Biological Management of Soil-Borne Pathogens Through Tripartite Rhizosphere Interactions with Plant Growth-Promoting Fungi

Abstract

Soil-borne plant pathogens pose a serious threat to global food security by causing extensive yield losses and compromising crop quality. Conventional chemical-based control methods often prove inadequate, environmentally harmful, and disruptive to beneficial soil microbiota, highlighting the urgent need for sustainable alternatives. Plant growth-promoting fungi (PGPF) have emerged as effective biocontrol agents capable of suppressing diverse soil-borne pathogens while simultaneously enhancing plant growth and resilience. This review synthesizes current knowledge on the tripartite interactions among plants, pathogens, and PGPF within the rhizosphere, with emphasis on their roles in disease suppression, rhizosphere competence, and plant health promotion. The findings highlight that PGPF such as Trichoderma, Penicillium, Aspergillus, non-pathogenic Fusarium, hypovirulent binucleate Rhizoctonia and sterile fungi can significantly reduce diseases caused by fungi, oomycetes, bacteria, nematodes, and protists through mechanisms including antibiosis, hyperparasitism, competition, and induction of systemic resistance. Evidence also indicates that consortium approaches and bioformulations enhance field efficacy compared to single-strain applications. Despite this progress, challenges such as variability in field performance, limited shelf life of inoculants, and gaps in understanding ecological interactions constrain large-scale use. Overall, the review underscores that PGPF-based strategies represent a promising and sustainable alternative to chemical pesticides, with strong potential for integration into holistic crop disease management under changing climatic conditions.

1. Introduction

Plant diseases that attack economically important crops pose a real threat to world agriculture. Annually, plant diseases cost around $220 billion to the global economy [1]. Plant diseases cause unadorned losses to humanity in numerous ways. Plant diseases can reduce attainable crop yield and lead to post-harvest spoilage and deterioration in quality. Each year, diseases account for an estimated 10–20% of crop yield [2]. An additional 10–15% of the global harvest is lost to post-harvest diseases [3]. Damage to food crops by diseases may reduce economic access to food, especially in resource-poor regions. Diseases may reduce the exportability of the crops and increase management expenditures. Plant disease can reduce the esthetic value of landscape plants and home gardens. In the past, devastating plant diseases caused natural calamities, such as the infamous Bengal famine and the 19th-century Irish potato famine, which altered the course of human history. In the coming days, the ongoing climate shift may exacerbate the adverse effects of plant diseases on crop productivity [4].

Of various plant diseases, soil-borne diseases are enormous problems for agricultural production. Soil provides a complex habitat for a synergistic combination of soil-dwelling plant pathogens, including notorious genera of nematodes, fungi, oomycetes, and bacteria [5]. The soil-borne pathogens infect a wide range of host plants, causing seedling damping-off, root decay, root-knot, root rot, root discoloration, yellowing, wilting, or stunting. Plants infected by soil-borne pathogens rarely survive to produce vigorous growth, often resulting in significant yield losses. In addition, many soil-borne pathogens exhibit an extraordinary ability to form long-lived, dormant resting structures that can survive adverse environments in the absence of hosts for many years and resume infection under favorable conditions. Consequently, soil-borne pathogens prove challenging to manage [6].

Various management approaches are being employed to address soilborne diseases [7]. Among them, chemical toxicants have always been a mainstay for soil-borne disease management. However, the field-scale application of chemical toxicants is expensive and ineffective in eliminating pathogens from the soil due to difficulties in reaching pathogen propagules. Additionally, they are not immediately effective in controlling soil-borne diseases that are already established. Furthermore, the application of these chemical toxicants is associated with detrimental consequences, including health hazards and environmental pollution [8]. In particular, the loss of microbial diversity in the rhizosphere is a direct consequence of the indiscriminate use of toxic chemicals in soil, leading to a greater presence and influence of soil-borne pathogens [9]. Therefore, the management of soil-borne pathogens requires a more holistic approach that considers the environment and natural microbial communities. Due to these tactics, many investigators are currently focusing on exploring alternatives to chemical pesticides to suppress soil-borne plant pathogens. In this regard, the application of microbial biocontrol agents has gained considerable interest among experts and crop producers.

The rhizosphere is a dynamic zone of intense biological activity. Complex interactions between plants, microbes, and soil-borne pathogens in the rhizosphere significantly influence plant functioning. In such a microenvironment, the tripartite interactions among plants, beneficial microorganisms, and pathogens determine the direction of plant disease suppression. As one of the heterogeneous microbial communities that inhabit the rhizosphere, plant growth-promoting fungi (PGPF) have been recognized as key players in stimulating plant vigor and the first line of defense in the fight against soil-borne diseases [10]. The introduction of PGPF in the crop rhizosphere is a promising and eco-friendly approach to controlling various soil-borne diseases and reducing pesticide usage in the soil. Apart from their biocontrol activity, the PGPF contribute to rhizosphere competence, modulate the microbial community composition, promote nutrient uptake, and improve stress resilience [11,12]. Their capacity to successfully colonize the rhizosphere and form stable associations with the plant roots is the basis for their functional efficacy against soil-borne pathogens. These tripartite interactions between plants, soil-borne pathogens, and PGPF are complex and require a thorough understanding to leverage their potential in integrated sustainable agriculture fully.

Although several reviews have summarized the plant growth-promoting and biocontrol functions of fungi such as Trichoderma, Penicillium, and Phoma [13,14,15], most have primarily focused on their physiological roles or taxonomic diversity rather than integrating ecological functionality with practical field performance. In contrast, this review aims to synthesize current knowledge on the multifaceted roles of PGPF in the rhizosphere, emphasizing their contributions to soil-borne disease suppression, plant growth promotion, and rhizosphere competence. It summarizes key findings on the mechanisms of PGPF-mediated pathogen suppression and their effectiveness against fungi, oomycetes, bacteria, nematodes, and protists. Special attention is given to recent advances in consortium applications, bioformulation, and delivery technologies, as well as the major challenges that hinder large-scale field application. The review ultimately highlights the potential of PGPF-based strategies as sustainable alternatives to chemical pesticides for integrated disease management.

2. The Rhizosphere: A Hotspot of Microbial Interactions

The rhizosphere is a domain created under the direct influence of the plant itself, where microorganisms constitute a major influential force (Figure 1). It is the narrow zone present at the interface of the roots of a living plant and the soil [10]. The domain of the rhizosphere zone varies with plant species and differs in biological and chemical features from the bulk soil zone or the edaphosphere. The rhizosphere zone extends from 2 to 80 mm from the root surface and is characterized by enhanced microbial activity and higher concentrations of root exudates [16]. Microbial activity is several-fold higher in the rhizosphere than in the edaphosphere [17]. Moreover, the microbial community in the rhizosphere is more active, diverse, and synergistic than that in bulk soil. The quantity and quality of the root exudates or rhizodeposits are the central drivers that determine the nature and composition of microbial assemblage in the rhizosphere. Approximately 40% of the carbon fixed by plants is released into the rhizosphere as root exudates or rhizodeposits, which attract microorganisms to utilize them as carbon sources [12]. The rhizodeposits also act as selective growth substrates and favorably influence the growth of specific organisms in the rhizosphere. Moreover, the rhizosphere is a battleground where complex interactions among microbial community members partly shape its structure [18].

The effects of various rhizosphere microorganisms on plant growth and development have been well documented [19,20]. The rhizosphere microbial community has members that exert diverse effects on plant growth and development. The consequences could be either beneficial, neutral, or detrimental, depending on the plant and microbe species. Many rhizosphere microbial members establish intimate associations with plant roots and benefit the plant in multiple ways, thereby constituting a significant factor in plant growth and health. Plant growth-promoting rhizobacteria (PGPR), nitrogen-fixing bacteria, PGPF, and mycorrhizal fungi are the prominent beneficial members of the rhizobiome. In addition, the rhizosphere harbors a wide range of microorganisms that have neutral effects on plant growth and development. At the same time, the rhizosphere may attract microorganisms that exert harmful effects on the plant. Microorganisms that negatively affect plant growth and health are primarily soil-borne pathogens. The soilborne pathogens can grow and thrive well both in the bulk soil and the rhizosphere. However, the rhizosphere provides the infection court where pathogens create a parasitic relationship with host plants, causing a significant problem for agricultural production. Whether beneficially or harmfully, the rhizobiome influences plant growth and disease tolerance, and its significance to plant health is receiving more attention.

3. Functional and Ecological Roles of PGPF in the Rhizosphere

PGPF are a diverse group of rhizosphere inhabitants capable of colonizing plant roots and enhancing crop performance across a wide range of hosts. They are effective root colonizers that establish themselves even in the presence of competing microflora, with their relative abundance in the rhizosphere varying by plant species, from 10 to 46% [21]. PGPF include members of Deuteromycota, Ascomycota, Basidiomycota, and Oomycota [12]. Among them, fungi belonging to the genera Trichoderma, Penicillium, Fusarium, Phoma, and Aspergillus are most frequently reported as promising candidates. In addition, non-pathogenic strains of otherwise pathogenic fungi, as well as sterile fungi without precise taxonomic placement, are also recognized as PGPF [19,22,23,24,25,26,27,28,29,30,31,32]. PGPF, such as hypovirulent binucleate Rhizoctonia, Rhodotorula, Limonomyces, and sterile fungi, belong to the phylum Basidiomycota [11]. PGPF are primarily saprotrophs and generally lack strict host specificity, enabling them to form associations with a broad spectrum of plants. Although mycorrhizal fungi share several beneficial traits, they differ from PGPF in being obligate symbionts with limited saprobic ability and narrower host ranges [33].

PGPF confer both short- and long-term benefits to monocots and dicots by supporting multiple stages of plant development. Notable effects include enhanced seed germination, increased seedling vigor, improved shoot and root growth, better root architecture, increased photosynthesis, enhanced flowering, and increased yield [11]. PGPF promote plant growth through two main pathways: direct and indirect mechanisms (Figure 2). Direct mechanisms involve processes within the plant, such as improved acquisition of essential nutrients (N, P, K, and trace minerals) and modulation of phytohormones (auxins, gibberellins, zeatin, and ethylene) [10,12]. Indirect mechanisms operate outside the plant, where PGPF alleviate the effects of biotic and abiotic stressors, thereby indirectly supporting plant growth.

However, functional traits observed in vitro do not always translate into ecological success under field conditions. For example, strains that strongly solubilize nutrients or produce antifungal metabolites in controlled assays may be outcompeted in complex rhizosphere communities. Conversely, ecologically dominant strains with moderate functional traits can enhance plant health through persistence and synergistic interactions with other microbes. Thus, the plant growth responses to PGPF vary widely depending on plant genotype, soil type, and environmental conditions [11]. Overall, PGPF simultaneously contribute functional benefits (nutrient mobilization, hormone modulation) and ecological services (rhizosphere competence, community structuring), making them integral to sustainable agriculture.

4. Rhizosphere Disturbance by Soil-Borne Plant Pathogens

Pathogens that survive and act in soil during part or all of their life cycle are called soil-borne plant pathogens [34]. Soil-borne pathogens are among the significant disturbances in the rhizosphere of most plant species. Ecologically, they exploit the edaphic and rhizosphere environments with high levels of efficiency and cause partial or complete impairment of plant growth. Soil-borne pathogens are notorious phytopathogens capable of infecting many plant species, including a wide range of important agronomic, horticultural, ornamental, and forest species. Some soil-borne pathogens cause substantial economic losses in crop yield and quality when susceptible varieties are grown in large areas and favorable environmental conditions prevail. Yield losses of 50–100% have been reported to be attributable to soil-borne microbial pathogens in many crops [35,36]. Moreover, some soil-borne pathogens elicit toxins in crop products. Most soilborne pathogens have a wide geographic range and occur in all countries to varying degrees. However, they may constitute the largest share of plant pathogens in some areas. In the United States of America, soil-borne plant pathogens are accountable for about 90% of the 2000 significant diseases of the main crops [37]. Soil-borne microbial plant pathogens may lead to either saprophytic or parasitic life during the entire or part of the life cycle. They are introduced into the soil through infected propagative materials, transplants, infected plant debris, infected volunteer and weed plants, moving irrigation and rainwater, and organic amendments. The extensive range of inoculum sources and pathogenic lifestyles of soil-borne microbes presents significant challenges to farmers and poses a formidable obstacle to crop cultivation.

Soil-borne plant pathogens usually infect below-ground plant organs or hypogeal parts, such as crowns and roots. Some pathosystems may also exhibit infection on developing hypocotyls, epicotyls, stems, and storage organs, such as tubers and pods. The root system damage by soil-borne pathogens results in impaired transportation of water and nutrients to the aboveground plant organs or epigeal. The extent of impairment in water and nutrient transport depends on several factors, including the growth stage of the plants at the time of infection, the degree of susceptibility or resistance of the plants, the virulence of the pathogen species, and existing environmental conditions [38]. The development of symptoms on the affected parts, necrosis of vascular tissues, and death of the plants are generally observed in plants infected with soil-borne pathogens. The infection process by soil-borne pathogens results from a series of chemical communications between the pathogens and the host plants. Soil-borne pathogens detect and turn towards their host plant via chemotropism. They locate and grow in the direction of a chemical gradient, such as root exudates [39], which may act as signals from the host plants to stimulate the pathogen to break dormancy, leading to germination/hatching and subsequent growth, or conversely, inhibit these processes [40]. A recent study on a plant pathogenic strain of Fusarium oxysporum has identified an evolutionarily conserved signaling pathway triggered by peroxidase proteins in tomato root exudates, which induced a chemotrophic response of the fungal hyphae towards the roots [41]. The initiation of infection is followed by a short incubation period in which the pathogen multiplies to the required level in the host plant and then expresses disease symptoms. It may be almost impossible to save infected plants at the time of symptom expression, as the pathogen would have already established itself in the internal plant tissues. Moreover, as soils are opaque, the correct diagnosis and prediction of most soil-borne diseases are difficult. Only destructive sampling can visualize symptoms on the roots and the crown of infected plants.

5. Diversity and Characteristics of Soil-Borne Pathogens

Soils harbor a substantial number of plant pathogens. Destructive soil-borne pathogens are found across nearly all microbial groups, including fungi, oomycetes, bacteria, protists, and nematodes (

Table 1. Major groups of soil-borne plant pathogens, associated diseases, and biological features.

Pathogen Group	Common Genera/Species	Disease(s) Caused	Key Features	References
Fungi	Sclerotium, Rhizoctonia, Sclerotinia, Fusarium, Macrophomina, Verticillium, Gaeumannomyces, Gibberella, Colletotrichum	Damping-off, root/stem/collar/tuber rots, wilts, take all, bakanae, anthracnose	Most destructive group; produces resting structures (sclerotia, chlamydospores); affects a wide range of crops	[42,43,44,45,46,47,48,49,50]
Oomycetes	Pythium, Phytophthora, Aphanomyces	Damping-off, crown rot, root rot, polycyclic leaf diseases	Produce durable oospores; Phytophthora species can also infect aerial parts	[45,51,52,53]
Protists	Plasmodiophora brassicae	Clubroot in crucifers	Obligate biotroph; survives as resting spores; infects root hairs and cortex	[54,55]
Bacteria	Ralstonia solanacearum, Pectobacterium carotovorum, Agrobacterium tumefaciens, Xanthomonas, Streptomyces	Wilts, soft rot, crown gall, scab, blackleg	Highly destructive; Ralstonia infects >200 species; soft rot affects many vegetables	[56,57,58]
Nematodes	Heterodera, Globodera, Meloidogyne, Pratylenchus, Radopholus	Cyst, root-knot, lesion, and burrowing nematode diseases	Feed on roots; impair water/nutrient uptake; often cause secondary infections	[59,60,61,62]
Viruses	Tobamovirus, Potexvirus, Tombusvirus, BNYVV, LBVV, GFLV	TMV, ToMV, rhizomania, big-vein, fan leaf, etc.	Some are transmitted abiotically or by soil-borne vectors (fungi, protists, nematodes)	[4,63,64,65]

). Among the different pathogen groups, fungi cause the most economically significant diseases and affect nearly all crops grown across diverse ecosystems. The common notorious genera of fungi identified as soil-borne plant pathogens include Sclerotium, Rhizoctonia, Sclerotinia, Fusarium, Gaeumannomyces, Macrophomina, and Verticillium. These pathogens are known to occur widely in many important agricultural and forest plants. They cause damping-off, root rots, stem rots, collar rots, tuber rots, and wilt diseases. Many fungal pathogens survive in the soil for many years without a host plant by forming long-lived, dormant resting structures such as microsclerotia, sclerotia, and chlamydospores. These structures resist adverse environmental conditions and remain viable even for several years. However, they resume activity rapidly when favorable conditions return to normalcy. Other genera, such as Colletotrichum, are causal agents of anthracnose in many important crops, including those that live in soil but affect the aerial parts of plants.

Oomycetes are among the economically notorious soil-borne pathogens. Most of them are species of genera, Pythium, Phytophthora, and Aphanomyces that cause damping-off, crown rot, and root rot in many host plants. Pythium spp. are highly virulent soil-borne pathogens. They are primarily known for infecting plants early in their growth by attacking the seeds or seedlings before or after germination (damping-off). Aphanomyces euteiches is a destructive soil-borne oomycete that causes root rot in legume crops such as lentils and peas [53]. The majority of Phytophthora species are characteristically terricolous, while several species that produce deciduous sporangia have partially adapted to an aerial lifestyle [66]. That is why several species of Phytophthora can also cause polycyclic leaf diseases due to their ability to produce airborne spores. In general, oomycete pathogens can survive for a long time (extending to several years) in the soil and plant debris as oospores, which are highly resistant to adverse environmental conditions.

A protist, Plasmodiophora brassicae, is a major obligate soil-borne pathogen that causes clubroot disease in cabbage and other cruciferous crops [55]. The pathogen has three phases in its life cycle. The first phase is pathogen survival in the soil as resting spores; the second phase is the primary infection of root hairs; and the third phase is the secondary infection within the root cortex. Finally, the resting spores germinate and release zoospores, which infect root hairs.

Bacterial pathogens that cause characteristic soil-borne diseases are typically fewer in number than fungi. Important bacterial soil-borne pathogens include Ralstonia (wilt), Pectobacterium (rots), Agrobacterium (crown gall), Xanthomonas (wilt), and Streptomyces (scab). They are highly destructive to many vegetable crops. Ralstoinia is most widely distributed among soil-borne bacterial pathogens and is capable of infecting more than 200 plant species. Ralstonia solanacearum causes enormous losses in several crops, including brinjal, chili, banana, potato, tomato, peanut, and tobacco [56]. Pectobacterium carotovorum subsp. carotovorum (Syn. Erwinia carotovora subsp. carotovora) is known to cause destructive soft rot disease in many vegetables, including potato, sweet potato, cabbage, carrot, onion, garlic, cucumber, eggplant, pepper, radish, tomato, and squash [57]. The bacterium also causes blackleg on potato stems. Agrobacterium tumefaciens is the causal agent of crown gall in many dicotyledonous hosts.

Most plant-parasitic nematodes are soil-borne root pathogens, while a small number of species feed mainly upon shoot tissues. Important soil-borne nematode pathogens include Heterodera (cyst), Globodera (cyst), Meloidogyne (root-knot), Pratylenchus (lesion), and Radopholus (burrowing) [67]. Cyst nematodes are common in temperate regions and can attack a few to many plant species, depending on the nematode species [59]. Root-knot nematodes occur in all regions of the world and attack a few thousand species of plants. Lesion nematodes are widespread and attack the roots of almost all crops and trees. The burrowing nematode is commonly observed in fields of tropical and subtropical regions. These plant-parasitic nematodes feed on the root systems, impeding the plant’s ability to absorb water and nutrients. In most cases, nematode infection induces morphophysiological changes in plant roots. The characteristic symptoms of nematode-infected plants include a decline in root biomass, alteration of the root structure and/or root enlargement. Nematode wounds on roots may also create openings for other pathogens to invade the roots, leading to a synergistic infection and a substantial increase in disease severity [61,62].

Of the many viruses that infect plants, a few are exclusively transmitted by soil. Some viruses that infect forest trees and crop plants do not have biotic vectors and are soil-borne. Viruses belonging to the genera Tobamovirus, Potexvirus, and Tombusvirus are pretty stable in the soil. Abiotic soil transmission of Tobacco mosaic virus (TMV) and Tomato mosaic virus (ToMV) is well documented in agricultural and greenhouse settings [68]. In addition, a few viruses that cannot exist in a free state in the soil environment utilize soil-borne fungi, protists, and nematode vectors for their transmission. Lettuce big-vein virus (LBVV) is transmitted by the fungal vector Olipidium brassicae [63]. Sugar beet rhizomania caused by Beet necrotic yellow vein virus (BNYVV) is transmitted by the soil-borne obligate root protist Polymyxa betae [64]. Nematodes of the genera Xiphinema, Longidorus, and Trichodorus are vectors of several plant viruses belonging to two genera Nepovirus and Tobravirus [65]. Grapevine fan leaf virus (GFLV) is the first plant virus demonstrated to be transmitted by the nematode vector Xiphinema index [69]. Soil-borne viruses infect plants through their roots, and symptoms of infection are typically expressed in the aerial plant parts much later [70].

6. Conventional Approaches to Controlling Soil-Borne Pathogens

Due to the complex soil environment and wide variation among the population, soil-borne pathogens are notoriously challenging to manage. Effective management of these pathogens requires a variety of strategies, including both chemical and non-chemical methods (Figure 3).

6.1. Chemical Control

Chemical control remains one of the most effective strategies for managing certain soil-borne diseases in crops. Since the non-chemical alternatives can be time-consuming and less effective against persistent pathogens, growers have increasingly turned to chemical fumigants and fungicides as alternatives to methyl bromide [71]. Chemical methods are particularly attractive in large-scale production systems due to their rapid action, ease of application, and broad-spectrum efficacy.

Several fungicide groups have demonstrated consistent activity against soil-borne fungi. Soil disinfestation is achieved by fumigating the soil with chemical fumigants, such as dazomet, methyl bromide, chloropicrin, and metam sodium. Of these, only the dazomet, a broad-spectrum soil fumigant, has been registered in most countries. Dazomet is used for controlling soil-borne diseases and pests in greenhouses and fields [72]. Additionally, a wide range of fungicides is available for controlling soil-borne fungal pathogens. Fungicides such as rothioconazole, tebuconazole, prochloraz, fludioxonil, guazatine, captan, thiram, mancozeb, thiophanate-methyl, thiabendazole, iprodione, boscalid, carbendazim, procymidone, strobilurins, carboxin, and azoxystrobin have been registered for controlling soil-borne pathogens under greenhouse and field conditions [72,73,74,75]. For example, Bubici et al. [73] reported significant reductions in Verticillium wilt in eggplant using strobilurins under both greenhouse and field conditions. Similarly, azoxystrobin is widely used against Rhizoctonia solani [76], while cyprodinil- and fludioxonil-based fungicides are recommended for Sclerotinia sclerotiorum [77].

Despite these successes, the drawbacks of long-term fungicide and fumigant use are increasingly evident. Continuous chemical applications may disrupt soil microbial communities, reduce soil fertility and productivity, and accelerate the development of fungicide resistance in pathogen populations [78]. Resistance issues are now widespread, diminishing the effectiveness of many commonly used fungicides. To mitigate this, rotating fungicides with different modes of action and integrating them into broader management programs are strongly recommended to delay resistance development.

6.2. Crop Rotation

Crop rotation is a widely emphasized practice for managing soil-borne pathogens by reducing the buildup of inoculum. Continuous monoculture creates favorable conditions for the persistence and proliferation of soil-borne pathogens. Crop rotation not only helps suppress pathogens but also enhances soil fertility, improves chemical and physical properties, supports better water management, and reduces soil erosion [35].

Rotation based on plant family rather than individual crops is generally more effective. For example, tomatoes should be rotated with legumes, cole crops, or lettuce, but not with other Solanaceae (eggplant, chili, potato), to reduce Fusarium oxysporum wilt. Crop sequences such as oat–potato, ryegrass–potato, or clover–potato have been shown to reduce Rhizoctonia solani inoculum levels and disease incidence [79]. Larkin et al. [80] demonstrated significant reductions in Rhizoctonia canker and black scurf in potato when rotated with barley or clover, compared to continuous potato cultivation.

Despite these benefits, crop rotation is not universally effective. Crop rotation effectively reduces infections caused by soil-invader pathogens, while it is insufficiently effective against soil-inhabitant pathogens [59]. Some of these soil inhabitants, such as Sclerotinia sclerotiorum, remain difficult to manage using crop rotation due to their broad host range [50]. Likewise, some produce long-lived survival structures like sclerotia, oospores, or chlamydospores, which limit the effectiveness of crop rotation and necessitate longer rotation periods [59]. For instance, crops susceptible to the same Rhizoctonia anastomosis group should not be rotated for at least three years, a strategy also relevant for managing sweet potato diseases such as black rot (Ceratocystis fimbriata), stem rot (Fusarium oxysporum), and scurf (Monilochaetes infuscans) [81]. However, not all Rhizoctonia strains are equally pathogenic to potato; for example, anastomosis group 3 (AG3) is considered the primary potato pathogen within the broader R. solani species complex subdivided into 13 groups (AG1–AG13) [82]. Thus, although crop rotation is a valuable tool, its effectiveness is limited by the pathogen’s host range, environmental persistence, and crop availability. Future research should focus on optimizing rotations and integrating them with other complementary management practices for more consistent control.

6.3. Soil Sterilization

Soil steam sterilization is a physical method used to disinfect soil in seed beds, high tunnels, and greenhouses by applying hot steam. This method can effectively suppress a broad spectrum of soil-borne organisms, including fungi, bacteria, nematodes, certain viruses, and weeds, by injecting hot water vapor into the soil using boilers and conductors. Steam sterilization of soil has several advantages. It is an efficient and practical technology for soil sterilization, which provides broad-spectrum control of soil-borne pathogens, insects, and weeds. Additionally, a short-duration treatment with steam can provide satisfactory control of soil-borne pathogens. Steaming soil at 80–100 °C for 30 min successfully controls most soil-borne pathogens and pests [7]. Control of Verticillium dahliae, Sclerotinia sclerotiorum, Sclerotium cepivorum, and Pythium ultimum appeared effective even when temperatures of 50–60 °C were applied for a few minutes [83].

Steam treatment, in some cases, has been shown to provide adequate control of soil-borne pathogens by outperforming chemical fumigants such as methyl bromide and chloropicrin [84]. For example, Afek and Orenstein [85] reported significant reductions in the incidence of Streptomyces scabies, Spongospora subterranae, Fusarium spp., Rhizoctonia solani, and Colletotrichum coccodes in potato tubers following steam application. Similarly, Fennimore et al. [86] demonstrated improved strawberry yields in California through the use of mobile steam applicators, while steam disinfestation was also found to be comparable to methyl bromide for root-knot nematode control in cut flower production in Florida [87].

The effectiveness of steam sterilization depends on the target pathogen, soil type, and treatment parameters such as temperature and duration. For instance, R. solani was eliminated by steaming tobacco trays at 80 °C for 30 min [88], whereas Fusarium oxysporum and R. solani in sandy-loam soil at 16 cm depth required three hours of steaming at the same temperature [89]. While most pathogens are sensitive to steam, some heat-resistant spore-forming fungi may survive. Therefore, integrating steaming with other techniques can enhance efficacy. For example, combining steam with exothermic chemicals such as potassium hydroxide (KOH) or calcium oxide (CaO) has been shown to suppress tobacco mosaic virus [90].

Despite its effectiveness, steam sterilization faces practical limitations. High fuel consumption, labor intensity, and time requirements reduce its appeal for large-scale open-field agriculture [90]. Consequently, steam disinfestation is more commonly applied in greenhouses, high tunnels, and container production systems. However, even in protected cultivation, economic viability is a concern. Samtani et al. [91] reported reduced net returns for growers due to high fuel and equipment costs. These challenges highlight the need for continued research into developing cost-effective, energy-efficient, and user-friendly steaming technologies. As concerns about environmental health, pesticide regulation, and food security intensify, steam sterilization—particularly when integrated with complementary approaches—remains a promising alternative for sustainable soil-borne disease management.

6.4. Soil Amendment

Soil amendment with organic materials is a valuable method for managing soil-borne diseases in addition to improving soil fertility, structure, and water-holding capacity. Herb plants that contain essential oils, organic acids, phenols, alcohols, and other biocidal compounds are successfully used for soil amendment [92]. Biofumigation of soil with plants from the families Brassicaceae and Alliaceae reduces soil-borne pathogens [93]. For example, mustard plants produce glucosinolates, which are enzymatically hydrolyzed into isothiocyanates. The isothiocyanates are volatile compounds and toxic to many soil organisms. Similarly, Allium tissues contain thiosulfinates and disulfides, which are as biocidal as methyl bromide against soilborne pathogens [93]. Organic manures derived from agricultural waste, composts, and peat have been widely proposed for managing soil-borne pathogens and pests. Pathogens such as Rhizoctonia solani, Thielaviopsis basicola, Verticillium dahliae, Fusarium spp., Phytophthora spp., Pythium spp., and Sclerotium spp. have been effectively suppressed through the application of organic amendments [94].

Beyond direct pathogen suppression, organic amendments support beneficial microorganisms in the soil, thereby enhancing microbial competition and reducing pathogen survival. Compost extracts enriched with rhizobacteria, Trichoderma, and Pseudomonas species have been shown to stimulate plant growth, improve resistance, and produce metabolites such as phenols and tannins that are antagonistic to pathogens [95]. By diversifying the soil’s nutrient base, amendments can shift microbial population equilibrium toward a more suppressive community, as supported by sequencing-based studies. Repeated applications further enhance soil respiration and chemical properties, contributing to long-term soil health.

Biochar, a carbon-rich byproduct of biomass pyrolysis, has also emerged as a promising soil amendment. Studies demonstrate its role in improving soil pH, cation exchange capacity, nutrient retention in light soils, and promotion of beneficial microbial populations [96]. Co-application of biochar with organic manures has been shown to modify soil properties in ways that favor beneficial microbes. For example, Jaiswal et al. [97] reported that biochar reduced disease severity caused by Pythium aphanidermatum in cucumber seedlings.

Although organic amendments have proven helpful in controlling soil-borne diseases, there are specific challenges associated with their widespread use in the field, which have been hindered by cost-effectiveness and practicality issues related to large-scale application [98,99,100]. Moreover, the efficacy of organic amendments is highly variable, depending on factors such as amendment type, application rate, soil structure, cation exchange capacity, pH, and electrical conductivity. Low amendment rates may minimize phytotoxic effects, while inappropriate rates or poor-quality materials can exacerbate disease severity [101,102]. Similarly, biochar concentrations above 3% have been linked to reduced efficacy or undesirable side effects [103]. Moreover, the raw material source and composting process strongly influence compost quality and disease suppression potential [104]. To address these challenges, integrated approaches are increasingly recommended.

6.5. Soil Solarization

Soil solarization is also a promising non-chemical method for controlling soil-borne pathogens. It is performed by placing transparent polyethylene sheets over moist soil surfaces during sunny summer days. It is a climate-dependent approach and can only be practiced in a specific season in a particular region.

Soil solarization is an eco-friendly, pre-planting method that uses solar energy to suppress soil-borne pathogens, nematodes, insects, and weed seeds. It is achieved by irrigating soil and covering it with transparent polyethylene sheets, which trap solar radiation and elevate soil temperatures in the upper layers [105]. The temperature of the topsoil may reach as high as 52 °C due to the solar heat. The increased temperature and the excessive moisture inactivate most soil-borne fungi, nematodes, and bacteria near the soil surface. Although soil solarization provides an effective method of soil disinfestation, the technique is climate-dependent, requiring regions and seasons with high solar radiation and elevated temperatures [105,106]. Thus, its application is limited in northern latitudes such as Canada, Europe, and parts of North America, where light intensity is insufficient.

Through direct thermal destruction and indirect modification of soil microbiota, solarization can eliminate or suppress many soil-borne pathogens, including Verticillium dahliae, Fusarium spp., Sclerotinia spp., Agrobacterium tumefaciens, Streptomyces scabies, nematodes, and several weed species [105]. Effectiveness depends not only on climate but also on mulching material, soil moisture, and duration of treatment. For instance, ethylene–vinyl acetate films increase soil temperature more effectively than standard polyethylene [107], while biodegradable options such as paraffin-wax emulsion mulch offer cost-effective and environmentally sustainable alternatives [108,109]. Pre-irrigation prior to solarization has been suggested to enhance heat penetration and thermal equilibrium, though more research is needed to clarify soil moisture–temperature interactions [110,111].

Although solarization is a relatively simple and cost-effective method for pathogen suppression, especially for organic growers, it requires extended treatment times and favorable climate conditions, which limit its adoption. Nevertheless, integration with other approaches can increase efficacy. For example, combining solarization with allelopathic cover crops such as Brassica spp. and Allium spp. has shown synergistic suppression of pathogens [112,113]. Hence, while solarization alone may not always be practical, its strategic use within integrated management frameworks can significantly enhance the control of soil-borne diseases.

6.6. Host Resistance

The deployment of resistant cultivars or varieties remains one of the most effective and economical tools for preventing soil-borne diseases. However, breeding resistant cultivars is a labor-intensive and time-consuming process that requires combining resistance genes with desirable agronomic and commercial traits. Furthermore, no cultivar is entirely resistant to all soil-borne diseases. Cultivars labeled “resistant” typically exhibit a higher level of protection than those labeled “tolerant,” but may still be vulnerable under high disease pressure.

Host resistance has been successfully applied in several pathosystems. In tomato, resistant rootstocks have been used effectively against Fusarium oxysporum f. sp. lycopersici, Fusarium oxysporum f. sp. radicis-lycopersici, Pyrenochaeta lycopersici, and Meloidogyne spp. [35]. Similarly, resistant potato clones maintained durable resistance to Verticillium wilt for five years under continuous cropping [7,114]. While conventional breeding remains a cornerstone of crop improvement, advances in biotechnology and genetic engineering offer additional avenues for developing resistance. A deeper understanding of host–microbe interactions enables the introduction of genes encoding proteins that degrade mycotoxins or suppress cell wall-degrading enzymes [115]. Although genetic engineering has shown promise, its acceptance by consumers and regulatory bodies remains limited [116].

Grafting represents another effective strategy for managing soil-borne diseases, particularly in high-value vegetable production. By grafting susceptible scions onto resistant rootstocks, several major diseases—including bacterial wilt, root-knot nematodes in solanaceous vegetables, and Fusarium wilt in cucurbits—have been successfully managed [117]. Grafting is also widely used to control Verticillium wilt in solanaceous crops. Given the extensive knowledge of Fusarium biology and the availability of resistant rootstocks, grafting has become a practical method to mitigate Fusarium-related risks. Beyond disease resistance, grafting can improve tolerance to abiotic stresses, enhance water and nutrient use efficiency, promote vigorous growth, and improve yield stability and quality [118].

Despite its advantages, grafting has limitations. Physiological incompatibility between scion and rootstock may cause disorders that reduce yield or fruit quality. For instance, transport of photosynthates was blocked when melon was grafted onto Cucurbita ficifolia due to incompatibility [119]. Other studies have observed reduced fruit quality in grafted tomatoes compared to non-grafted controls [120]. Research on the use of auxin-related compounds to accelerate vascular tissue differentiation offers a potential solution to such challenges.

6.7. Microbial Biocontrol

Biological control offers a sustainable alternative, where antagonistic microorganisms are applied to suppress soil-borne pathogens through mechanisms such as parasitism, production of antifungal metabolites, competition for nutrients and infection sites, and induction of systemic resistance in plants [55]. Several microbial genera are successfully used as biological control agents (BCAs) against soil-borne pathogens. Commercially important bacterial and fungal BCAs include Gliocladium, Bacillus, Burkholderia, Coniothyrium, Paecilomyces, Phlebiopsis, Coniothyrium, Pseudomonas, Rhizobium, Serratia, Streptomyces, and Trichoderma [7,121,122]. These BCAs have been effective against root rot and root-knot diseases caused by soil-borne pathogens across various crops, including tomato, okra, mung bean, and bell pepper [123,124,125,126]. These BCAs produce large quantities of fungitoxic metabolites and act as strong mycoparasites, suppressing both foliar and soil-borne pathogens, as well as plant-parasitic nematodes [125]. Some BCAs secrete cell wall-degrading enzymes (e.g., chitinases, glucanases) that facilitate colonization and degradation of fungal cell walls, spores, and sclerotia [121], while some directly penetrate, disintegrate, and destroy fungal cells [127]. Some also inhibit the germination of spores and sclerotia, mainly by competing for nutrients [128,129].

Bacterial BCAs such as Bacillus amyloliquefaciens produces antifungal compounds effective against pathogens such as Alternaria panax, Botrytis cinerea, Colletotrichum orbiculare, Penicillium digitatum, Pyricularia grisea, and S. sclerotiorum [130]. Likewise, metabolites from Streptomyces species, such as prenylated indole derivatives, inhibit Colletotrichum orbiculare, Phytophthora capsici, Corynespora cassiicola, and Fusarium oxysporum [131].

In addition to antagonistic bacteria and fungi, arbuscular mycorrhizal fungi (AMF) contribute to biological control. By colonizing root surfaces and forming fungal mats, AMF create a physical barrier, compete with pathogens, enhance nutrient uptake, and secrete compounds that are antagonistic to pathogens. Vesicular–arbuscular mycorrhizas (VAMs), the most common AMF association, are formed with almost all cultivated agronomic, horticultural, and fruit crops [132]. VAMs have been reported to reduce Rhizoctonia-induced damage in multiple plants, suppress Verticillium wilt in cotton, and mitigate Fusarium crown and root rot, as well as Phytophthora nicotianae infections in tomato [7].

Although biological control is an important component of sustainable soil-borne disease management, its success is often variable under field conditions. The effectiveness of BCAs is influenced by soil type, environmental conditions, crop genotype, and interactions with native microbial communities. Therefore, consistent results are more likely when BCAs are applied as part of an integrated disease management (IDM) strategy, in combination with cultural, physical, and regulatory measures, while maintaining overall soil health.

7. Plant Growth-Promoting Fungi in Soil-Borne Disease Suppression

Biological control is a practical approach to managing plant pathogens and promoting a sustainable crop production system. Until now, many PGPF have been characterized and applied for the biocontrol of plant pathogens, including fungi, oomycetes, bacteria, protists, and nematodes, in both greenhouse and field conditions. Inoculating plants with PGPF results in reduced disease incidence and improved growth in treated plants compared to those inoculated solely with pathogens (Figure 4).

7.1. Soil-Borne Fungal Diseases

Soil-borne fungal pathogens, such as Rhizoctonia, Sclerotium, Fusarium, Colletotrichum and Sclerotinia, are commonly associated with damping-off, root rot, and wilt diseases in many plants. These diseases reduce seedling establishment and cause severe economic damage to crops. The PGPF have long been known to be able to suppress these pathogens successfully (Table 2). Of the various PGPF, Trichoderma spp. are among the most studied biocontrol agents of soil-borne plant pathogens [133]. The treatment of tomato seeds with T. koningii Rifai successfully inhibited S. rolfsii damping-off and furnished significantly greater seedling counts than uncoated control seeds [134]. T. asperellum isolates (Tri2, Tri3, and Tri6), individually and in combination, effectively promote tomato growth and suppress southern blight caused by S. rolfsii [133]. The isolates exhibited multiple plant growth-promoting traits and significantly inhibited the pathogen’s mycelial growth and oxalic acid production. Consortium treatments (dual or triple isolates) outperformed individual applications by enhancing seed germination, growth, and yield, while reducing disease severity and damping-off [133]. Isolates of T. atroviride and T. virens significantly increased the emergence of perennial ryegrass (Lolium perenne L.) in the presence of R. solani by 60–150% and 35–212%, respectively. A similar significant increase in the emergence of red clover (Trifolium pratense L.) in the presence of Sclerotinia trifoliorum was shown by treatment with T. atroviride and T. hamatum isolates [45]. In many other similar studies, Trichoderma isolates effectively controlled the damping-off disease of various crops in the greenhouse and field [44,135]. The application of Trichoderma to soil, either before or at planting, has also been reported to control soil-borne pathogens [136,137]. For instance, soil application of T. viride significantly reduced the red rot disease of sugarcane caused by Colletotrichum falcatum [138]. In addition, soil application of T. viride appeared superior for controlling seedling blight, color rot, stem rot, and root rot in Jute [139].

Other PGPF, such as Penicillium and non-pathogenic strains of Aspergillus and hypovirulent binucleate Rhizoctonia have also been used to protect plants against damping-off disease [12]. Inoculating cucumber seedlings with Penicillium viridicatum GP15-1 was effective as a biocontrol agent of damping-off disease caused by R. solani R02, leading to a significant reduction in seedling mortality and disease severity [43]. The inoculation of sunflower plants with Penicillium citrinum and Aspergillus terreus reduced the stem rot caused by S. rolfsii and improved plant growth characteristics [140]. Hypovirulent non-pathogenic Rhizoctonia successfully controlled Rhizoctonia diseases in various plants [141].

Fusarium wilt disease caused by Fusarium oxysporum is one of the most damaging and yield-limiting factors in many plants. Trichoderma species have frequently been evaluated against Fusarium wilt pathogens and have demonstrated significant potential in controlling the disease. Three species of Trichoderma (T. viride, T. harzianum, and T. virens) significantly decreased wilt incidence caused by Fusarium oxysporum f. sp. ciceris in chickpea under greenhouse conditions [142]. In addition, the combination of T. harzianum and carboxin for seed treatment was found to be superior, which improved seed germination by 12.0–14.0%, grain yields by 42.6–72.9%, and lessened wilt incidence by 44.1–60.3% in the field [142]. Similarly, incorporating soil treatment with T. harzianum isolate, Azadirachta indica leaf extract, and seed treatment with Provax-200 WP (Hossain Enterprise C.C. Limited, Dhaka, Bangladesh) significantly improved grain yields and reduced wilt incidence in chickpea in the field [47]. Field pot trials demonstrated that Fusarium oxysporum infestation significantly hindered chickpea growth; however, treatment with Trichoderma species, either individually or in consortia, significantly reduced disease incidence (22.2–11.1%) and severity (86–92%) [143]. These treatments also enhanced shoot growth parameters by up to 75% over two years. The findings highlight the potential of Trichoderma spp. as effective biocontrol agents for managing chickpea wilt under diverse environmental conditions.

Numerous studies using various species of Trichoderma have exhibited significant reductions in the incidence and severity of Fusarium wilt disease caused by Fusarium oxysporum. f. sp. lycopersici in tomatoes [8,144]. Six Trichoderma isolates were screened in vitro, where T. harzianum AMUTH-1 and T. asperellum AMUTV-3 showed the strongest antagonistic activity, while T. virens AMUTS-1 was the least effective [144]. Both top-performing isolates also produced indole-3-acetic acid and siderophores and exhibited high enzymatic activity. Pot trials confirmed the efficacy of T. harzianum AMUTH-1, which enhanced plant growth by 9–28%, increased biomass by 15–21%, and reduced FOL soil populations by 88%. Its performance was comparable to the chemical fungicide carbendazim, highlighting its potential as an effective bio-management agent against tomato Fusarium wilt. Significant suppression of Fusarium wilt was noted when tomato seedlings were treated with Penicillium sp. EU0013 and its benomyl-resistant mutant EU0013_90S [145]. In the growth chamber, suppression of tomato wilt disease was observed when a suspension of Phytophthora cryptogea zoospores was sprayed on the green parts of tomato cv. Danish Export (susceptible) and Elin F1 (moderately resistant) [146]. Non-pathogenic isolates of Fusarium oxysporum and Fusarium solani have been reported as potential biocontrol agents against Fusarium oxysporum f. sp. radicis-lycopersici, causing a significant reduction in wilt incidence of tomatoes [147,148,149]. Integration of the endophytic T. asperellum prr2 and rhizospheric Trichoderma sp. NRCB3 in the treatment resulted in a 47% reduction in Fusarium wilt incidence of banana, caused by Fusarium oxysporum f. sp. cubense (Foc) race 1 [150]. Two non-pathogenic Fusarium oxysporum Ro-3 and Ra-1 reduced the Fusarium wilt of banana (Foc R1) by 80% on cv. “Rasthali” in a field trial [150]. Another non-pathogenic Fusarium oxysporum isolate, UPM31P1, alone or in combination with Serratia marcescens isolate UPM39B3, reduced banana fusarium wilt (Foc TR4) under greenhouse conditions. In the field, this strain delayed the onset of Fusarium wilt and reduced the disease incidence by 75% at 15 weeks post-transplanting [151].

Verticillium dahliae is a serious soil-borne plant pathogen that causes vascular wilt diseases in a diverse range of crops, including eggplant. In a study, T. virens HZA14 has shown the strongest antagonistic activity against the fungus, significantly inhibiting mycelial growth and conidial germination. Moreover, HZA14 promoted plant growth and reduced disease severity by 96.59% at 30 days post-inoculation [152].

Hypovirulent binucleate Rhizoctonia has been reported to be an effective biocontrol agent of Fusarium crown and root rot [153]. Applications of four isolates (G1, L2, W1, and W7) of hypovirulent binucleate Rhizoctonia both at seeding and transplanting stages (double application) resulted in a consistent and significant reduction in fusarium wilt of tomato caused by Fusarium oxysporum f. sp. lycopersici [154]. Similarly, treatments of spinach with hypovirulent binucleate Rhizoctonia isolates significantly reduced fusarium wilt disease (Fusarium oxysporum f. sp. spinaciae) and discolouration severity by 56–100% and 52–100%, respectively [155].

Take-all, caused by Gaeumannomyces graminis var. tritici, is a common soil-borne disease that causes root rot in wheat, rye, barley, and other Poaceae species worldwide [156]. PGPF have a broad spectrum of activity and are especially active against the take-all pathogen. Applying isolates of T. virens and T. koningii as seed coatings or soil treatments effectively reduced take-all severity by 25–55% and increased dry shoot weight by 27 to 59% and dry root weight by 23 to 58% compared with the control [157].

Bakanae disease threatens rice production in Asia. Fifty isolates, including three Talaromyces flavus (Tf1, Tf2, Tf3) and various endophytes, were screened through dual culture and enzymatic assays. Six promising isolates were selected for further investigation. Glasshouse trials confirmed significant disease inhibition, with Tf1 and Tf2 showing the highest efficacy (95%), followed by Trichoderma sp. (94%), F. equiseti (87%), Tf3 (70%), and Fusarium sp. (66%) [158]. T. asperellum (SKT-1) was also reported to be a valuable fungal biocontrol agent against various seed-borne diseases of rice, including “Bakanae” disease [159].

The use of T. viride alone or in combination with Pseudomonas fluorescens as seed treatments and soil application significantly reduced dry root rot incidence in chickpea caused by Macrophomina phaseolina [42]. Seed treatment with T. viride resulted in substantially higher germination, while both seed and soil applications yielded higher yields than the control [42]. These results indicate that PGPF have significant potential as biocontrol agents against soil-borne fungal pathogens.

Table 2. Biological control of soil-borne fungal pathogens in various host plant species by PGPF.

Disease	Pathogen Name	Host Plant	PGPF Species	Effect on Disease	Reference
Damping off	Rhizoctonia solani	Pea	Trichoderma harzianum T-3	Inhibited 77.22% mycelial growth and reduced seedling mortality	[44]
		Perennial ryegrass	T. atroviride T. virens	Increased seedling emergence by 60–150% (T. atroviride) and 35–212% (T. virens)	[45]
		Cucumber	Penicillium viridicatum GP15-1	Reduced damping-off by 47% and 74% at 0.5% and 1.0% inoculum levels	[43]
	Sclerotinia trifoliorum	Red clover	T. atroviride T. hamatum	Enhanced seedling emergence up to 55% and growth up to 10.6 g shoot weight	[45]
	Sclerotium rolfsii	Tomato	T. koningii Rifai	Increased seedling emergence by 20% over untreated control	[134]
		Tomato	T. asperellum Tri2, Tri3, and Tri6	Suppressed damping-off by 87–92%	[133]
Southern blight	Sclerotium rolfsii	Tomato	T. asperellum Tri2, Tri3, and Tri6	Inhibited mycelial growth by 72.22–83.33%	[133]
Stem rot	Sclerotium rolfsii	Sunflower	Penicillium citrinum LWL4 Aspergillus terreus LWL5	Reduced stem rot severity (quantitative data not reported)	[140]
Fusarium wilt	Fusarium udum	Pigeon pea	T. harzianum T-75	Reduced wilt and wet root rot incidence (percentage not reported)	[160]
	Fusarium oxysporum f. sp. ciceris	Chickpea	T. harzianum	Inhibited radial growth by 75.89% in vitro	[47,142]
		Chickpea	T. asperellum and T. harzianum strains 1 and 2	Reduced disease incidence by 22.2% and 11.1% and severity by 86–92%	[143]
	Fusarium oxysporum f. sp. lycopersici	Tomato	Rhizoctonia G1, L2, W1, and W7	Reduced FCRR lesions by 74–93% depending on distance	[153,154]
			T. harzianum	Inhibited mycelial growth by 95.18%	[161]
			T. harzianum AMUTH-1	Enhanced plant growth by 9–28%, increased biomass by 15–21%, and reduced pathogen populations by 88%	[144]
			T. virens	Reduced disease incidence by 54.66% compared to control	[8]
			T. atroviride	Reduced disease incidence by 69%	[162]
			Fusarium oxysporum Fo-B2	Suppressed wilt by 14–87% under different conditions (growth chamber, greenhouse, field)	[149]
			Penicillium oxalicum	Reduced wilt by 28–72% under greenhouse and field conditions	[163]
			Phytophthora cryptogea	Completely suppressed wilt (100% suppression)	[146]
	Fusarium oxysporum f. sp. lycopersici race 1	Tomato, cabbage	Penicillium sp. EU0013	Suppressed disease by 32–78%	[145]
	Fusarium oxysporum f. sp. cubense race 1	Banana	T. asperellum prr2 Trichoderma sp. NRCB3	Reduced disease incidence by 47%	[150]
			Fusarium oxysporum Ro-3 and Ra-1	Reduced wilt by 80%	[164]
	Fusarium oxysporum f. sp. cubense TR4		Fusarium oxysporum isolate UPM31P1	Delayed symptoms by 6 weeks with 95–96% plant survival	[151]
	Fusarium oxysporum f. sp. spinaciae	Spinach	Rhizoctonia G1, L2, W1, and W7	Reduced lesion development by 55–98% depending on distance	[153,155]
	Fusarium oxysporum f. sp. physali	Cape gooseberry	T. virens GI006	Reduced wilt severity by up to 72%	[165]
Verticillium wilt	Verticillium dahliae	Tomato	Penicillium oxalicum	Reduced wilt incidence by 72% under greenhouse and field conditions	[163]
	Verticillium dahliae	Eggplant	T. virens HZA14	Inhibited mycelial growth and conidial germination; reduced disease severity by 96.59%	[152]
Bakanae	Gibberella fujikuroi	Rice	T. asperellum SKT-1	Suppressed bakanae disease by 95%	[159]
			Talaromyces flavus (Tf1, Tf2, Tf3), Fusarium equiseti, Fusarium sp., and Trichoderma sp.	Reduced disease by 67–95% depending on the isolate	[158]
Take-all	Gaeumannomyces graminis var. tritici	Wheat	T. virens (T65, T90, T96, T122), T. koningii T77	Reduced disease severity by 25–55%	[157]
Dry root rot	Macrophomina Phaseolina	Chickpea	T. viride	Reduced root rot incidence by 78–86%	[42]

Table 2. Biological control of soil-borne fungal pathogens in various host plant species by PGPF.

Disease	Pathogen Name	Host Plant	PGPF Species	Effect on Disease	Reference
Damping off	Rhizoctonia solani	Pea	Trichoderma harzianum T-3	Inhibited 77.22% mycelial growth and reduced seedling mortality	[44]
		Perennial ryegrass	T. atroviride T. virens	Increased seedling emergence by 60–150% (T. atroviride) and 35–212% (T. virens)	[45]
		Cucumber	Penicillium viridicatum GP15-1	Reduced damping-off by 47% and 74% at 0.5% and 1.0% inoculum levels	[43]
	Sclerotinia trifoliorum	Red clover	T. atroviride T. hamatum	Enhanced seedling emergence up to 55% and growth up to 10.6 g shoot weight	[45]
	Sclerotium rolfsii	Tomato	T. koningii Rifai	Increased seedling emergence by 20% over untreated control	[134]
		Tomato	T. asperellum Tri2, Tri3, and Tri6	Suppressed damping-off by 87–92%	[133]
Southern blight	Sclerotium rolfsii	Tomato	T. asperellum Tri2, Tri3, and Tri6	Inhibited mycelial growth by 72.22–83.33%	[133]
Stem rot	Sclerotium rolfsii	Sunflower	Penicillium citrinum LWL4 Aspergillus terreus LWL5	Reduced stem rot severity (quantitative data not reported)	[140]
Fusarium wilt	Fusarium udum	Pigeon pea	T. harzianum T-75	Reduced wilt and wet root rot incidence (percentage not reported)	[160]
	Fusarium oxysporum f. sp. ciceris	Chickpea	T. harzianum	Inhibited radial growth by 75.89% in vitro	[47,142]
		Chickpea	T. asperellum and T. harzianum strains 1 and 2	Reduced disease incidence by 22.2% and 11.1% and severity by 86–92%	[143]
	Fusarium oxysporum f. sp. lycopersici	Tomato	Rhizoctonia G1, L2, W1, and W7	Reduced FCRR lesions by 74–93% depending on distance	[153,154]
			T. harzianum	Inhibited mycelial growth by 95.18%	[161]
			T. harzianum AMUTH-1	Enhanced plant growth by 9–28%, increased biomass by 15–21%, and reduced pathogen populations by 88%	[144]
			T. virens	Reduced disease incidence by 54.66% compared to control	[8]
			T. atroviride	Reduced disease incidence by 69%	[162]
			Fusarium oxysporum Fo-B2	Suppressed wilt by 14–87% under different conditions (growth chamber, greenhouse, field)	[149]
			Penicillium oxalicum	Reduced wilt by 28–72% under greenhouse and field conditions	[163]
			Phytophthora cryptogea	Completely suppressed wilt (100% suppression)	[146]
	Fusarium oxysporum f. sp. lycopersici race 1	Tomato, cabbage	Penicillium sp. EU0013	Suppressed disease by 32–78%	[145]
	Fusarium oxysporum f. sp. cubense race 1	Banana	T. asperellum prr2 Trichoderma sp. NRCB3	Reduced disease incidence by 47%	[150]
			Fusarium oxysporum Ro-3 and Ra-1	Reduced wilt by 80%	[164]
	Fusarium oxysporum f. sp. cubense TR4		Fusarium oxysporum isolate UPM31P1	Delayed symptoms by 6 weeks with 95–96% plant survival	[151]
	Fusarium oxysporum f. sp. spinaciae	Spinach	Rhizoctonia G1, L2, W1, and W7	Reduced lesion development by 55–98% depending on distance	[153,155]
	Fusarium oxysporum f. sp. physali	Cape gooseberry	T. virens GI006	Reduced wilt severity by up to 72%	[165]
Verticillium wilt	Verticillium dahliae	Tomato	Penicillium oxalicum	Reduced wilt incidence by 72% under greenhouse and field conditions	[163]
	Verticillium dahliae	Eggplant	T. virens HZA14	Inhibited mycelial growth and conidial germination; reduced disease severity by 96.59%	[152]
Bakanae	Gibberella fujikuroi	Rice	T. asperellum SKT-1	Suppressed bakanae disease by 95%	[159]
			Talaromyces flavus (Tf1, Tf2, Tf3), Fusarium equiseti, Fusarium sp., and Trichoderma sp.	Reduced disease by 67–95% depending on the isolate	[158]
Take-all	Gaeumannomyces graminis var. tritici	Wheat	T. virens (T65, T90, T96, T122), T. koningii T77	Reduced disease severity by 25–55%	[157]
Dry root rot	Macrophomina Phaseolina	Chickpea	T. viride	Reduced root rot incidence by 78–86%	[42]

7.2. Soil-Borne Oomycete Disease

Oomycetes belong to the genus Pythium, and Phytophthora are recognized as major soil-borne pathogens of various soil-borne diseases in a diverse range of host plants. Species of these fungi are the common causes of damping-off disease in a wide range of plants. The use of antagonistic microorganisms for the biological control of the damping-off disease has drawn extensive interest in recent years. Numerous studies have demonstrated the potential of PGPF in the biological control of damping-off disease of crop plants caused by Pythium and Phytophthora (Table 3). Among the PGPF, Trichoderma spp. are extensively used as biocontrol agents to control Pythium and Phytophthora. A carbendazim-resistant mutant, T. harzianum strain M1, was employed as seed treatment and found to contain the damping-off disease of tomato caused by Pythium aphanidermatum in the greenhouse and field [166]. The efficacy of five Trichoderma isolates in controlling damping-off and root rot of tomato caused by Pythium aphanidermatum was evaluated [167]. All isolates inhibited pathogen growth and suppressed zoospore germination. Greenhouse trials revealed that the combined application of the isolates increased plant survival by 74.5%, while field trials showed a 57.2% reduction in root rot and an 87.5% increase in survival. The combined inoculation also enhanced defense enzyme activity, chlorophyll content, growth, and fruit yield. These findings suggest that a consortium of Trichoderma isolates is an effective biocontrol strategy against Pythium aphanidermatum in tomato [167]. Several other isolates of Trichoderma spp. have also been used as a bio-fungicide for the control of damping-off in tobacco, tomato, and Chinese Kale (Brassica alboglabra) caused by Pythium aphanidermatum [168,169,170]. Isolates of T. atroviride and T. hamatum showed a 25–42% increase in the emergence of white clover (Trifolium repens L.) in the presence of Pythium ultimum [45]. Treatments with Penicillium brevicompactum, Penicillium solitum and T. atroviride strongly reduced the root rot severity and improved plant anchorage, and marketable yields of the tomato plants grown in Rockwool infested with Pythium ultimum under greenhouse conditions [171]. These findings suggest that application of PGPF is an effective biocontrol strategy against Pythium in a wide range of plants.

Phytophthora root rot, caused by Phytophthora capsici, is a destructive disease affecting many plants grown in greenhouses and fields [172]. Adequate chemical controls of the disease are limited. Several potential PGPF have been tested as biological control agents for this disease. The most promising have been the isolates of Trichoderma and Penicillium. For instance, the addition of T. harzianum in the substrate resulted in a significant reduction in the Phytophthora collar rot (Phytophthora cactorum) of pear [173]. Greenhouse experiments tested the effect of Penicillium striatisporum Pst10 treatment on Phytophthora root rot in chili pepper and recorded 80% and 72% healthy plants in soil infested with Pst10 conidia 7 and 14 days after planting, respectively [52]. Talaromyces pinophilus was reported to control damping-off disease caused by Pythium aphanidermatum and R. solani in cumber [174]. Aphanomyces euteiches is a challenging root pathogen causing substantial losses in pulse crops in many areas globally [53]. Fungicides did not appear to be effective for the control of Aphanomyces root rot. However, suppression of Aphanomyces euteiches was demonstrated by T. harzianum T-22 in vitro [175]. Moreover, the application of Trichoderma resulted in the improvement of biomass and root length in Aphanomyces euteiches-infected plants. It becomes clear that the application of PGPF could play a significant role in controlling oomycete diseases in crops.

Table 3. Biological control of soil-borne oomycete pathogens causing damping off and root rot in various host plant species by PGPF.

Disease	Pathogen Name	Host Type	PGPF Species	Effect on Disease	Reference
Damping off/Root rot	Pythium aphanidermatum	Tomato	Trichoderma harzianum (Th), T. asperellum (Ta), T. virens (Tvs1), T. virens (Tvs2) and T. virens (Tvs3)	Combined application increased plant survival by 74.5% in the greenhouse, a 57.2% reduction in root rot, and an 87.5% increase in survival in the field	[167]
	Pythium aphanidermatum	Tomato	T. harzianum	Reduced damping-off up to 74% in the greenhouse and field	[166]
	Pythium aphanidermatum	Chinese kale	T. harzianum	Reduced disease incidence by approximately 33.6% compared to the control	[168]
	Pythium ultimum	White clover	T. atroviride T. hamatum	Increased seed emergence by 25–42%	[45]
	Pythium diclinum	Wheat	G. roseum T. harzianum	Reduced disease incidence by approximately more than 95% in both pre- and post-emergence damping-off.	[51]
	Pythium ultimum	Tomato	Penicillium brevicompactum Penicillium solitum strain 1 T. atroviride	Reduced disease incidence in rockwool systems by 32.9%, 54.8%, and 50.4%, respectively	[171]
	Phytophthora capsici	Chili	Penicillium striatisporum Pst10	At seven days, all treatments produced total suppression (100% relative reduction compared to the 95% control). At 14 days, SLCF + Conidia + CPM produced the highest reductions (92% reduction) and SLCF + Conidia (85% reduction), but SLCF alone produced 80% and conidia alone produced 72%.	[52]
	Aphanomyces euteiches	Lentil	T. harzianum T-21	48% inhibition of Aphanomyces euteiches mycelial growth	[175]

Table 3. Biological control of soil-borne oomycete pathogens causing damping off and root rot in various host plant species by PGPF.

Disease	Pathogen Name	Host Type	PGPF Species	Effect on Disease	Reference
Damping off/Root rot	Pythium aphanidermatum	Tomato	Trichoderma harzianum (Th), T. asperellum (Ta), T. virens (Tvs1), T. virens (Tvs2) and T. virens (Tvs3)	Combined application increased plant survival by 74.5% in the greenhouse, a 57.2% reduction in root rot, and an 87.5% increase in survival in the field	[167]
	Pythium aphanidermatum	Tomato	T. harzianum	Reduced damping-off up to 74% in the greenhouse and field	[166]
	Pythium aphanidermatum	Chinese kale	T. harzianum	Reduced disease incidence by approximately 33.6% compared to the control	[168]
	Pythium ultimum	White clover	T. atroviride T. hamatum	Increased seed emergence by 25–42%	[45]
	Pythium diclinum	Wheat	G. roseum T. harzianum	Reduced disease incidence by approximately more than 95% in both pre- and post-emergence damping-off.	[51]
	Pythium ultimum	Tomato	Penicillium brevicompactum Penicillium solitum strain 1 T. atroviride	Reduced disease incidence in rockwool systems by 32.9%, 54.8%, and 50.4%, respectively	[171]
	Phytophthora capsici	Chili	Penicillium striatisporum Pst10	At seven days, all treatments produced total suppression (100% relative reduction compared to the 95% control). At 14 days, SLCF + Conidia + CPM produced the highest reductions (92% reduction) and SLCF + Conidia (85% reduction), but SLCF alone produced 80% and conidia alone produced 72%.	[52]
	Aphanomyces euteiches	Lentil	T. harzianum T-21	48% inhibition of Aphanomyces euteiches mycelial growth	[175]

7.3. Suppression of Soil-Borne Bacterial Pathogens

Bacterial wilt, caused by Ralstonia solanacearum, is a common and destructive disease in the cultivation of solanaceous vegetables. The management of bacterial wilt with PGPF has been investigated for decades (

Table 4. Biological control of soil-borne bacteria, nematodes, and protists in various host plant species by PGPF.

Disease	Pathogen Name	Host Type	PGPF Species	Effect on Disease	Reference
Bacterial wilt	Ralstonia solanacearum	Tomato	Trichoderma spp. isolate T1	Reduced bacterial wilt incidence by more than 61.66% and decreased the Ralstonia solanacearum population in the soil by over 92%	[58]
			Trichoderma spp. AA2	Prevented 92–97% of the infection in the field	[177,178]
		Potato	T. asperellum T34	Reduced disease severity in the greenhouse and field
			T. asperellum (T4 and T8)	Reduced about 46–52% across years and locations	[176]
Common scab	Streptomyces scabies	Potato	T. viride	Reduced potato common scab incidence by about 41%	[181]
			T. viride	Reduced early blight disease incidence by 65.48%	[182]
Soft rot	Pectobacterium carotovorum subsp. carotovorum	Chinese cabbage	T. pseudokoningii SMF2	Reduced infection in the field, with up to 82.08% protection	[183]
		Potato	T. viride T. virens T. harzianum	Reduced soft rot incidence by up to 96.8% with T. viride and T. virens and 73.6–90.4% with T. harzianum)	[184]
Root-knot	Meloidogyne javanica	Tomato	T. atroviride	Reduced RKN incidence by 53.5–91.7%	[185]
	Meloidogyne incognita	Tomato	T. asperellum T34 T. harzianum T22	Reduced by 71% and 54% by T34, respectively, while T22 reduced 48% of the number of eggs per plant	[186]
	Meloidogyne incognita	Tomato	T. harzianum T-78	Reduced severe disease incidence in Arabidopsis from ~20% to 0%, representing a 100% reduction	[187]
	Meloidogyne incognita	Tomato	Pochonia chlamydosporia isolates M10.43.21	Reduced infection (32–43%), reproduction (44–59%), and fecundity (14.7–27.6%)	[188]
	Meloidogyne incognita	Arabidopsis	Fusarium oxysporum, strain Fo162	Reduced disease incidence approximately 35–53%	[189]
	Meloidogyne incognita	Tomato	Fusarium oxysporum strain Fo162	Showed 26–45% less nematode penetration, 21–36% less galls and a 22–26% reduction in the number of egg masses in the roots	[190]
	Meloidogyne incognita race 3	Melon, Squash	Fusarium oxysporum strain Fo162	Reduced early root penetration up to 69–73%	[191]
	M. graminicola	Rice	Fusarium graminicola	Reduced nematode penetration (55%) and increased the male-to-female ratio (nine times)	[192]
Cyst nematodes	Globodera pallida G. rostochiensis	Potato	Pochonia chlamydosporia	Reduced the multiplication rate of potato cyst nematodes by approximately 48–51% in field conditions	[193]
	G. pallida	Potato	T. harzianum ThzID1-M3	Reduced Globodera pallida infection and reproduction by 49% and 60%, respectively	[194]
Burrowing nematode	Radopholus similis	Banana	Fusarium oxysporum, Fusarium diversisporum	Reduced disease (nematode) incidence by approximately 29–39% after 5 days and 22–45% after 15 days of inoculation	[195]
Club root	Plasmodiophora brassicae	Cauliflower	Trichoderma spp. isolate TC32 TC45 and TC63	In the glasshouse experiment, Trichoderma isolates TC32, TC45, and TC63 reduced clubroot disease severity in Chinese cabbage seedlings by approximately 56.76%, 83.78%, and 59.46%, respectively, while in the field trial, the same isolates reduced disease incidence by about 58.33%, 27.78%, and 27.78%, respectively, compared to the untreated control	[196]
	Plasmodiophora brassicae	Rapeseed	Trichoderma strains ReTk1 and ReTv2	Reduced clubroot disease incidence in rapeseed by approximately 32.82–52.52%	[55]
	Plasmodiophora brassicae	Chinese cabbage	T. harzianum LTR-2	Reduced disease incidence (45.4%) and pathogen abundance	[197]
	Plasmodiophora brassicae	Cabbage	T. hamatum T. harzianum	Reduced the incidence of clubroot disease by 45.4%	[198]
	Plasmodiophora brassicae	Chinese cabbage	T. harzianum T4	Reduced the incidence of clubroot disease by 79.3%	[199]
	Plasmodiophora brassicae	Arabidopsis	Acremonium alternatum	Reduced gall formation and the disease index by up to 50%	[200]
Rhizomania	Polymyxa betae	Sugar beet	T. harzianum	Reduced pathogen population by approximately 46–68%	[201]
	Polymyxa betae	Sugar beet	Fusarium oxysporum Strain Fo47	Reduced the incidence of disease by 44.7%	[202]

). Delayed development and reduced incidence of potato wilt were observed with the application of T. asperellum (T4 and T8) [176]. Trichoderma-treated tomato plants showed a significant improvement in plant growth and fruit yield under field conditions. Treatments with Trichoderma isolate T1 significantly reduced bacterial wilt incidence and severity compared to the control [58]. Trichoderma isolate T1 performed superiorly among the treatments, reducing disease incidence by more than 61.66% and 53%, respectively, at two experimental sites [58]. In the field, Trichoderma spp. AA2 alone prevented 92% of bacterial wilt infections in tomatoes and, combined with Pseudomonas fluorescens PFS, contained 97% of the infections [177]. T. asperellum T34 reduced the severity of bacterial wilt in potatoes under greenhouse and field conditions [178]. Other studies have also shown the potential of different Trichoderma species as biocontrol agents for bacterial wilts in various crops [179,180].

Potato scab is a significant plant disease caused by Streptomyces spp. Antagonistic fungi have been reported as biocontrol agents of potato scab pathogens. Fifteen fungal strains of the genera Penicillium, Eupenicillium, Fusarium, Chaetomium, Mortierella, Kionochaeta, Cladosporium, and Pseudogymnoascus isolated from potato field soils showed antagonistic activity against three well-known potato scab pathogens: Streptomyces scabiei, Streptomyces acidiscabiei, and Streptomyces turgidiscabiei [203]. In Dalat City, Vietnam, a field trial showed excellent effects of T. viride in controlling potato common scab, with scab tuber incidence in the control experiment at 89.2%, compared with 52.7% in T. viride treatment [181]. Likewise, tuber treatment with T. viride @ 8 g/kg at planting provided effective control of potato common scab disease [182].

Pectobacterium carotovorum subsp. carotovorum is a destructive soil-borne pathogen that causes blackleg and soft rot disease in potatoes. Biological control by Trichoderma spp. is one of the most effective methods for controlling plant diseases. The spore preparation of T. pseudokoningii SMF2 significantly reduced the bacterial soft rot infection in Chinese cabbage in the field, giving protection of up to 82.08%, which was considerably higher than the control effect of agricultural streptomycin (69.81%) [183]. Furthermore, treating tubers with T. viride and T. virens simultaneously or two hours before pathogen inoculation effectively reduced soft rot symptoms, whereas T. harzianum was found to be effective when applied simultaneously or two hours after pathogen inoculation [184]. These studies show that PGPF are capable of giving significant control of soil-borne bacterial pathogens in many crops.

7.4. Soil-Borne Nematode Diseases

The plant pathogenic nematodes constitute a significant menace to the agricultural production of a diverse range of crops worldwide. Due to the considerable toxicity hazards of chemical nematicides, developing sustainable control strategies against nematodes is necessary. In this regard, PGPF is considered an exciting biocontrol alternative to destructive nematode plant pathogens (Table 4). The genus Trichoderma is one of the core groups of PGPF, extensively studied as biological control agents against nematodes. T. harzianum T-78 protected tomato roots against the root-knot nematode M. incognita at the different stages of the infection [187]. Treatment with T. atroviride controlled root infection by M. javanica, causing a 42% reduction of the number of galls, 60% reduction of the number of egg masses, and 90% reduction of the number of adult nematodes inside the roots of tomatoes grown under greenhouse conditions [185]. Similarly, two commercial formulations of T. asperellum (T34) and T. harzianum (T22) induced resistance to M. incognita in tomatoes and reduced the number of eggs per plant [186]. Other strains of Trichoderma spp. were also reported to provide significant protection against the root-knot nematode [204,205].

Cyst nematodes cause severe yield losses in different crops worldwide. Numerous parasites and antagonists have been evaluated for developing biological control agents against cyst nematodes. The fungus Pochonia chlamydosporia represents an important natural control agent of potato cyst nematodes Globodera pallida and Globodera rostochiensis. Significant reductions in the nematode multiplication rate were observed in potato plants grown in Pochonia chlamydosporia-treated plots (48% and 51% control, respectively) in two field experiments conducted in consecutive years [193]. T. harzianum was reported to be effective in controlling potato cyst nematode Globodera pallida. Significant reduction in infection and reproduction rate of Globodera pallida in potato roots was observed when the soil was amended with GFP-transformed T. harzianum strain (ThzID1-M3) [194]. Soil amendment with the non-transformed strain of T. harzianum (ThzID1) also reduced the reproduction rate of Globodera pallida by 43% and 48% in two consecutive potato crop cycles under greenhouse conditions [206].

Non-pathogenic Fusarium spp. have been reported to grow endophytically and lessen root-knot nematode infection. Inoculation of Arabidopsis thaliana with Fusarium oxysporum strain Fo162 systemically reduced M. incognita infection by lowering the number of M. incognita juveniles infecting the roots and, thereby, the number of galls produced [189]. The same Fusarium oxysporum strain also systemically decreased M. incognita infection, development and fecundity on tomatoes [190] and cucurbitaceous crops [191]. Isolates of Fusarium spp. have shown the ability to control burrowing nematode Radopholus similis infection on banana roots in glasshouse experiments. Pre-inoculation of banana seedling root systems with Fusarium oxysporum and Fusarium diversisporum reduced R. similis root penetration by 29–39% and 22–41% at 5 and 15 days after nematode inoculation, respectively [195]. The endophyte Fusarium moniliforme gave significant protection against Meloidogyne graminicola in rice [192]. The fungal egg parasite Pochonia chlamydosporia isolate M10.43.21 was able to colonize the roots of tomato and reduced M. incognita infection by 32–43%, reproduction by 44–59%, and female fecundity by 14.7–27.6% [188]. None of the Pochonia chlamydosporia isolates provided protection against M. incognita in cucumber. The presented reports have established the utility of PGPF as biocontrol agents of nematode infection in different plant species.

7.5. Soil-Borne Protist Diseases

Clubroot disease, caused by the obligate protist Plasmodiophora brassicae, is a major soil-borne threat to Brassica crops worldwide. Numerous studies have demonstrated that several PGPF, particularly Trichoderma species, can effectively suppress this disease (Table 4). For instance, incorporating Trichoderma-colonized crushed maize residues (isolates TC32, TC45, and TC63) into topsoil significantly reduced clubroot severity on cauliflower roots under both glasshouse and field conditions [196]. Similarly, Trichoderma applied as an inoculum within an organic fertilizer containing actinomycetes successfully prevented and controlled clubroot disease [207]. Two endophytic Trichoderma strains, ReTk1 and ReTv2, isolated from healthy rapeseed roots, strongly inhibited resting spore germination and reduced root-hair infection, root index, and disease severity in infested soils [55]. In addition to disease suppression, these strains promoted plant growth by enhancing shoot and root length, leaf diameter, and biomass accumulation. The protective effects are likely mediated through activation of plant defense pathways involving jasmonic acid, ethylene, salicylic acid, auxin, and phenylpropanoid signaling.

In soils heavily infested with Plasmodiophora brassicae, inoculation with T. harzianum LTR-2 reduced clubroot incidence by 45.4% in Chinese cabbage and markedly decreased the relative abundance of the pathogen in the rhizosphere [197]. Soil drenching with conidial suspensions of T. hamatum and T. harzianum (1.5 × 10⁶ CFU per polybag) also decreased disease incidence and enhanced cabbage growth [198]. Moreover, T. harzianum T4, applied alone or in combination with the fungicide cyazofamid or Bacillus subtilis XF-1, provided superior control of clubroot and increased the fresh weight of Chinese cabbage [199]. The control efficacy of T. harzianum (79.3%) was significantly higher than that of B. subtilis (63.1%) and statistically comparable to cyazofamid (93.2%). These results suggest that T. harzianum can serve as an environmentally friendly biofungicide for managing clubroot and improving yield in vegetable crops.

Endophytic species of the genus Acremonium have also shown promise as biocontrol agents against Plasmodiophora brassicae. Arabidopsis plants co-inoculated with Acremonium alternatum and Plasmodiophora brassicae showed a reduction of up to 50% in gall formation and disease index compared to plants inoculated with the pathogen alone [200]. Interestingly, even autoclaved spores or spore extracts of A. alternatum suppressed clubroot, indicating that viable spores were not essential for disease control. These findings suggest that Acremonium alternatum and related PGPF species may offer valuable biocontrol options for managing clubroot disease.

Polymyxa betae, another soil-inhabiting plasmodiophorid, is generally a minor pathogen but can damage young beet roots. Its greater significance lies in its role as a vector of Beet necrotic yellow vein virus (BNYVV), the causal agent of rhizomania, one of the most devastating diseases of sugar beet. Managing rhizomania is challenging due to the persistent and soil-borne nature of Polymexa betae, making vector control the most effective management strategy.

Biological suppression of Polymexa betae using antagonistic fungi has shown promising results. Soil inoculation with T. harzianum reduced root infection by 25% in glasshouse trials and lowered the cystosorus population of Polymexa betae, while simultaneously increasing sugar beet root weight [201]. Similarly, the non-pathogenic Fusarium oxysporum strain Fo47 exhibited strong biocontrol potential against Polymexa betae, comparable to T. harzianum 908 [202]. When applied via soil or seed treatment, Fo47 significantly reduced Polymexa betae activity and survival, as confirmed by DAS-ELISA, and effectively suppressed BNYVV infection. Among application methods, soil treatment provided the highest efficacy, underscoring the importance of delivery mode in optimizing biocontrol performance.

8. Mechanisms of PGPF-Mediated Soil-Borne Disease Suppression

Various mechanisms are involved in PGPF-mediated biological control of soil-borne pathogens. Most described mechanisms are direct (when PGPF act on the pathogen), while several are indirect (when PGPF modulate plant responses or the rhizosphere so the pathogen is disadvantaged). The direct protective tools include antibiosis, hyperparasitism, and competition for nutrients or colonization niches (Figure 5). Indirect mechanisms primarily involve plant growth promotion and induction of systemic resistance (ISR/SAR) (Figure 5). Although these mechanisms are often presented separately in the literature, in practice, they commonly act in concert, and attributing field efficacy to a single mechanism without multifactorial evidence is rarely justified. PGPF widely differ in their relative reliance on each mechanism, and the conferred biocontrol action is typically the result of multiple, interacting processes rather than a single mode of action.

8.1. Antibiosis

Many PGPF bioagents are known antagonists of soil-borne plant pathogens. The PGPF antagonists control soil-borne pathogens through the process of antibiosis, a crucial mechanism of biocontrol. Antibiosis refers to the phenomenon in which the antagonist produces various metabolites, such as antibiotics, lytic enzymes, toxins, or volatile compounds, which are detrimental to the pathogens. PGPF produce a diverse array of metabolites that have demonstrated antifungal properties against various soil-borne pathogens (Figure 6). Isolates of Trichoderma can produce volatile and non-volatile antibiotics, which are active against a range of plant pathogens [208]. Strains of T. virens are efficient biocontrol agents against soil-borne plant pathogens [8,45,157].

Trichoderma can produce an antibiotic, gliovirin, which plays a crucial role in the biocontrol of the damping-off pathogen Pythium ultimum [209]. Another antibiotic, gliotoxin, is mainly produced by T. virens [209]. Gliotoxin showed an inhibitory effect against the R. solani, which causes damping-off disease of zinnias, cucumber, pea, and perennial ryegrass [43,44,45,210]. Gliotoxin is also inhibitory to Pythium ultimum, but at a relatively higher concentration (30 µg/mL). T. viride and T. harzianum and their culture filtrates showed inhibitory action against Fusarium proliferatum and Fusarium verticillioides [211]. The mycoparasitic activity of T. harzianum was observed against two fusarial pathogens, while no mycoparasitism was detected between T. viride and pathogens, indicating that, depending on Trichoderma species, more than one mechanism may have been involved against the pathogen. Palmitic acid and acetic acid were the main bioactive constituents of T. viride and T. harzianum strains, respectively [211]. The harzianic acid was also reported as one of the main constituents of T. harzianum extract and acted as an anti-mycotic agent against Sclerotinia sclerotiorum, Pythium irregulare, and Rhizoctonia solani [212]. Harzianic acid promotes plant growth and is regarded as a new siderophore due to its ability to bind with Fe³⁺ [213].

An unsaturated lactone, 6-Pentyl pyrone (6-PP), produced by T. harzianum and T. atroviride strains, possessed antifungal and plant growth-promoting properties [214]. Production of 6-PP was observed by strains of T. koningii, which suppressed the mycelial growth and caused morphological alterations in the filamentous fungal hyphae [215]. 6-PP regulates the production of mycotoxin in plant pathogens by downregulating the Vel complex and Fub10 genes, key players in regulating the expression of the Fub cluster and the synthesis of aflatoxin [215,216,217]. 6-PP regulates the TOR signaling pathway, influencing various developmental processes, including growth, sporangium formation, encystment, zoospore release, and pathogenicity [218]. Alteration of organic acid metabolism via the Krebs cycle may affect the physiology of plant pathogens. 6-PP alters metabolic pathways in plant pathogens, affecting their ability to acquire nutrients and energy for growth and survival [219].

The inhibition of Phytohthora capsici has been reported to occur through the production of toxic metabolites by Penicillium striatisporum Pst10 [52]. The production of griseofulvin, dechlorogriseofulvin, and curvulinic acid was detected in the culture filtrates of Penicillium canescens and Penicillium janczewskii, exhibiting inhibitory activity against the plant pathogenic fungus R. solani [220]. Another compound, ito, purified from Penicillium canescens extracts, was entirely inhibitory for the mycelial growth of R. solani and several other plant pathogenic fungi in vitro [221]. The volatile organic compounds (VOCs) producing non-pathogenic Fusarium oxysporum strain CanR-46 is a promising biocontrol agent of Verticillium dahliae. Nineteen VOCs were identified in Fusarium oxysporum (Fo) strain CanR-46, with eremophila-1 (10),11-diene being the most prominent, which inhibited mycelial growth, delayed conidial germination, suppressed germ-tube elongation, and caused hyphal shriveling and collapse of V. dahlia [222]. Some PGPF biocontrol agents produced metabolites which acted against plant pathogenic nematodes, as alternariol 9-methyl produced by non-pathogenic Alternaria sp. against the pine wilt nematode Bursaphelenchus xylophilus [223], VOCs produced by Daldinia cf. concentrica against M. javanica [224] and chaetoglobosin A, chaetoglobosin B, flavipin, 3-methoxyepicoccone and 4,5,6-trihydroxy-7-methylphthalide produced by Chaetomium globosum against M. incognita [225].

PGPF Phoma sp. are also an abundant source of potent antimicrobial compounds. Two metabolites, epoxydines A and epoxydon B, along with four known and related metabolites, were purified from the endophyte Phoma sp. isolated from the halotolerant plant Salsola oppositifolia, which were shown to have antifungal activity against the fungus Microbotryum violaceum [226]. An α-tetralone derivative, (3S)-3,6,7-trihydroxy-α-tetralone, was purified from a Phoma endophyte, isolated from the Chinese medicinal plant Arisaema erubescens, and shown to have antifungal activities against Fusarium oxysporum and Rhizoctonia solani [227]. A new anthraquinone derivative, 7-(γ, γ)-dimethylallyloxymacrosporin, along with five known analogs, macrosporin, 7-methoxymacrosporin, tetrahydroaltersolanol B, altersolanol L, and ampelanol, were identified from the endophyte Phoma sp. L28 and shown antifungal activity against Colletotrichum musae, Fusarium graminearum, Colletotrichum gloeosporioides, Penicillium italicum, Fusarium oxysporum f. sp. lycopersici, and Rhizoctonia solani [228]. A new phenolic compound, phomodione, along with two other compounds, usnic acid and cercosporamide, isolated from the culture of an endophyte, Phoma pinodella, showed fungicidal activity against Pythium ultimum, Rhizoctonia solani and Sclerotinia sclerotiorum [229]. Four antifungal compounds, viridicatol, tenuazonic acid, alternariol, and alternariol monomethyl ether were purified from Phoma sp. WF4 isolated from Eleusine coracana (L.) Gaertn, which causes intense breakage of Fusarium graminearum hyphae in vitro [230]. These well-known examples have demonstrated that many PGPF produce antibiotics and other metabolites that seem to be critical for controlling different soil-borne pathogens.

Although metabolite discovery is robust, several practical questions remain unresolved, limiting the explanatory power of antibiosis for field disease suppression. For instance, many metabolites inhibit pathogens at concentrations achievable in vitro, but the actual concentrations in the rhizosphere, their persistence, and diffusion distances are rarely quantified. Dual culture or cell-free filtrate assays may artificially amplify antibiosis (high local concentrations, direct contact) and do not reflect spatial heterogeneity or adsorption to soil particles. To confirm that antibiosis is the dominant mechanism in the field, in situ verification is essential, including the use of mutant strains (biosynthetic gene knockouts/knockdowns), isotopic labeling of metabolites in soil, and metabolomics of the rhizosphere.

8.2. Hyperparasitism

Biological control of soil-borne plant pathogens by many PGPF relies on hyperparasitism. The role of the hyperparasitism mechanism by the biocontrol agent is immense since it lives in or on the pathogens (the host) and utilizes them as a nutrient source. Bacteria and viruses are recognized to parasitize some soil microorganisms, but fungi are the most prevalent parasitic organisms in the soil. Hyperparasitism by fungi is a complex process that occurs in several phases. In this mechanism, the hyphae of parasite fungus grow towards the target pathogen by remotely recognizing it (chemotropism and recognition), attach on the host surface and intensively coil around it (attachment and coiling), secret lytic enzymes to lyse pathogen cell wall (secretion of extracellular enzymes), and penetrate the cell wall and digest host–pathogen cell (penetration and digestion).

Among the PGPF, Trichoderma is well known for having hyperparasitic strains. While encountering host pathogens, hyperparasitic Trichoderma strains detect the pathogens, grow toward them, attach to the host surface, and coil around the pathogens [231]. Eventually, the Trichoderma form appressoria and release extracellular hydrolytic cell wall-degrading enzymes, mostly glucanase and chitinase, leading to the entry of Trichoderma hyphae into the host cells and collapse the host–pathogen [209]. The mycoparasitic strains of T. harzianum controlled Rhizoctonia solani, Sclerotinia sclerotiorum, Phytophthora spp., and Pythium ultimum through direct parasitism of pathogen hyphae [209,232,233,234]. The reduction in root rot in pepper was related to intense hyperparasitism, where T. harzianum hyphae coiled around Phytophthora hyphae, resulting in the disintegration and lysis of the host fungus hyphae [173]. According to Ezziyyani et al. [233], hyphae of T. harzianum were seen enveloping, severing, and disintegrating Phytophthora capsici hyphae, thereby preventing the growth of the pathogen. The hyphae of the Bakanae disease fungus Gibberella fujikuroi on the embryo of rice seeds were penetrated by the hyphae of its biocontrol agent T. asperellum SKT-1, leading to the degradation of the cell walls of G. fujikuroi [159]. Isolates of T. virens were reported to coil around the hyphae of Gaeumannomyces graminis var. tritici [157].

Hyperparasitism is also involved in the biological control of nematodes by PGPF. of 18 strains of Trichoderma species (T. harzianum, T. virens, T. atroviridae, T. rossicum, T. tomentosum,) and six strains of nematode-trapping fungi (Arthrobotrys tortor, Arthrobotrys oligospora, Monacrosporium cionopagum and Monacrosporium haptotylum), T. harzianum strains showed the most potent egg-parasitic ability against Caenorhabditis elegans [235]. Trichoderma isolates (T. asperellum, T. atroviride, and T. harzianum) exhibited nematode biocontrol activity against M. javanica in pot experiments with tomato plants, where females and egg masses were found to be parasitized by the fungus (T. asperellum-203) [236]. Hyphae of T. harzianum formed a loop and trapped 2nd-stage juveniles of M. incognita. Subsequently, Trichoderma penetrated the nematode body and replaced all internal organs with fungal growth, leading to the death of the nematode [237]. The gelatinous matrix plays the primary role in the process of Trichoderma conidial attachment to the nematode M. javanica [236]. The eggs of M. incognita are parasitized and destroyed by Acremonium implicatum [238]. Likewise, Fusarium oxysporum isolated from banana parasitized, paralyzed, and killed the root-lesion nematode Pratylenchus goodeyi [239]. The fungal antagonist Pochonia chlamydosporia acts against root-knot and cyst nematodes by directly parasitizing their eggs [188]. Therefore, using hyperparasitic fungi from different groups as biocontrol agents appears to be a promising strategy for controlling soil-borne plant-parasitic nematodes in agriculture.

Despite extensive evidence of hyperparasitism under laboratory and greenhouse conditions, its ecological significance in open-field environments remains constrained by encounter probability and spatial dynamics. Effective hyperparasitism requires direct physical contact between antagonist and pathogen; however, soil heterogeneity, patchy pathogen distribution, and low antagonist densities often limit such encounters. Pathogen refugia—including deep-buried sclerotia or protected egg masses—further reduce accessibility. Consequently, field efficacy depends strongly on inoculum density, timing of application, and the antagonist’s root colonization and persistence abilities.

Moreover, disease progression in the field may outpace the establishment of hyperparasites, particularly in rapidly developing epidemics. Conversely, the degradation of resilient structures such as sclerotia can require extended periods, making hyperparasitic control more episodic and delayed rather than immediate or uniform.

8.3. Competition

From a biological control point of view, the term competition is defined as the higher activity of a biological agent to access limiting nutrients and colonize a niche, making it inaccessible to pathogens. Nutrients and colonization substrate are essential for the survival and subsequent proliferation of all microorganisms. Competition between microorganisms is universal since the amount of a crucial substrate or nutrient is most often insufficient. Beneficial and pathogenic microorganisms compete for nutrients and colonization niches in the root zone, depriving each other of these resources, thereby ensuring their own persistence and causing the death or inactivity of the different microorganisms. Competition for nutrients and colonization space is a classic mechanism of biocontrol by many PGPF agents. Usually, PGPF are often aggressive competitors in the root zone, characterized by rapid development and a high capacity for colonization [12], which enables the PGPF to quickly establish a niche quickly [43]. Additionally, PGPF demonstrated a competitive ability to absorb scarce nutrients [11]. Due to these two characteristics, PGPF promote the competitive exclusion of soil-borne pathogens from infection sites, hence preventing the spread of soil-borne illnesses. For example, T. harzianum T35 was able to control the Fusarium wilt pathogen Fusarium oxysporum due to its superior ability to compete for nutrients and rhizosphere colonization [240]. PGPF are aggressive competitors in the root zone and are characterized by faster growth and high colonization ability [12], which helps them rapidly establish in the niche [43].

Moreover, PGPF showed a competitive ability to acquire limited nutrients [11]. With these two traits, PGPF cause competitive exclusion of soil-borne pathogens from infection sites and control soil-borne diseases. For instance, the Fusarium wilt pathogen Fusarium oxysporum was controlled by T. harzianum T35 due to its superior ability to compete for nutrients and colonize the rhizosphere [240]. Trichoderma spp. produced siderophore in iron deficiency conditions and competed with Pythium for the availability of iron in the soil [241], thereby inhibiting the growth of soil-borne fungal pathogens. The inoculation of T. harzianum resulted in a significant decrease in the Phytophthora population in the substrate, probably due to exhaustion of the nutrient supply by the biocontrol agent [173]. The suppression of take-all and common root rot in wheat by Phoma sp. GS6-1, Phoma sp. GS7-4 and non-sporulating fungus GU23-3 appeared to be due to obstructive pathogen colonization on the wheat root systems in the presence of biocontrol agents [242]. An increase in PGPF inoculum concentration in the soil resulted in less frequent colonization by both fungal pathogens. At the same time, the addition of Cochliobolus sativus and Gaeumannomyces graminis var. tritici inoculum in the soil at higher concentrations did not affect the colonization ability of the PGPF in roots, indicating the high competitive root colonization ability of Phoma and sporulating fungi [242]. Prior colonization of wheat roots by these fungi reduces the availability of infection sites for pathogen colonization. Therefore, wheat grown in soil amended with Phoma sp. GS7-4 for ten days, subsequently inoculated with Gaeumannomyces graminis var. tritici, and cultivated for four weeks, showed less disease [242]. These results suggest that the competitive advantage of PGPF provides benefits to these plants by potentially enhancing their ability to cope with pathogens and/or utilize limited resources.

Although competition can be an effective mechanism for disease suppression, it is inherently context-dependent. The outcomes of niche-based competition may depend on which organism colonizes the area first, known as the priority effect. At the same time, factors such as nutrient availability, pH, redox potential, and adsorption to soil minerals can influence the effectiveness of nutrient-based competition. Additionally, highly competitive PGPF may outcompete other beneficial microbes, thereby altering community functions. Empirical evidence of such trade-offs is limited but warrants a comprehensive investigation. Mechanistic field studies are essential for quantifying root colonization dynamics, measuring niche occupancy (e.g., via qPCR or fluorescent tagging), and linking colonization processes to disease outcomes across different soils and cropping systems.

8.4. Plant Growth Promotion

The PGPF-mediated suppression of most soil-borne pathogens is due, at least partially, to the promotion of the growth of infected plants by PGPF [243]. In the presence of soil-borne pathogens, plants exhibit disrupted development and become more susceptible to pathogenic activity. However, PGPF diminish the adverse effects of pathogens on plant growth and indirectly helps to biocontrol the pathogens. The treatment of tomato seeds with T. koningii Rifai resulted in significantly greater seedling counts, plant height, and fresh weight in protected plants compared to the unprotected control plants [134]. One or more isolates of T. atroviride significantly improved the seedling growth of the three pasture species in the presence of R. solani, Sclerotinia trifoliorum, and Pythium ultimum [45]. T. virens inoculated into tomato seed and soil indirectly augmented plant growth in the presence of the tomato wilt pathogen [8]. Equally, in the presence of the tomato wilt pathogen, T. atroviride isolate LU140 significantly increased tomato plant growth by 50% or more, while none of the Trichoderma isolates consistently increased all plant growth parameters in the absence of the pathogen [162]. In banana, integration of endophytic T. asperellum prr2 with rhizospheric Trichoderma sp. NRCB3 resulted in a 45% increase in the bunch weight in the presence of Fusarium oxysporum f. sp. cubense (Foc) race 1 [150]. Likewise, inoculation of T. harzianum and T. virens into potting substrates improved the biomass and root length in Aphanomyces euteiches-infected lentil plants [175]. Yu et al. [199] suggested that T. harzianum T4 not only reduced the incidence of clubroot by inhibiting spore germination but also by promoting the growth of Brassica chinensis.

Hypovirulent binucleate Rhizoctonia increased the fresh weight of tomato stems and leaves in plants inoculated with Fusarium oxysporum f. sp. lycopersici under greenhouse conditions [153,154]. Similarly, the fresh weight of spinach leaves in plants treated with hypovirulent binucleate Rhizoctonia isolates G1, L1, W1, and W7 increased significantly by 53–63%, compared with untreated and pathogen-challenged plants [155]. These reports show that PGPF promote plant growth under the pathogen-inoculated condition, and such plant growth promotion ability is partly attributed to their disease suppression ability [243]. Generally, substantial damage from the pathogen infection is observed in the inoculated plants. However, the application of PGPF helps plants improve performance and minimize the overall adverse effects of pathogens. In this way, plant growth-promoting activities by PGPF appear to play an indirect role in the biocontrol of plant diseases. Therefore, fungal antagonists with plant growth-promoting traits have advantages as biocontrol agents in agriculture.

Distinguishing direct pathogen suppression from indirect tolerance arising from improved plant health remains methodologically challenging but is essential for accurate interpretation of plant–microbe interactions. Experimental designs such as split-root systems, the use of mutant strains that lack plant growth-promoting (PGP) traits but retain colonization ability, and carefully controlled pathogen challenge assays can help decouple direct antimicrobial effects from host-mediated tolerance—yet such rigor is often absent in current studies. PGPF also modulate plant hormone balances, including auxin, ethylene, gibberellin, and cytokinins, leading to growth promotion but sometimes inadvertently altering susceptibility to specific pathogens through hormonal crosstalk. From a sustainability standpoint, enhanced growth and yield stability under disease pressure represent valuable outcomes even when pathogen levels are not substantially reduced; however, distinguishing true disease suppression from mere symptom masking is critical for designing durable management strategies. Future research should employ experimental approaches that partition direct and indirect effects—such as split-root systems, hormone profiling, and PGP-deficient mutants—while integrating phenotypic assessments with transcriptomic and metabolomic analyses to elucidate the host pathways modified by PGPF activity.

8.5. Induction of Systemic Resistance

Induction of systemic resistance (ISR) is one of the standard mechanisms by which PGPF-inoculated plants protect themselves against a wide range of plant pathogens. ISR is a plant defense mechanism where PGPF trigger enhanced resistance to pathogens in the plant [11]. This resistance is not a direct attack on the pathogen but rather a preconditioning of the plant to respond more effectively to future attacks. ISR primarily relies on signaling pathways involving jasmonic acid (JA) and ethylene (ET), rather than salicylic acid (SA), which is more associated with Systemic Acquired Resistance (SAR) (Figure 7). While SA signaling is primarily associated with SAR, ISR can also involve SA, particularly in certain plant species or under specific conditions [22]. Unlike SAR, ISR typically sensitizes or primes plants to activate JA- and ethylene ET-inducible defense genes. This priming process prepares the plant to respond more rapidly and robustly to pathogen attacks, enhancing its resistance. Although SAR and ISR differ in their triggers and signaling pathways, NPR1 (Non-expressor of Pathogenesis-Related genes 1) plays a crucial role in both forms of plant immunity. NPR1 acts downstream of SA and JA/ET, facilitating the expression of PR genes and other defense responses during SAR and ISR.

Many PGPF are known to trigger ISR in plant roots, which protects plants from infection caused by soil-borne plant pathogens. Trichoderma spp. are the most widely used inducers of resistance to soil-borne plant pathogens. Cotton roots grown from T. virens-treated seeds showed an increase in terpenoid synthesis and peroxidase activity compared to untreated controls [244]. The intermediates of the terpenoid synthesis pathway, desoxyhemigossypol, and hemigossypol, were strongly inhibitory to R. solani and the final product, gossypol, was toxic to the pathogen only at a higher concentration [244]. This indicates the importance of induced defense responses, particularly the elevated terpenoid synthesis, in cotton roots by T. virens in the biological control of R. solani-infected seedling disease. T. virens treatment in seeds or soil reduced the incidence of Fusarium wilt disease and induced the expression of defense-related enzymes (peroxidase, polyphenol oxidase, and phenylalanine ammonia-lyase) compared to untreated controls [8], suggesting that induction of resistance in tomato by T. virens played an essential role in defense against Fusarium wilt disease. Similarly, the combined application of five Trichoderma isolates in controlling damping-off and root rot of tomato caused by Pythium aphanidermatum enhanced defense enzyme activity, such as peroxidase, polyphenol oxidase, and chitinase [167]. In a study aimed at identifying effective biocontrol agents against Fusarium fujikuroi in Basmati rice, three Talaromyces flavus (Tf1, Tf2, Tf3) and various endophytes were found to enhance defense gene expression [158]. These findings emphasize the modulation of plant defense responses as a common mechanism for the biological control of bakanae disease in rice.

Inoculation with T. asperellum alone or with S. rolfsii increased glucanase, chitinase, and peroxidase activity in bulbs, roots, and leaves of all three onion varieties compared to uninoculated controls, where the highest levels of enzyme activity were observed in plants that had been dual-inoculated with T. asperellum and S. rolfsii. Plants of the variety with the most increased enzyme activities showed the lowest severity of the disease [245], implying that T. asperellum mediates the protection of onions against infection by S. rolfsii principally through the constitutive and induced activity of glucanase, chitinase, and peroxidase enzymes. Root colonization by Trichoderma spp. in tomato primed salicylic acid-regulated defenses, limiting nematode root invasion and subsequently enhanced jasmonic acid-regulated defenses, annulling the deregulation of jasmonate-dependent immunity by the nematodes, leading to the inhibition of nematode galling and fecundity [187]. Application of T. harzianum-fortified vermicompost protected tomato plants from fusarium wilt and induced an elevated accumulation of peroxidase, polyphenol oxidase, phenylalanine ammonia-lyase, superoxide dismutase, and total phenol content in the treated plants [161].

The biocontrol capacity of T. asperellum against tomato bacterial wilt Ralstonia solanacearum under field conditions was associated with increased levels of peroxidase, polyphenol oxidase, phenylalanine ammonia-lyase, β-1,3-glucanase, and total phenol content in the T. asperellum-treated plants, indicating involvement of the induction of plant resistance mechanisms by T. asperellum in the biocontrol of R. solanacearum in tomato plants [176]. Treatment with T. atroviride isolates significantly reduced tomato fusarium wilt incidence when spatial and temporal separation existed between the Trichoderma isolates and Fusarium challenge [162]. These imply that Trichoderma may prime plant defense responses to protect plants against soil-borne pathogens. In rapeseed, root colonization by two endophytic Trichoderma strains, ReTk1 and ReTv2, triggered defense responses by upregulating genes associated with the jasmonate, ethylene, salicylic acid, auxin, and phenylpropanoid pathways [55]. This is the first report demonstrating that endophytic Trichoderma from rapeseed roots can reduce clubroot severity through induced defense mechanisms such as ISR and SAR.

While many PGPF are known to induce ISR, the specific elicitors, microbe-associated molecular patterns (MAMPs), secondary metabolites, or volatile organic compounds responsible for these effects are often unknown. Discovering conserved elicitors would enhance mechanistic understanding and facilitate the design of targeted bioformulations. Moreover, ISR typically functions through priming—enabling faster or stronger defense responses upon pathogen challenge—rather than through constitutive activation of defense pathways. While priming minimizes fitness costs, it is difficult to quantify and requires time-series challenge assays supported by molecular markers. The efficacy and specificity of ISR are also strongly context-dependent, varying with plant genotype, soil conditions, nutrient status, and the surrounding microbial community; an elicitor effective in one cultivar or environment may be ineffective in another. Furthermore, the potential growth–defense trade-off warrants attention, as enhanced defensive readiness may divert resources from growth under low disease pressure. ISR frequently acts in concert with other mechanisms such as antibiosis and competitive exclusion, making it essential to study these synergistic effects in combination rather than isolation. To advance predictive understanding and practical use of ISR, future research should focus on isolating and characterizing elicitors through biochemical purification and mutant screening, quantifying priming responses using transcriptomic and proteomic time-series analyses, and conducting multi-site field trials to evaluate the durability and trade-offs of ISR across diverse environmental contexts.

9. Rhizosphere Competence: A Key Trait of Effective PGPF Biocontrol Agents

Rhizosphere competence refers to the ability of microorganisms to proliferate and function within the developing rhizosphere. Rhizosphere competence is a significant determinant for an organism to be an efficient biocontrol agent. The microbe that can survive and establish itself in the rhizosphere in the presence of native microflora has a higher ability to protect plants from harmful soil microorganisms effectively than those that cannot. Several previous studies have reported that rhizosphere-competent PGPF colonizes the rhizosphere and prevents the colonization of soil-borne pathogen populations. Pre-inoculation of tomato seedlings with hypovirulent binucleate Rhizoctonia followed by challenge with Fusarium oxysporum f. sp. lycopersici suppressed pathogen population in stems and roots under greenhouse conditions [153,154,155]. Low population densities of Fusarium oxysporum f. sp. spinaciae were found in the roots, both inside and outside paper pots, of plants treated with all four isolates of hypovirulent binucleate Rhizoctonia. These results suggested that the rhizosphere competence of the antagonists may play a significant role in controlling soil-borne pathogens in many plants.

The establishment of biocontrol microorganisms along the root length or depth is not necessarily homogeneous and usually varies across different portions of the roots [12]. Therefore, rhizosphere competence is measured based on population density as a function of root depth [134]. The population density of PGPF may vary with root depth and reveal the site of maximum colonization by PGPF in the root. For instance, rhizosphere-competent strains of Trichoderma colonize the rhizosphere, having higher population density in the upper and lower segments of roots than in the mid-segments. An isolate of T. koningii was rhizosphere competent and detected in the rhizosphere at all depths, but with a significantly higher establishment in the upper and lower root portions [134]. Hossain et al. [43] found a significantly greater density of Penicillium viridicatum GP15-1 in the upper root region than in the middle and lower part of the cucumber roots during the first two weeks of seedling growth. The occurrence of high fungal densities in the upper root regions at the early growth stage may result from increased exudates from the germinating seeds. On the contrary, the lower population densities of the fungus in the bottom root segments than the upper root regions may be attributed to the faster root growth of plants than the hyphae of the fungus [12]. Another reason might be the position of the primary root exudation zone, which is assumed to be located behind the root apex.

The root population of Penicillium viridicatum GP15-1 showed a gradual increase with seedling age. The fungus colonized the entire root system after three weeks of seedling growth, resulting in an equal level of fungal isolation frequency in three root regions [43]. Similar findings were also reported by Jayaraj et al. [166] and Prasad et al. [160], who recorded a steady increase in rhizosphere population of T. harzianum with plant age in tomato and pigeon pea, respectively. These clearly indicate that seedling age significantly affects the extent of root colonization by the biocontrol agents. The rhizosphere competitiveness and effectiveness of biocontrol agents inevitably depend on their capability to survive, multiply and colonize the rhizosphere. The rhizosphere competent biocontrol agents can increase their population and grow around the host roots with increasing seedling age and ultimately constitute stable populations able to elicit beneficial effects on plants. The efficient and complete colonization by the biocontrol agents allows the root system to resist the pathogen establishment and its successive infection. The utilization of specific nutrients is vital for the efficient and competitive colonizing abilities of PGPF. Only fungi with a large nutrient base can grow with root growth and colonize the distal root region. PGPF, such as T. koningii, multiplied more on tomato roots in S. rolfsii-infested soil than in the non-infested soil [134]. The augmented exudation from roots infected by the pathogen might provide a food source for the antagonist that attacks the pathogen structures in the absence of host roots. Since some of these pathogen structures could have died, the antagonists may have used them as a food base for colonizing the rhizosphere.

10. Mass Production and Formulation Strategies for PGPF Delivery

The selection of appropriate commercial methods for mass production and delivery of antagonists is a significant step in making biocontrol agents available for farmer use. Agro-industrial waste and byproducts serve as economical substrates for microbial growth and biomass production (Figure 8). Solid-State Fermentation or Liquid Fermentation is employed to mass produce biocontrol agents, including PGPF. Solid or semi-solid substrate fermentation is beneficial for fungi that do not sporulate in liquid or survive the liquid fermentation process. Moreover, solid-state fermentation resembles the natural environment and provides an ideal habitat for filamentous fungi to produce vigorous conidia and mycelia. Because of these reasons, solid-state fermentation systems have often been preferred to produce inoculum of fungal biocontrol agents in the genera Penicillium, Trichoderma, Coniothyrium, Gliocladium, Chaetomium and Laetisaria. A solid-state formation system requires very minimal facilities for implementation and is advantageous in countries where agricultural wastes are available and labor is plentiful. Various grain seeds and meals, bagasse, straws, wheat bran, sawdust, peat, and other organic substances, individually or combinedly, are used as substrates. By growing on these substrates, aerial conidia of biocontrol agents with high viability and effectiveness are obtained. The mass production of aerial conidia of Trichoderma spp. by solid-state fermentation using cereal grains is a well-known process [246]. The highest production of conidia of Penicillium oxalicum, a fungal antagonist of Fusarium oxysporum f. sp. lycopersici was observed on peat/vermiculite (1:1, wt/wt) plus a meal of cereal grains (barley) or leguminous seeds (lentil) [247]. Spent mushroom compost, farmyard manure, vermicompost, sorghum grain, wheat grain, and broken maize grain-based materials were evaluated for mass production of T. harzianum T5 and efficacy of the biocontrol agent against R. solani in cowpea. Of these substrates, the spent mushroom compost produced by T. harzianum T5 was found superior in reducing seedling mortality and promoting seedling growth [248]. T. harzianum was multiplied on jhangora (Echinochloa frumentacea), mandua (Eleusine coracana), sorghum (Sorghum bicolor), polygonum (Polygonum hydropiper), rice (Oryza sativa), and wheat (Triticum aestivum)-based substrates, out of which Jhangora proved to be the superior substrate [249]. Adding cow dung compost in the treatment further reduced the disease incidence and improved tomato yield [249]. The key benefit in using organic substrates is that they are rich in carbon and nitrogen, which help the inoculated PGPF grow, persist and sustain for a longer duration. Although a solid fermentation system has many benefits, this production system is marked with several limitations. These include unsuitability for industrial-scale production, time-consuming, labor-intensive, a shortage in automation, and a lack of standardization of fungal inoculum [250].

On the other hand, liquid fermentation technology is a sophisticated system widely used to produce microbial products such as organic acids, enzymes, antibiotics, and other drugs on an industrial scale. The multiplication of conidia in liquid media is considered the most efficient and economical method for the mass production of microbial bioagents [251,252]. Until now, this has been the typical approach for producing various fungal agents for the biocontrol of insects and weeds [253]. Its application for the mass production of antagonists for plant pathogens is not widely adopted. However, Kobori et al. [254] and Lopes et al. [255] confirmed the feasibility of a liquid fermentation system for mass production of submerged conidia and microsclerotia of T. harzianum and T. asperellum, respectively. Recent years have seen an increase in the number of studies using the liquid substrate to optimize conditions for mass production of different propagules of biocontrol agents of plant pathogens [252,254]. Temperature, pH, photoperiod, and carbon–nitrogen ratio are assumed to be factors affecting the conidial production of biocontrol agents in a liquid fermentation system. As de Rezende et al. [246] showed, the optimal conditions for the highest conidial production of T. asperelloides LQC-96 through liquid fermentation included an initial pH of 3.5, a carbon: nitrogen ratio of 200:1 at 30 °C, without glycerol, and under a 24 h photoperiod. These conditions also maximized conidial production of T. erinaceum T-12 and T-18, and T. harzianum T-15, but only LQC-96 effectively parasitized S. sclerotiorum, preventing myceliogenic germination of sclerotium [246]. The liquid fermentation system represents several shortcomings. Some microorganisms, particularly filamentous fungi, require high oxygen transfer for growth and sporulation, and produce fewer conidia in liquid fermentation than in solid fermentation. For example, Penicillium oxalicum produced 250-fold fewer conidia in liquid than in solid fermentation at 30 days after substrate inoculation [247]. The liquid production system requires large installation systems and involves high initial costs. This method is inappropriate for small-scale production.

Developing an accessible and effective delivery system for the microbial agent is crucial for the effective biocontrol of pathogens. A feasible, efficient delivery system enables biocontrol agents to survive well in ecosystems and retain their biocontrol efficacy. Moreover, some of the ingredients used in the preparations may have priming effects on seed germination and the biocontrol agent’s colonization ability. A number of delivery systems for the application of PGPF as biocontrol agents are known. Seed treatment with a conidial suspension is considered the most uncomplicated and least expensive delivery system for many PGPF. Conidial coating of seeds requires less amount of inoculum of biocontrol agents than any other application technique. Moreover, a biocontrol agent applied as a seed inoculant gets an early opportunity to proliferate and establishes itself on the emerging radicle and developing roots of the germinating seed and provides potential benefits to the plants beyond the seedling emergence stage. It is also possible to use stored PGPF-coated seeds to control soil-borne pathogens, particularly when stored at the appropriate temperature. Trichoderma-treated seeds still provided significantly higher seedling counts, plant height, and plant fresh weight than uncoated control seeds after storage for up to 4 months [134]. However, extended storage periods may reduce the biocontrol efficacy and the effect of PGPF on plant growth to some extent. For example, storage of tomato seeds coated with conidia of the biocontrol agent T. koningii at 6 or 20 °C for more than two months negatively affected the final number of established tomato plants. Storage for three months or longer reduced the effectiveness of T. koningii treatment on seedling emergence and plant fresh weight, while storage for four months impaired plant height [134]. Therefore, different storage durations and conditions of formulated biocontrol products should be evaluated in conjunction with field studies to determine how storage affects the efficacy of biocontrol agents.

11. Challenges and Future Priorities

Important soil-borne pathogens associated with soil-borne diseases are often considered a complex of genetically diverse species, making them problematic pathogens to tackle. These pathogens have either a broad host range or a virulence inclination for particular hosts. For instance, the multinucleate R. solani species is divided into 14 anastomosis groups [82], while the binucleate Rhizoctonia spp. are distributed into 19 anastomosis groups. Rhizoctonia oryzae and R. zeae are multinucleate species with the teleomorphs Waitea circinata var. circinata and Waitea circinata var. zeae, respectively. Wide variation exists within- and between-AGs in virulence and host range. Broad genetic diversity of Fusarium spp. has also been reported, with more than 1000 species being known [256]. Sclerotium rolfsii is characterized by large variability and complexity in terms of host range and virulence. A vast host range also exists for most plant-pathogenic lines within Pythium species, notably Pythium ultimum, which is reported to attack over 719 host plants [257]. The genus Phytophthora is even more complex in terms of taxonomy, which has been evolving very constantly. Recent studies frequently propose new Phytophthora species [258,259]. The complexity in the characterization of the pathogens’ ever-changing diversity, virulence pattern, host range, and effective antagonists is considered the primary challenge, which impedes effective management of soil-borne diseases.

Accurate and timely identification of the pathogens associated with soil-borne diseases is crucial for the dissection of the etiology of outbreaks and for adopting appropriate measures for their management. Most often, the specific causes of soil-borne diseases cannot be determined accurately based on visual observation of the symptoms. In the laboratory, identification is performed by using culture- and sequencing-based techniques. Separately, each method has merits and limitations, and most often, both are used to complement each other in identifying the pathogen. Culture-based approaches provide important observations on cultural traits such as morphology, growth, virulence, or fungicide resistance of the pathogen. Culture-based methods may also prove essential in confirming novel or unexpected species in a sampling location, thus being considered for identification purposes [260]. However, most culture-based techniques are time-consuming and ineffective in uncovering the true diversity of the pathogen species present in a given sampling area [261]. In contrast, next-generation sequencing can identify the common species diversity of the pathogen existing in a sample. However, sequencing-based techniques cannot characterize the cultural traits of the pathogens [262]. Recently, several PCR-based methods are known to rapidly detect and identify specific pathogens causing soil-borne diseases [263]. However, the timely detection of species diversity of pathogens using these modern PCR techniques is still a significant challenge. Performing such tests also warrants sophisticated laboratories, expensive equipment, and highly trained professionals [264]. These requirements prevent their adoption on a broader scale. Therefore, the techniques that could simplify the detection, on the one hand, and be economically sustainable, on the other, still need to be developed.

12. Conclusions and Future Perspectives

The rhizosphere is a complex ecosystem that harbors intricate interactions among diverse microorganisms. Being an active component of rhizosphere microbial communities, PGPF provides effective and reliable cooperation mechanisms for managing soil-borne plant pathogens. Understanding the belowground interactions of plants with PGPF that influence soil-borne disease dynamics in natural ecosystems is crucial for maximizing the cooperation advantage. However, the enormous number of soil-borne pathogens involved, along with various other biotic and abiotic components that affect plant-microbe intrinsic interactions, has made this complicated. Although advances in next-generation sequencing techniques can describe overall microbial assembly in the rhizosphere, this vital step alone will not reveal mechanisms of interaction. At first, experimental studies should be conducted to examine interactions between PGPF and individual soil-borne pathogen species in the rhizosphere. Once these baseline studies are completed, a multi-species approach is needed to reveal the more complex interactions among multiple PGPF species and different fungal pathogens. More studies are required to clarify the roles of other rhizosphere players and to link the various interactions occurring in the rhizosphere to develop a durable soil-borne disease management strategy.