential biocontrol agent. Its different types of products can increase productivity and the plant growth, and it can be applied as a good biocontrol agent without negatively influencing other microorganisms in the soil. The genus Trichoderma possesses mycoparasitic potential against pathogenic fungi [126]. It also has high potential for degrading pollutants [127,128]. At first, Trichoderma colonizes between living plant cells, resembling the early stages in an attack by soil-borne pathogens, and to start colonization, conidial germ tubes or hyphae growing toward and near the root in the rhizosphere almost adhere to the root epidermis [129,130].

However, Pfordt et al. [131] reported that T. afroharzianum has been found as a pathogen causing ear rot disease on maize in Italy, France, and Germany, leading to massive infections on maize cobs, which has been confirmed even in other studies [132,133]. In 2020, T. afroharzianum was reported for the first time in Europe as an ear rot disease in maize [132]. The T. afroharzianum ear rot was characterized by a massive production of gray–green spores in the interkernel regions and on the outer surface of the husks, causing a significant reduction in the dry matter content and the premature germination of kernels [132,133]. The most important activities of Trichoderma spp. are shown in Figure 2.

4. Journey of Trichoderma spp. Species

In the year 1794, the name Trichoderma was introduced, and in 1865, the sexual stage of T. viride (Hypocrea rufa) was reported. In 1932, the first evidence that T. lignorum (Hypocrea virens) has mycoparasitic and biocontrol abilities was presented, and in 1934, the first anti-microbial compound from Trichoderma spp., namely gliotoxin, was discovered. In 1957, the discovery of the effect of light on T. viride was reported. In general, when in darkness, Trichoderma grows indefinitely as mycelium, and a brief pulse of light applied to the actively growing zone of the mycelium leads to the formation of dark green mature conidia, forming a ring at what was the edge of the colony when light was applied; the first event induced by light is a fast, first-order, photochemical reaction that does not need the presence of molecular oxygen and is independent of temperature [134]. In 1972, the demonstration of biocontrol activity of T. harzianum against Sclerotium rolfsii in field conditions was reported, and in 1983, the cloning of the first Trichoderma species, which was T. reesei, was performed. In 1986, the report on the expression of growth promotion in the root was published, while in 1987, the successful transformation of T. reesei was reported, and in 1989, the first registration of a commercial formulation was reported. Evidence of the cloning of lectin-coated fibers by Trichoderma species was presented in 1992, and in 1998 and 1999, the identification of factors that induced the genes for mycoparasitism and the demonstration of Trichoderma internal colonization of plant roots was accomplished. In 2011, a genome comparison of three species of Trichoderma was conducted [135], and in 2022, five new Trichoderma species were reported [136,137,138,139].

5. Trichoderma spp. and Prospects for Application in Agriculture, Horticulture, and Organic Farming

Some scientific publications have shown that Trichoderma species can also significantly influence plant phytohormone networking and production by the secretion of enzymes that can change plant ethylene levels [140].

T. viride and T. longibrachiatum have shown effective larvicide impacts against dengue mosquitoes such as Aedes albopictus and Aedes aegypti [141]. T. asperellum also possesses both plant-growth-promoting and biocontrol activities [142]. It has also been reported that the combined application of T. koningii and T. virens with extracts of Chlorella vulgaris are significantly effective against severe disease-late wilt (LWD) of maize incited by Cephalosporium maydis Samra under both field and greenhouse conditions [143]. Previous studies confirmed the IAA production potential of Trichoderma species, including T. harzianum, T. asperellum, T. longibrachiatum, T. pinnatum, T. virens, T. asperelloides, T. guizhouense, T. atrobrunneum, T. simmonsii, and T. paratroviride [144]. It has been reported that one of the major and effective ways to control phytopathogenic microorganisms and to reduce the adverse impacts of heavy metals on plants is via the application of T. harzianum [145]. The presence of alfalfa seedlings with Trichoderma increased the available nutrient (K, P, and N) content in the soil and the alfalfa biomass [146], as Trichoderma acts as a nutrient mobilizer, improving the yield, yield components, and quality traits of the crops [147]. Trichoderma spp. have been found to degrade chlorpyrifos, benzimidazole fungicide, 2,2-dichlorovinyl dimethyl phosphate, and penthiopyrad [148]. T. hamatum can be considered for its plant-growth promotion [149] and various biocontrol activities, and it also possesses different beneficial activities such as antioxidative activity [150], antimicrobial properties [151], herbicidal activity [152], and insecticidal activity [153,154].

Trichoderma spp. has shown biocontrol activity by producing certain hydrolytic and antibiotic enzymes, such as β-1,3-glucanase and chitinase, which facilitate cell-wall degeneration and, ultimately, cause the death of pathogenic microorganisms [155]. Transcriptional parameters such as MYBs, WRKYs, and MYCs have shown important functions in priming as they act as regulatory nodes in the transcriptional network of systemic defense after stress recognition, and when it comes to long-lasting priming, Trichoderma spp. may have roles in the plants’ epigenetic regulation via DNA (hypo)methylation, histone replacement and modification, RNA-directed DNA methylation (RdDM), and DNA (hypo)methylation, and the inheritance of epigenetic markers can improve growth promotion and enhance the resistance of plants [156,157]. The most effectual biocontrol characteristics are pertain to T. harzianum, T. virens, T. pseudokoningii, T. koningii, T. asperellum, T. longibrachiatum, T. viride, and T. polysporum, which have a considerable effect on the development of plant diseases caused by F. culmorum, F. oxysporum, Verticillium dahliae, Gaeumannomyces graminis var. tritici, Pythium aphanidermatum, Sclerotium rolfsii, and R. solani in both field and greenhouse conditions [158].

Some researchers have reported that since many Trichoderma species are fungal parasitoids and symbiotic, they need to produce secondary metabolites and degradation enzymes to obtain nutrients from the host; thus, they have been developed as biocontrol factors for plant diseases [159]. T. hamatum has shown antibacterial effects on Xanthomonas campestris pv. armoraciae, and Xanthomonas euvesicatoria [160,161], Bacillus subtilis, Staphylococcus aureus, Pseudomonas aeruginosa, Serratia, and Acidovorax avenae [162], and Ralstonia solanecearum [160,163]. T. hamatum has also shown antifungal activity against Rhizoctonia solani in radish [164], Sclerotinia sclerotiorum in lettuce [164], Magnaporthe oryzae in Arabidopsis thaliana [165,166,167,168], Sclerotinia asari in Asarum rhizosphere [169], F. proliferatum, F. solani, and F. oxysporum in Aconitum carmichaelii Debx [170], Lasiodiplodia theobromae in Macadamia integrifolia [170], and Sclerotinia sclerotiorum in Arabidopsis thaliana [171]. Different species of Trichoderma, like. T. asperellum, T. atroviride, T. harzianum, T. viride, T. citrinoviride, T. koningii, and T. hamatum, can produce 6-pentyl-alpha-pyrone (6PP), which is a lactone with a coconut-like aroma that has special potency for increasing root hair development and root branching [172,173] and for improving plant health and growth [174]. The occurrence of Trichoderma spp. species in different environments is shown in

Table 2. Occurrence of Trichoderma spp. in different environments.

Environment	Trichoderma spp. Species	References
Desert soil	T. afroharzianum, T. atrobrunneum, T. longibrachiatum	[175]
Forest soil	T. afroharzianum, T. asperellum, T. atroviride, T. citrinoviride, T. fertile, T. harzianum, T. longibrachiatum, T. oblongisporum, T. pararogersonii, T. paraviridescens, T. pleurotum, T. piluliferum, T. polysporum, T. rossicum, T. saturnisporum, T. viridescens	[176,177]
Soil from garlic crops	T. asperelloides, T. azevedoi, T. hamatum, T. koningiopsis, T. longibrachiatum, T. peberdy	[178]
Soil from maize crops	T. asperellum, T. brevicompactum, T. fertile, T. hamatum, T. harzianum, T. koningiopsis, T. longibrachiatum, T. pleuroticola, T. virens	[179]
Soil from onion crops	T. afroharzianum, T. asperelloides, T. asperellum, T. azevedoi, T. erinaceum, T. lentiforme, T. longibrachiatum, T. peberdyi	[178]
Soil from rice crops	T. asperellum, T. atroviride, T. brevicompactum, T. capillare, T. erinaceum, T. fertile, T. hamatum, T. harzianum, T. koningiopsis, T. longibrachiatum, T. polysporum, T. saturnisporum, T. spirale, T. velutinum, T. virens	[179]
Soil from wheat crops	T. asperellum, T. atroviride, T. brevicompactum, T. erinaceum, T. hamatum, T. harzianum, T. koningiopsis, T. virens	[179]
Soil from plant roots	T. afroharzianum, T. asperelloides, T. asperellum, T. guizhouense, T. harzianum, T. reesei, T. strigosum, T. virens	[180]
Soil from tree bark	T. atroviride, T. erinaceum, T. harzianum, T. hebeiensis, T. longibrachiatum, T. parareesei, T. reesei	[181]
From decaying wood	T. atroviride, T. citrinoviride, T. cremeum, T. gamsii, T. harzianum, T. koningii, T. koningiopsis, T. longibrachiatum, T. longipile, T. paraviridescens, T. trixiae, T. viride, T. viridescens	[182]
From lignocellulosic compost	T. asperellum, T. citrinoviride, T. harzianum, and T. lixii	[183,184]

.

Compounds synthesized by Trichoderma spp. that are involved in plant interactions are IAA in T. virens, GA₃ in Trichoderma spp., ABA in T. virens and T. atroviride, ethylene in T. atroviride, jasmonic acid (JA) in T. asperellum, and salicylic acid (SA) in T. atroviride [185]. A novel type II hydrophobin secreted by the biocontrol strain MK1 of T. longibrachiatum was characterized and isolated, and the corresponding gene (Hytlo1) was shown to have multiple functions in the Trichoderma–plant pathogen three-way interactions, while the purified protein showed direct antifungal and plant-growth promotion (PGP) activities as well as microbe-associated molecular patterns [185]. In this experiment, leaf infiltration with hydrophobin systemically enhanced the resistance to pathogens and activated defense-related responses involving phytoalexin, oxylipin, superoxide dismutase, reactive oxygen species, and pathogenesis-related formation or activity; moreover, hydrophobin stimulated root formation and growth, and a targeted knock-out of Hytlo1 significantly decreased both the antagonistic and PGP effects of the wild-type strain [185]. Polyketides in T. virens and Trichoderma sp. SCSIO41004; terpenes in T. virens, T. harzianum P1-4, T. citrinoviride, and T. harzianum R5; VOCs in T. atroviride and T. arundinaceum; and hydrophobin in T. virens, T. atroviride, and T. asperellum have different functions, such as in plant-growth promotion, and facilitate the plant–microbe interactions in the rhizosphere [186,187]. Claudia et al. [186] showed that the product of the TvCyt2 gene from T. virens encoded a new protein homologous to cytochrome p450, which is down-regulated at the beginning of the Trichoderma–Arabidopsis interaction, and Arabidopsis plants co-cultivated with the OETvCyt2 strains showed a stronger induction of systemic acquired resistance than plants co-cultivated with the WT strain, as well as increases in biomass and fitness, which show that the TvCyt2 gene is involved in secondary metabolite biosynthesis, and this can increase the antagonistic activity toward phytopathogenic fungi and the capacity to promote plant growth [186].

Some of the species of Trichoderma are active in regulating different genes in plants, such as T. asperelloides, which can up-regulate the MDAR gene in Arabidopsis and cucumber, which can increase osmo-protection and oxidative stress [188]; T. atroviride and T. virens, which can up-regulate AtERD14 in Arabidopsis and mitigate cold stress effects; T. parareesei, which can up-regulate PYL4, ERF1, ACCO1, and NCED3 in rapeseed, thus improving tolerance to salinity and drought; T. longibrachiatum in wheat, which can up-regulate CAT, POD, and SOD and increase the resistant of plants to salinity [189]; T. harzianum in tomato, which can improve the tolerance of seedlings to cold via P5CS and TAS14 [190]; T. harzianum, which regulates GST1 and Lox in potato, which can improve plant resistance to diseases [191]; and T. asperellum, which can up-regulate PdPapARF1 in poplar, which can promote growth and defense responses [192].

Some parameters that may encourage the market for Trichoderma-based biofungicides are that they should be broad-spectrum in action, show consistent field performance, have an extensive lifespan, be a cost-effective product, have easy accessibility and improved delivery systems, and there should be social awareness of their benefits among farmers [193]. Trichoderma spp. as potential biocontrol agents (BCAs) can be used for the effective management of different soil, foliar, and post-harvest plant pathogens, and they have gained more attention in recent years.

Some of the identified genes from Trichoderma species have different roles during the biocontrol interaction with phytopathogens, such as Tvsp1 from T. virens, which can protect cotton seedlings against R. solani [194]; Tag3 from T. asperellum, which is responsible for glucanase production for cell-wall degradation [195]; TgaA and TgaB from T. virens, which has shown biocontrol effectiveness for the management of R. solani and Sclerotium rolfsii [196]; ThPG1 from T. harzianum, which is needed for beneficial interactions between T. harzianum and the host [197]; ThPRT2 from T. harzianum, which has shown mycoparasitism activity against Botrytis cinerea [198]; tri5 of T. brevicompactum IBT40841, which has antifungal activity and has been used in the production of trichodermin against fungi causing infections in the human body [199], TvGST of T. virens, which provides enhanced tolerance against cadmium stress [200]; TrCCD1 of T. reesei, which can facilitate pigment production and hyphal growth [201]; egl1 of T. longibrachiatum, which shows antagonistic activity against Pythium ultimum [202]; qid74 of T. harzianum, which has roles in plant biofertilization and the root architecture [203]; tac1 of T. virens IMI 304061, which shows mycoparasitism against S. rolfsii and R. solani [204]; TrCCD1 of T. reesei, which can promote conidia formation and elongation of fungal hyphae; XI 1 of Trichoderma strain Y, which is helpful in hemicellulose breakdown [205]; tvhydii1 of T. reesei, which is important in mycoparasitism and plant–fungus interactions [206], gpr1 of T. atroviride, which is needed for the stability of cell walls and hyphal growth [207]; ipa-1 of T. virens, which has a role in antibiosis against R. solani [208]; TasXyn24.2 and TasXyn29.4 of T. asperellum, which can induce resistance and increase growth in seedlings [208], and agl1 of T. atroviride, which can be used for the biological control of plant pathogens. It has been reported that the application of grains (200 g + sugar (1%) + T. harzianum) showed 12.96% effectiveness in the management of chili wilt disease [209], and the application of vermicompost fortified with Trichoderma induced a reduction of 10.01% in the incidence of wilt in chili [209]. A mixture of ground grain + sugar solution (1%) + T. harzianum and the combined application of decomposed cow dung + a Trichoderma formulation has positive impacts on maize seeds [210], while the application of partially crushed grain + sugar (1%) solution + distilled water and the combined application of beech, fir, and chestnut + conidial suspensions of T. atroviride + distilled water + soy flour could increase the yield [211].

Guzman-Guzman et al. [212] reported that the biocontrol mechanisms of Trichoderma spp. against potential pathogens include antibiosis, parasitism, secondary metabolite production, plant defense system induction, and competition. Different Trichoderma species used in agriculture have different biocontrol characteristics; for example, T. atroviride, T. viride, T. longibrachiatum, T. virens, T. asperellum, and T. harzianum have demonstated parasitism, competition, plant defense induction, priming, secondary metabolite production, and antibiosis [213,214]. Chan et al. [215] reported that the T. harzianum strain CE92 can be used as a potential biocontrol agent for pathogenic wood rot fungal species such as Rigidoporus microporus, Phellinus noxius, and Fulvifomes siamensis. De Oliveira et al. [216] reported that T. harzianum is recommended for the biological control of the root-lesion nematode Pratylenchus brachyurus, which is an important nematode in sugarcane, sunflower, potato, millet, cotton, corn, and soybean, while Wu et al. [217] found that octahydronaphthalene derivatives from an endophytic fungus Trichoderma sp. can be used for managing Botrytis cinerea. Tamandegani et al. [218] also found that T. asperellum (Iran 3062C), which was isolated from potato fields in Hamedan, Iran, showed a strong ability to induce systemic resistance against cucumber mosaic virus (CMV) that involved the jasmonic acid (JA)/ethylene (ET)/salicylic acid (SA) signaling pathways. Biocontrol mechanisms applied by the Trichoderma genus against fungal pathogens include the use of plant-resistance elicitors, the stimulation of antioxidative enzymes, and phytoalexin production by the plants via Trichoderma and its metabolites, as well as mechanisms like mycoparasitism, utilization of the activity of proteases, glucanases, and chitinases, competition for space and nutrients, and the production of antifungal and antibiotic components such as polyketides, peptaibols, anthraquinones, pyrones, and terpenoids.

T. virens 6PS-2 was effective in controlling apple replant disease and in improving the growth and fruit quality of apple [219], while T. virens could improve defense pathways [220] and enhance plant growth promotion in Arabidopsis when applied as an important biocontrol agent [220]. T. harzianum could increase the tolerance of avocado seedlings to P. cinnamomic [221], and it can be used as biological control agent to control post-harvest pathogens such as Diaporthe sp. and Phomopsis perseae in avocado plants [222]. T. harzianum also can significantly control chickpea Fusarium wilt [223,224]. It is also effective in the control of root-knot nematode disease in cowpea [225]. Gupta et al. [226] reported that T. harzianum can induce a higher root canopy and a better root biomass and final yield in finger millet. Its application was also effective against dry root rot in mung bean [227,228]. Pandey et al. [229] found that T. harzianum could enhance the activity of antioxidative enzymes and decrease lipid peroxidation during drought stress in rice plants. The application of an organic additive with T. harzianum could reduce the levels of Sclerotium rolfsii, which is the main pathogen for potato [230]. Limdolthamand et al. [231] could decrease the infection of northern corn leaf blight in sweet corn and improve the growth of sweet corn plants. T. asperellum could improve the resistance of plants against Colletotrichum graminicola by increasing lignification in plants and by enhancing the activity of antioxidative enzymes [232], and it was effective in controlling Fusarium wilt in stevia plants [233]. Changes in the yield and yield components of various horticultural and agricultural plants following the application of different species of Trichoderma spp. are presented in

Table 3. The effects of different species of Trichoderma spp. on the yield and yield components of some agricultural and horticultural plants.

Plant	Plant Family	Trichoderma Species	Key Points	References
Apple (Malus robusta)	Rosaceae	T. virens 6PS-2	It was effective in controlling apple replant disease (ARD) and improved the growth and final quality of fruits.	[234]
		T. asperellum	Significant reduction in the negative impacts caused in the host by F. proliferatum was reported.	[234]
Arabidopsis (Arabidopsis thaliana)	Brassicaceae	T. virens	It could secrete 1-octen-3-ol, which enhanced plant resistance against pathogens by activating JA/ET-dependent defense pathways.	[235,236]
		T. virens	It could be used for biocontrol goals, balancing between herbicidal activity and plant-growth promotion.	[220]
Avocado (Persea americana Mill)	Lauraceae	T. harzianum; T. hamatum	They could increase the tolerance of plants to P. cinnamomi.	[221]
		T. harzianum	It could be used as a biological control agent to suppress post-harvest pathogens like Phomopsis perseae, Diaporthe sp., Colletotrichum gloeosporioides, and Neofusicoccum parvum.	[237]
		T. atroviride; T. virens	They could promote the control of avocado white root rot.	[238]
Banana (Musa sp. L.)	Musaceae	T. harzianum ALL42 and IBLF006; T. asperellum T00	They could promote plant growth and reduce the negative impacts of Meloidogyne javanica.	[239,240]
		T. longibrachiatum	It could promote the performance of banana seedlings.	[241]
		T. asperellum	Inoculation with it could increase the root potassium and phosphorus content.	[242]
		T. piluliferum	It is an important biocontrol agent for anthracnose caused by Colletotrichum musae.	[243]
Bean (Phaseolus vulgaris L.)	Fabaceae	T. harzianum	It can induce plant resistance to R. solani by increasing the synthesis of squalene and ergosterol and by promoting the stability and integrity of plant cell membranes.	[244,245,246]
		T. viride	It can enhance the levels of total phenols, polyphenol, peroxidase, phenylalanine ammonia-lyase, and photosynthetic pigments and protect plants against fungal infections.	[247]
		T. longibrachiatum AD-1	It can be used to control root rot diseases caused by Fusarium spp. RT-qPCR revealed that applying a cell-free culture filtrate of Trichoderma in common beans resulted in significant up-regulation of the defense-related genes PR1, PR2, PR3, and PR4.	[248]
		T. gamsii IT-62	It could lead to increased soil fertility and significantly improve the root and shoot weight and levels of total protein, and photosynthetic pigments.	[249]
		T. gamsii IT-62	It can be used to control common bean damping-off caused by pathogens.	[250]
		T. asperellum BRM-29104	It can be used against white mold caused by Sclerotinia sclerotiorum.	[251]
Black pepper (Piper nigrum L.)	Piperaceae	T. viride; T. harzianum	They can significantly protect black pepper plants from anthracnose by increasing the chlorophyll content, increasing the overall plant health, suppressing the disease incidence and improving the innate defense system and plant health.	[252,253,254,255]
Cacao (Theobroma cacao L.)	Malvaceae	T. asperellum PR11	It could be used against cacao black pod rot (BPR) caused by Phytophthora megakarya.	[256,257,258]
Canola (Brassica napus L.)	Brassicaceae	T. harzianum (ARCTr281, ARCTr272, and ARCTr418)	They were effective antagonists in controlling canola rot disease and increasing plant traits.	[259]
Cassava (Manihot esculenta Crantz)	Euphorbiaceae	T. aureoviride URM5158	It could manage cassava root rot.	[260]
Castor (Ricinus communis L.)	Euphorbiaceae	T. asperellum 7316, T. asperellum N13	They showed special antagonistic ability against the fungal pathogen (Alternaria ricini).	[261,262]
Chickpea (Cicer arietinum L.)	Fabaceae	T. harzianum	It was effective in the control of chickpea Fusarium wilt.	[223]
		T. harzianum	It could reduce the adverse impacts of salt stress and fungal diseases.	[224]
		T. harzianum; T virens	They could increase root and shoot lengths and grain yield as well as reduce the dry root rot incidence.	[263]
Chili (Capsicum frutescens L.)	Solanaceae	T. asperellum; T. harzianum; T virens; T. pseudokoningii	They could increase the resistance of plants to Colletotrichum truncatum by enhancing the activity of defensive and antioxidative enzymes in plants, decreasing the accumulation of reactive oxygen in plants.	[264]
Chinese cabbage (Brassica rapa L.)	Brassicaceae	Trichoderma spp.	They could increase nutrient uptake and increase tolerance to environmental stresses as well as improve the quality of products.	[265]
Citrus (Citrus L.)	Rutaceae	T. harzianum	It can affect Guignardia citricarpa and deactivate the hydrolytic enzymes of pathogens.	[266]
Cacao tree (Theobroma cacao L.)	Malvaceae	T. hamatum	It could increase stomatal conductance, green fluorescence emission, net photosynthesis, and improve drought tolerance.	[267]
Coffee (Coffea L.)	Rubiaceae	T. asperellum GD040	It is suggested for managing coffee anthracnose caused by Colletotrichum cairnsense.	[268]
Cotton (Gossypium hirsutum L.)	Malvaceae	T. virens	It can increase terpenoid synthesis and is toxic to R. solani.	[269]
		T. virens and T. longibrachiatum	They could metabolize pathogen propagule germination against R. oryzae.	[270,271]
		T. hamatum	It has a great capacity to control leaf worm (Spodoptera littoralis).	[272]
		T. viride	It decreased the root rot incidence and improved yield and dry matter production.	[273]
		T. viride NBAITv23; T. harzianum NBAIITh1	Because of their antifungal activities, they can be used against R. solani, which is the cotton seed rotting pathogen.	[274]
Cowpea (Vigna unguiculata L.)	Fabaceae	T. harzianum	It was effective in the control of root-knot nematode disease.	[275]
Cucumber (Cucumis sativus L.)	Cucurbitaceae	T. atroviride	It can lead to resistance to R. solani by increasing the accumulation of volatile organic compounds, increasing the activity of antioxidative enzymes in the plant, and reducing lipid peroxidation.	[276,277]
		T. longibrachiatum	It can increase plant resistance against Botrytis cinerea by increasing the contents of jasmonic acid, salicylic acid, and ethylene.	[278]
		T. asperellum	In high-salinity conditions, it could increase the level of abscisic acid, auxins, and gibberellin.	[279]
		T. asperellum	It could enhance local defense responses and plant root colonization with the secretion of swollenin.	[280]
		T. asperellum FJ035	It was effective against cucumber Fusarium wilt and improved the plant height, root length, fresh weight, stem thickness, and quality.	[281]
		T. asperellum; T. pseudokoningii	They have shown high potential as biocontrol fungi against cucumber Fusarium wilt.	[282]
		T. koningiopsis	An alternative bioherbicide against different fungi of the cucumber plants due to its ability to produce enzymes that increase its phytotoxic effects.	[283]
Dragon fruit (Hylocereus costaricensis)	Cactaceae	T. asperellum K1-02	It has shown antifungal activity against stem canker caused by the fungus Neoscytalidium dimidiatum.	[284]
Eucalyptus trees (Eucalyptus globulus)	Myrtaceae	T. asperellum; T. longibrachiatum	They could effectively suppress the growth of Neofusicoccum parvum and Lasiodiplodia theobromae fungal species.	[285]
Faba bean (Vicia fabae L.)	Fabaceae	T. viride, T. harzianum, T. virens, T. atroviride, T. longibrachiatum	They can be used to reduce the growth of Alternaria spp., R. solani, Botrytis spp., Penicillium spp., Aspergillus spp., F. solani, and F. oxysporum.	[286,287]
Finger millet (Eleusine coracana L.)	Poaceae	T. harzianum	Its application induced a higher root canopy and a better root biomass and final yield.	[288]
Forage cactus (Nopalea cochenillifera L.)	Cactaceae	Trichoderma spp.; T. aureoviride URM 6668	They have shown high efficiency against the soil fungi F. solani and Lasiodiplodia theobromae.	[289]
Forskolin (Coleus forskohlii (Willd.) Briq.)	Lamiaceae	T. viride	Its inoculation could enhance the root biomass and forskolin content and reduce nematode infections.	[290]
Grapevine (Vitis vinifera L.)	Vitaceae	T. koningiopsis	It could be used to reduce copper levels and fight against Plasmopara viticola, the causal agent of downy mildew.	[291]
		T. harzianum	It has positive impacts in controlling soil-borne plant pathogens like F. solani, F. oxysporum, and Macrophomina phaseolina.	[292]
		T. simmonsii; T. afroharzianum; T. gamsii; T. orientale	They could significantly improve D-glucose and the D-fructose concentrations.	[293]
		T. harzianum T118	Its application induced higher total antioxidative activity and levels of ascorbate peroxidase and flavonoids.	[294]
Groundnut (Arachis hypogaea L.)	Fabaceae	T. viride JAU60	It can be used to combat the oxidative burst produced by invading pathogens, especially against Aspergillus niger Van Tieghem, which causes collar rot.	[295,296]
		T. longibrachiatum; T. asperellum	They showed an important role in the resistance to Sclerotium rolfsii.	[297]
		T. asperellum SH16	It was important in controlling diseases such as root rot, stem rot, and pod rot.	[298]
		T. asperelloides SKRU-01	It can be used for mitigating the negative impacts of Aspergillus species infestation and for increasing aflatoxin B1 degradation.	[299]
		T. harzianum ITEM 3636	It could be used against F. solani and reduced the severity of brown root rot.	[300,301]
		T. viride F7	It could enhance peanut performance and decrease peanut Cd concentrations.	[302]
Jerusalem artichoke (Helianthus tuberosus L.)	Asteraceae	T. harzianum	It is suggested for the biological control of southern stem rot caused by Sclerotium rolfsii.	[303]
Lettuce (Lactuca sativa L.)	Asteraceae	T. azevedoi CEN1241	It could increase the levels of volatile organic compounds and decreased the negative impacts of white mold caused by the fungus Sclerotinia sclerotiorum.	[304]
		T. asperellum T76-1	It could inhibit fungal growth of two leaf-spot fungal pathogens, namely Curvularia aeria and Corynespora cassiicola.	[305]
		T. spirale T76-1	It could decrease the native effects of leaf spot caused by Curvularia aeria and Corynespora cassiicola.	[306]
		T. harzianum T22; T. atroviride P1	They could alleviate abiotic stresses and improved plant growth.	[307]
Mango (Mangifera indica L.)	Anacardiaceae	T. asperellum T8a	It can enhance the control of anthracnose via cellulase activity as well as mango production.	[308]
		T. pinnatum LS029-3	It could improve the activity of mango defense enzymes such as total phenol, peroxidase, and polyphenol oxidase and reduced the content of ascorbic acid content and glutathione enzyme, and thus be useful against mango stem-end rot disease.	[309]
Maize (Zea mays L.)	Poaceae	T. viride; T. harzianum	They are effective against F. verticillioides and F. proliferatum strains.	[310,311]
		T. asperelloides; T. longibrachiatum	These two species increase seedlings’, wet biomass and increase the resistance of plants against late wilt.	[312]
		T. harzianum	It elicited plant defense responses through the secretion of Hyd1 hydrophobin.	[313]
		T. harzianum	It induced ISR in plants via ET or JA pathways via the secretion of cellulases.	[314]
		T. asperellum GDFS1009	It could significantly reduce maize stalk rot caused by F. graminearum.	[315]
		T. gamsii	It could improve plant growth and increase the resistance of plants to F. verticillioides.	[316]
Milk thistle (Silybum marianum (L.) Gaertn.)	Asteraceae	Trichoderma strain M7, KHB, G124-1, G46-3, and G46-7	They could promote growth and increased the production of silymarin, isosilybin, and silychristin.	[317]
Monterey pine (Pinus radiata)	Pinaceae	T. hamatum	Its application in seedlings and roots could increase the dry root weight, shoot growth promotion, and root penetration.	[318,319]
Mulberry (Morus spp.)	Moraceae	T. pseudokoningii	It could decrease the negative impacts of soil-borne diseases and improved plant growth.	[266]
Mung bean (Vigna radiata L.)	Fabaceae	T. harzianum	It was effective against dry root rot.	[228]
Muskmelon (Cucumis melo L.)	Cucurbitaceae	T. asperelloides PSU-P1	It revealed antifungal characteristics and increased the defense response against gummy stem blight through cell-wall-degrading enzymes and defense-related enzymes.	[320]
Mustard (Brassica juncea L.)	Brassicaceae	T. viride 1433 mutant strains	They could improve the tolerance of plants to Pythium aphanidermatum in both field and lab experiments.	[321]
Oil palm (Elaeis guineensis)	Palmaceae	T. asperellum T76-14	It is an important choice to improve plants against Ganoderma boninense infection.	[322]
Olive (Olea europaea L.)	Oleaceae	T. harzianum strain Ths97	It could increase plant tolerance to F. solani.	[323]
Onion (Allium cepa L.)	Amaryllidaceae	T. viride	The combined application of T. viride and AMF altered amino acid concentrations.	[324]
		T. viride	The combined application of T. viride and AMF significantly improved the levels of total free amino acids, the soluble protein content, and onion biomass.	[324]
		T. asperellum	In the presence of heavy metals, it could decrease lipid peroxidation and regulate the level of proline in the plants.	[325]
		T. longibrachiatum	It could decrease electrolyte levels elevated by infection and salinity and decrease the damage caused by infection with Sclerotium cepivorum.	[326]
		T. azevedoi CEN1241; T. koningiopsis CEN1513; T. asperelloides CEN1559	They could increase the weight of onion bulbs promote seedling growth, and be useful against soil fungi, especially Sclerotium rolfsii.	[327]
		T. harzianum; T. atroviride	They could mitigate the adverse effects of Fusarium basal rot caused by F. oxysporum f. sp. cepae.	[328]
Pak Choi (Brassica campestris spp. Chinensis)	Brassicaceae	T. viride	Its inoculation can increase plant growth, with significant impacts on suppressing clubroot disease (Plasmodiophora brassicae).	[329]
		T. harzianum	It could boost plant growth and the activity of antioxidative enzymes such as peroxidase, glutathione reductase, catalase, superoxide dismutase, and ascorbic acid peroxide.	[330]
Pearl millet (Pennisetum glaucum (L.) R.Br.)	Poaceae	T. virens	Its oligosaccharides can increase resistance against downy mildew disease.	[331]
		T. asperellum DL-81	It is suggested as an important biological control agent of downy mildew disease.	[332]
Pepper (Capsicum annuum L.)	Solanaceae	T. polysporum T1	It was effective in the control of leaf curl virus (PeLCV) by releasing salicylic acid.	[333]
		T. atroviride T32l; Trichoderma sp. N97	Sustainable candidates for the biological control of root rot pathogen and pepper wilt.	[334,335]
		T. asperellum	It has a positive effect in controlling root-knot nematodes arising from Meloidogyne incognita.	[336]
		T. virens HZA14	It could reduce the disease incidence and delayed the occurrence of chili pepper blight caused by Phytophthora capsici.	[337]
		T. simmonsii	It could increase crop nutrition and stimulated the plant tolerance to P. capsici.	[338]
Peppermint (Mentha × piperita L.)	Lamiaceae	T. viride Tv-1511	Its inoculation can enhance concentrations of pulegone, menthol, and menthone.	[339]
Pigeon pea (Cajanus cajan L.)	Fabaceae	T. asperellum IIPRTH-31; T. afroharzianum IIPRTh-33	They could be effective in the biocontrol of Fusarium wilt through defense-related enzymes.	[340]
		T. harzianum; T. viride	They could increase growth and resistance against Fusarium sp.	[341]
Pine (Pinus sylvestris)	Pinaceae	T. harzianum	It could increase plant tolerance to Phytophthora cinnamon under greenhouse conditions.	[342,343]
Pomegranate (Punica granatum L.)	Punicaceae	Trichoderma spp. (strains ABSA18, TSA17, and ABSA16)	They were effective against pathogenic fungi of pomegranate such F. chlamydosporum, F. oxysporun, A. niger, and A. alternata.	[344]
Potato (Solanum tuberosum L.)	Solanaceae	Trichoderma spp.	It could be used as an important alternative against Alternaria solani, which is the main pathogen causing early blight in potato.	[345]
		T. brevicompactum	It was effective in the biological control of potato wilt disease (F. solani).	[346]
Rambutan (Nephelium lappaceum L.)	Sapindaceae	T. harzianum	It could reduce the occurrence of post-harvest diseases caused by pathogens such as Botryodiplodia theobromae, Colletotrichum gloeosporioides, Gliocephalotrichum microchlamydosporum and improve the color and quality of the fruits.	[347]
Rice (Oryza sativa L.)	Poaceae	T. harzianum	It could increase the activity of antioxidative enzymes and reduce lipid peroxidation during drought stress.	[348]
		T. hamatum KUFA 0042	It showed high biocontrol activity against R. solani and Bipolaris oryzae.	[349]
		T. asperellum T12	It was effective in the biocontrol of sheath blight.	[350]
Roselle (Hibiscus sabdariffa L.)	Malvaceae	T. viride	It could reduce the mycelial growth of different pathogens such as R. solani, F. nygamai, and Phoma exigua.	[351]
Rye (Secale cereale L.)	Poaceae	T. harzianum	It could increase the plant tolerance to R. solani and Sclerotium rolfsii under both field and greenhouse conditions.	[352]
		Trichoderma spp.	They have a positive influence on the growth and final yield of plants.	[353]
Ryegrass (Lolium multiflorum L.)	Poaceae	T. atroviride	It could promote resistance against Pyricularia oryzae in ryegrass through physical and biochemical defenses.	[354]
Soybean (Glycine max L.)	Fabaceae	T. viride	It can be used as a biocontrol agent against two fungal pathogens, namely Pythium arrhenomanes and F. oxysporun. It could promote the root system and enhance the root and shoot systems.	[355]
		Trichoderma strains	They have shown positive effects against charcoal rot caused by Macrophomina phaseolina (Tassi) Goid.	[272]
		Trichoderma spp.	They could improve the absorption of Mn and K and reduce the severity and incidence of diseases.	[356]
		T. koningiopsis	It is an important alternative for weed control.	[357]
		Trichoderma spp.	Trichoderma-based products could control the spiral nematode (Helicotylenchus dihystera).	[358]
		T. harzianum; T. viride; T. koningii	They could significantly inhibit the mycelial growth of F. oxysporum, F. solani, and R. solani.	[359]
		T. harzianum ALL 42	It has shown special potential in the biological control of Pratylenchus branchyrus, an important nematode.	[275]
Sorghum (Sorghum bicolour L.)	Poaceae	T. asperellum	It can improve the resistance of plants to Colletotrichum graminicola by increasing lignification in plants and improving the activity of antioxidative enzymes.	[232]
Spinach (Spinacia oleracea L.)	Amaranthaceae	T. harzianum	It could reduce the negative impacts of salt stress and improve the fresh and dry weight, root length, chlorophyll content, and mineral contents.	[360]
Stevia (Stevia rebaudiana)	Asteraceae	T. asperellum	It was effective in fighting against Fusarium wilt.	[233]
Strawberry (Fragaria × ananassa Duch.)	Rosaceae	T. atrobrunneum	It could increase plant tolerance to Armillaria mellea.	[361]
		T. harzianum	It was appropriate for preventing and controlling gray mold in plants.	[362]
Sugar beet (Beta vulgaris spp. vulgaris)	Amaranthaceae	T. atroviride	It can induce stress-related defense genes, such as the expression of a pathogenesis-related gene (PR-3), in plants.	[363]
		T. viride TVB1	It could decrease root rot disease and improve root yield.	[364]
		T. harzianum	It could reduce the incidence of Sclerotium root rot and enhanced the green foliage, sucrose yield per ha, and the root yield.	[365]
		T. harzianum; T. asperellum	They can be considered potential biocontrol agents for controlling R. solani-induced sugar beet damping-off disease.	[366]
Sugarcane (Saccharum officinarum L.)	Poaceae	T. harzianum	It could increase soil carbon sequestration, photosynthesis, yield, and growth in sugarcane ratoon.	[367]
Sunflower (Helianthus annuus L.)	Asteraceae	T. longibrachiatum	It could increase the activity of antioxidative enzymes in plants in the presence of heavy metals.	[368,369]
		T. harzianum T22	It could increase the tolerance of plants to Alternaria alternata in lab experiments.	[370]
		T. viride	Its application together with P. fluorescens could increase the oil content and growth of plants.	[371]
		T. harzianum T22	It could decrease sclerotia formation caused by Sclerotinia sclerotiorum in sunflower.	[372]
		T. harzianum TRIC8	It was effective in improving the resistance of plants to downy mildew disease caused by Plasmopara halstedii.	[373]
Sweet sorghum (Sorghum bicolor (L.) Moench)	Poaceae	T. viride	It had an important role in reducing NH3 volatilization and simultaneously improved the effectiveness of nitrogen fertilizers.	[374]
Sweet corn (Zea mays convar. saccharata var. rugosa)	Poaceae	T. harzianum	It reduced the infection of northern corn leaf blight in sweet corn as well as improved plant growth.	[375]
Sword lily (Gladiolus hybridus)	Iridaceae	T. hamatum	It could increase chlorophyll a and b levels and the uptake of both macro and micronutrients and enhanced inflorescence elongation.	[376]
Tea (Camellia sinensis L.)	Theaceae	T. reesei TRPATH01	It could increase the shoot height, stem diameter, and fresh weight and improved the resistance of plants to Fusarium dieback caused by F. solani.	[377]
		T. reesei	It can be considered for the biological control of gray blight.	[348]
		T. asperellum TC01	It could be applied to fight against Colletotrichum gloeosporioides C62. It could increase the root dry weight, shoot dry weight, stem diameter, and shoot height.	[348]
Tobacco (Nicotiana tabacum L.)	Solanaceae	T. nigricans T32781	It could result in lower Cd uptake and contamination in plants and improved tobacco growth.	[378]
Tomato (Solanum lycopersicum L.)	Solanaceae	T. viride	Its inoculation could significantly increase the root fresh weight and shoot fresh weight. Its application was more effectual in controlling early blight disease caused by Alternaria alternata.	[379,380]
		T. harzianum	It could improve the final yield and inhibited the radial growth of F. oxysporum f. sp. lycopersici.	[381,382,383]
		T. harzianum; T. viride	Both of them could be used against root galling and the nematode reproduction of Meloidogyne javanica.	[384,385,386]
		T. harzianum; T. viride	They could promote growth and increase the yield of tomato plants.	[384]
		T. harzianum TR05; T. viride TR06; T. asperellum TR08	They have been suggested as biological control agents of collar rot.	[387]
		T. hamatum	Its application on seedlings could enhance lateral development.	[388]
		T. simmonsii; T. atrobrunneum	They are effective in suppressing disease development and colony growth of soil-borne pathogens.	[389,390]
		T. koningii	It could increase the activity of antioxidative enzyme in plants at high temperatures as well as regulate the level of starch, proline, phenols, and proteins.	[391]
		T. harziaum	At low temperatures, it could decrease lipid peroxidation, regulate the level of osmolites, and increase the water content of the leaves.	[391]
		T. harziaum	During drought stress, it could increase the level of abscisic acid, gibberellin, and auxins in the plant.	[392]
		T. asperellum	It is promising for the successful management of collar rot disease (Agroathelia rolfsii).	[393,394]
		T. harziaum; T. atroviride	They could secret 6PP, which can increase the leaf area and plant height, develop the root system, and enhance the lycopene content in fruits.	[395,396]
		T. longibrachiatum	It could influence genes involved in the mitigation of stress damage.	[397]
Tuberous begonias (Begonia × tuberhybrida)	Begoniaceae	T. hamatum	Its application to root tubers could increase the blooming size of the flowers and chlorophyll production and promote the uptake of boron, iron, and zinc.	[398]
Water hyssop (Bacopa monnieri L.)	Plantaginaceae	T. harzianum; T. asperellum	Their application was effective against Alternaria alternata causing leaf blight.	[399]
Wheat (Triticum aestivum L.)	Poaceae	T. longibrachiatum	It could increase the level of salicylic acid, reduce the level of hydrogen peroxide, and improve the activity of antioxidative enzymes in plants under salinity conditions.	[400]
		T. harzianum sensu lato TSM39	It is a potential biocontrol agent against Bipolaris sorokiniana, the causal agent of wheat spot blotch.	[400]
		T. harzianum; T. pseudokoningii	They have been introduced as having herbicidal potential in the control of Rumex dentatus L.	[401]
		T. gamsii MK361 138	It could reduce the severity of crown rot disease and improve growth parameters.	[402]
		T. harzianum; T. viride	They showed higher efficiency against Alternaria alternata, which can cause black point disease in wheat.	[403,404]
		T. atroviride Vel1	It is involved in mycoparasitism, sporulation, secondary metabolite production, and disease control and is especially appropriate for controlling the wheat root rot disease caused by F. graminearum.	[405]
Wild blueberries (Vaccinium angustifolium)	Ericaceae	T. harzianum T-22; T. atroviride IC-11	Its combination with calcium polysulphide could manage botrytis blossom blight in wild blueberry.	[406,407]

.

6. Conclusions

Endophytic fungi are very important in agricultural production because of their synergistic association with plants and their strong ability to stimulate plant growth because of their synthesis of phytohormones in response to biotic and abiotic stressors; these make them unique options as biofertilizers and biostimulants as well as as biocontrol factors against different types of diseases. Different species of Penicillium can significantly improve the fresh and dry weight of shoots, as well as stimulate the chlorophyll content. They can also improve the photosynthesis rate and the P and N content. P. janthinellum can be used to control phytophthora root rot in azalea, while P. citrinum YW322 can be applied to control ginseng root rot caused by Fusarium, and P. citrinum BTF08 can be applied against the pathogenic F. oxysporum s. sp. cubense race 4 in banana. P. chrysogenum can be used to control fungal diseases in cotton, and it is also appropriate for controlling root-knot nematodes in cucumber. P. citrinum can enhance the yield and chemical metabolites in choy sum, while P. chrysogenum strain 34-P can increase the fresh and dry biomass of maize, and P. chrysogenum (PenC-JSB9) is suitable for increasing the root and shoot length of pearl millet. Species of Trichoderma spp. are known as growth enhancers, stimulators of resistance in plants, biopesticides, and biofertilizers. T. harzianum is effective against dry root rot in mung bean, and T. asperelloides PSU-P1 can enhance the defense response against stem blight diseases in muskmelon. T. viride Tv-1511 can boost the concentrations of menthone, menthol, and pulegone in peppermint plants, while T. asperellum IIPRTH-31 and T. afroharzianum IIPRTH-33 can be used to control Fusarium wilt in pigeon pea plants. Among the different species, T. viride, T. longibrachiatum, T. atroviride, T. hamatum, and T. koningii have been reported to show nematicidal characteristics. Trichoderma spp. produces various secondary compounds with numerous beneficial impacts, such as xylanases, epipoly-thiodioxopiperazines, pyrones, peptaibols, volatile terpenes, nonvolatile terpenes, polyketides, siderophores, and cerato-plantanins. The most important impacts of Trichoderma inoculation are the destruction of pathogenic organisms and plant growth promotion. Their strains are considered to be among the most useful fungi in agriculture, horticulture, industrial enzyme production, and bioremediation. In conclusion, the application of Penicillium spp. and Trichoderma spp. is a promising method and an environmentally friendly practice for improving the growth and final yield of plants, and novel practices involving such biostimulants should be integrated in new farming systems. Areas that should be considered in future research include studying their mechanisms of action, assessing their long-term effects while considering sustainability and the effects of climate change, how to integrate both Trichoderma spp. and Penicillium spp. into sustainable agriculture, and investigating the effects of their combined application.