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Review

Microbial Antagonists for the Control of Plant Diseases in Solanaceae Crops: Current Status, Challenges, and Global Perspectives

by
Takalani Whitney Maake
* and
Phumzile Sibisi
Department of Agriculture and Animal Health, University of South Africa, Private Bag X6, Florida 1710, South Africa
*
Author to whom correspondence should be addressed.
Bacteria 2025, 4(3), 29; https://doi.org/10.3390/bacteria4030029
Submission received: 25 March 2025 / Revised: 23 May 2025 / Accepted: 25 June 2025 / Published: 28 June 2025
(This article belongs to the Special Issue Harnessing of Soil Microbiome for Sustainable Agriculture)
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Abstract

Postharvest losses of Solanaceae crops, which include potatoes (Solanum tuberosum), tomatoes (Solanum lycopersicum), bell peppers (Capsicum annuum), and others, are one of the major challenges in agriculture throughout the world, impacting food security and economic viability. Agrochemicals have been successfully employed to prevent postharvest losses in agriculture. However, the excessive use of agrochemicals may cause detrimental effects on consumer health, the emergence of pesticide-resistant pathogens, increased restrictions on existing pesticides, environmental harm, and the decline of beneficial microorganisms, such as natural antagonists to pests and pathogens. Hence, there is a need to search for a safer and more environmentally friendly alternative. Microbial antagonists have gained more attention in recent years as substitutes for the management of pests and pathogens because they minimize the excessive applications of toxic substances while providing a sustainable approach to plant health management. However, more research is required to make microbial agents more stable and effective and less toxic before they can be used in commercial settings. Therefore, research is being conducted to develop new biological control agents and obtain knowledge of the mechanisms of action that underlie biological disease control. To accomplish this objective, the review aims to investigate microbial antagonists’ modes of action, potential future applications for biological control agents, and difficulties encountered during the commercialization process. We also highlight earlier publications on the function of microbial biological control agents against postharvest crop diseases. Therefore, we can emphasize that the prospects for biological control are promising and that the use of biological control agents to control crop diseases can benefit the environment.

1. Introduction

Agriculture is the backbone of the economy in Africa, contributing significantly to the gross domestic product (GDP) across the continent [1]. Potatoes from the family Solanaceae, are the fourth largest food crop [2]; in terms of food consumption [3,4], they are a crop of global importance for food [5] and are consumed by more than one billion people [6]. Nutritionally and financially, the cultivation of potatoes is worthy of attention from the world because they contain vitamins and minerals and are consumed daily [7]. Although potatoes can be stored for a long time compared to other crops, potato tubers can be constrained by preharvest factors and postharvest losses due to postharvest diseases [8]. Preharvest factors include any conditions or activities that affect crops before harvesting [9]. These factors include inappropriate cultural practices, nutritional imbalances, genetic composition, harvesting methods, quality of water for irrigation, microbial invasion, insect pest inoculum remnants, and more [10,11].
Postharvest diseases are infections that occur in fruits, vegetables, and seeds after they have been harvested [12] and are mainly caused by phytopathogens [13]. These organisms include oomycetes, fungi, bacteria, nematodes, and viruses that cause diseases like warts, powdery scabs, and late and early blight. These organisms pose a serious threat to crop productivity worldwide [14]. Phytopathogens from Rhizoctonia sp., Fusarium sp., Alternaria sp., Penicillium sp., and Pseudomonas sp. produce toxigenic metabolites (citrinin, alternariol, toxoflavin, fumonisin, and coronatine) [15], which compromise the quality and usability of harvested crops, contributing to the consumer’s final decision to eat or reject the food [16]. This is why effective protection against pathogens is so important.
Agrochemicals have been successfully employed to reduce postharvest pathogens [17]. However, reducing agricultural production inputs like agrochemicals is of great importance, while maintaining a lucrative yield of high-quality goods is becoming more and more necessary because of the global sustainability agenda [18].
Due to growing concerns about the impact of agrochemicals on the environment, crop quality, nutrient constituents, the development of pesticide resistance in pests, and consumer health, farmers are eager to seek solutions for management practices other than agrochemicals. South Africa, as the largest agrochemical user in sub-Saharan Africa, with over 3000 registered pesticide products [19], has started to ban some of the registered products like glyphosate-based herbicides, triazine herbicides, 2,4-dichlorophenoxyacetic acid (2,4-D), and chlorpyrifos, among others [20]. The recent trend is now shifting toward safer and more eco-friendly alternatives, such as the use of biological control microorganisms, natural compounds (essential oils and phytohormones), and physical treatments (advanced oxidation process) [21], to control postharvest diseases and decay without contaminating the environment [22]. Biological control agents (BCAs) have been regarded as a promising alternative to conventional pesticides [23], with a wide array of microbial antagonists being developed in the past few decades for the management of fungal and bacterial diseases [24,25]. Biological control agents, also known as antagonists, refer to the use of microorganisms to control insects, weeds, and pathogens that affect plants [26,27].
Evidence has shown a significant increase in the number of studies conducted between 2005 and 2025 regarding bacterial and fungal BCAs [14,28,29]. When the term “Biological control agents” was added to a Google Scholar search with the keyword “Plants”, the number of records retrieved was roughly 6218 (2015–2025). The bibliometric data were extracted from the SCOPUS database (https://www.scopus.com/ (accessed on 10 January 2025)) and constructed using the VOS viewer processing software (v1.6.9., Leiden University, Leiden, The Netherlands) (Figure 1a). The network analysis showed the distribution of articles related to BCAs in plants. The network analysis was reduced to BCA use in Solanaceae species, which showed 132 articles with the following keywords: Solanales, Solanaceae, invasive species, Anthonomus, biological control, Solanum maritium, Solanum melongena, Lycopersicon esculentum, Solanum varium, Capsicum annuum, Solanum tuberosum, and South Africa (Figure 1b). While South Africa focuses on the development and use of BCAs as natural enemies to invasive weeds [29,30], the Scopus database showed that most published manuscripts on BCAs are from China [31], with 1247 (Figure 1c). The United States of America (USA), India, Italy, Brazil, and Spain were also ranked as the top leading countries after China in postharvest research involving BCAs based on the number of research papers published and uploaded to Scopus since 2015–2025, as indicated by the extracted and screened document in Figure 1c.
The application of microbial antagonists has significant advantages, such as causing less harm than chemical pesticides, decomposing quickly, and being highly specific against the target disease and pathogen [32]. Although pathogen populations can be controlled by antagonistic microorganisms, the mode of action is not always known. Not only does the nature of the mode(s) of action determine how a pathogen population is affected by the antagonist but the characteristics of the microbial antagonist also depend on the utilized mode of action [33]. Therefore, knowledge of the mechanisms of action in the management of pests–pathogens is a key factor in achieving an efficient reduction of the pathogen in their host. Several strains cover a single mechanism, while others use a combination of them [24,34].
Various beneficial microbial antagonists have been reported for the management of plant health, but they require effective acceptance, together with the standardization of bioformulation. The present review focuses on the recent development of microbial control agents and their mechanisms of action, as well as the development of microbial pesticides and their potential applications for agricultural productivity.

2. Biodiversity of Antagonistic Microbes

Antagonism is a phenomenon whereby microorganisms colonize the rhizosphere or aerial parts of the plants without causing any harm to the plant while preventing the colonization of pathogens [35]. These microorganisms are referred to as biological control agents, biopesticides, or microbial antagonists [36]. Microbial antagonists for the control of postharvest diseases have gained more attention in recent years as substitutes for chemical pesticides because they provide a sustainable approach to plant health management and assist in minimizing the excessive applications of toxic substances. The antagonistic microbes belong to different bacterial phyla, including Bacillota, Actinomycetota, Pseudomonadota, and Bacteroidota [1], while fungal phyla include Ascomycota, Basidiomycota, Glomeromycota, and Mucoromycota [37]. Many microbial antagonists naturally occur on the surfaces of vegetables and fruits, while others are found in closely related surroundings, such as the roots and soil [17]. They possess mechanisms that allow them to efficiently protect plants from diseases caused by plant pathogenic microbes [38]. A list of some of the microbial antagonists isolated from Solanaceae crops and successfully used as BCAs for the management of postharvest diseases is reported in Table 1.
Acinetobacter is known for producing diffusible and volatile antifungal compounds by suppressing the disease through the mechanism of inducing plant resistance [55]. Other modes of action have been suggested as possible mechanisms behind the biological control activity of these strains, viz., siderophores and the production of HCN and lytic enzymes. Acinetobacter sp., as a BCA, has similar characteristics to Pseudomonas sp. for metabolizing various aromatic compounds like naphthalene, carbaryl, phthalate isomers, etc., as a sole source of carbon and energy [56]. The multifunctional endophytic isolate Acinetobacter lwoffii, Bac109, has previously been shown to be more effective than the commercial antifungal hygromycin B against various pathogenic strains like Fusarium oxysporum, Bipolaris papendorfii, Rhizoctonia sp., and Phoma sp. [57].
Bacillus species have a long history in crop growth-promoting applications under unfavorable growth conditions such as heat and drought [58]. The majority of species from the Bacillus genus have been shown to exhibit antagonistic activity against phytopathogenic microorganisms in agricultural crops such as tomatoes, potatoes, and peppers [59]. This genus is one of the most studied genera in terms of its production of antibiotic substances such as bacteriocins and peptide antibiotics, which are produced by Bacillus subtilis. Bacillus subtilis has been tested previously with satisfactory results to produce antifungal activity against Botrytis cinerea, a phytopathogenic fungus, through various modes of action, including the production of diffusible molecules (both antimicrobial molecules and siderophores); the production of hydrolytic enzymes; the production of volatile organic compounds; and competition for nutrients and space [60]. Bacillus subtilis has also been shown to produce the AiiA gene, which encodes for AHL-lactonase, an enzyme that breaks down N-acyl-homoserine lactones, to decrease the symptoms of diseases caused by Erwinia carotovora [61]. Bacillus amyloquefaciens secretes volatile organic compounds that inhibit Ralstonia solanacearum and Penicillium digitatum [39].
Enterobacter has been well documented as an effective BCA against Ralstonia solanacearum (Smith) [62], the bacterium that causes bacterial wilt in potato and eggplant. Enterobacter cloacae PS14 reduced potato wilt disease severity by 25%, while increasing the yield by 40% through the induction of plant systemic resistance and by suppressing the pathogen’s modes of action [63]. The induction of systemic resistance can be confirmed by observing an increase in the total phenol and salicylic acid contents [64]. In tomatoes, E. cloacae TR1 suppresses pathogen growth by producing antifungal volatile organic compounds with 3-methylbutan-1 against B. cinerea [65].
Paenibacillus is known to produce many secondary metabolites, such as lipopeptide antibiotics, volatile compounds, lytic enzymes, and antifungal proteins [66]. The genus was originally included within Bacillus but was later reclassified as a separate genus [63].
Pseudomonas strains are commonly found in natural environments like soil and on crops such as potatoes, tomatoes, and tobacco [67]. They produce antibiotics to achieve biological control of plant diseases [68]. Pseudomonas syringae has been previously recorded to suppress silver scurf caused by Helminthosporium solani and dry rot caused by Fusarium spp. in potatoes [69]. Studies have shown that Pseudomonas protegens, P. clororaphis, and P. brassicacearum can reduce hair root disease caused Agrobacterium rhizogens by up to 95% in tomatoes [70,71].
Serratia is a Gram-negative plant growth-promoting bacterium. Serratia ureilytica reduces the damping-off of tomato seeds caused by Pythium cryptoirregulare, while Serratia marcescens produces two known metabolites, oocydin A and biosurfactant serrawetin, which have previously shown activity against fungi and oomycetes [72].
Trichoderma is an endophytic fungus that can grow in plant tissue without causing disease through a symbiotic relationship between the host and the phytopathogens, while protecting the host and consequently improving its growth rate. Trichoderma controls various plant fungal and nematode diseases, including Rhizoctonia solani, Fusarium oxysporum, Botrytis cinerea, Pythium ultimum, Sclerotinia sclerotiorum, Colletotrichum spp., and Pseudocercospora spp. [73]. A total of 15 Trichoderma species are responsible for antifungal activities: T. erinaceum, T. hebeiensis, T. taxi, T. bissettii, T. aggressivum, T. gamsii, T. reesei, T. citrinoviride, T. koningiopsis, T. phayaoense, T. longibrachiatum, T. viride, T. virens, T. viren, T. asperelloides, and T. asperellum [74,75,76]. A total of five species play a role in nematode resistance: T. harzianum, T. hamatum, T. atrobrunneum, T. lignorum, and T. strigosellum [77,78,79]. Although studies suggest that Trichoderma produces antimicrobial peptides as a nematicide effect, the mechanism through which it occurs remains unclear [80]. The Trichoderma harzianum, T-22, species is known to have various beneficial abilities as a BCA, such as producing enzymes and metabolites that have antagonistic effects on fungi, bacteria, and nematode pathogens [81]. This species competes with pathogens for nutrients and space by colonizing the root systems and surrounding soil of plants [63,82].

3. Solanaceae Diseases

Bacterial soft rot is a postharvest disease that poses a serious threat to potato production worldwide [83]. Infected tubers become soft and watery and develop a foul odor. This disease is caused by two genera, Pectobacterium and Dickeya. Pectobacterium was previously known as Erwinia [84]. The contamination of potato tubers occurs during harvest, handling, and washing. The pathogen remains dormant within the plant until favorable environmental conditions, like humidity, cause a shift from latency to disease development. In South Africa, the disease has contributed to yield losses and is caused by climate change and P. brasiliense [85]. Pectobacterium brasiliense prevails at temperatures between 20 °C and 38 °C during the potato growing seasons in South Africa. The disease can be managed by spraying chemicals with copper on the wounded area to reduce the spread of bacteria to healthy plants. BCAs that have an induced systemic resistance mechanism as their mode of action can induce plant systemic resistance against soft rot by activating the salicylic acid-dependent pathway [86].
Rhizoctonia disease, also known as black scurf, is a fungal disease caused by Rhizoctonia solani that affects potato tubers. Although it is not destructive, it can reduce the value of potatoes because it makes potatoes hard, with black patches on their surfaces [87]. The disease can be managed using fungicide, resistant cultivars, crop rotation, and the avoidance of planting potatoes deeply [88]. Infection can occur at any time during the growing season throughout the world, including South Africa. Rhizoctonia disease was first recorded in South Africa in 1918, and currently, all 10 anastomosis groupings (AG) of Rhizoctonia solani associated with black scurf have been isolated in South Africa [89]. It was only recently, in 2023, that a destructive black scurf disease was recorded in Lesotho, the neighbouring country of South Africa [90]. Although most of the Trichoderma species have not been approved as BCA, in vitro studies have shown that Trichoderma species (T. viride, T. herzianum, T. helicum, T. asperellum, and T. hamatum) suppress the growth of Rhizoctonia solani by 70% [91] through different modes of action, including competition for the substrate, antibiosis, and mycoparasitism [92]. Trichoderma harzianum and T. viride are registered as active BCAs.
Ralstonia bacterial wilt, caused by Ralstonia solanacearum and Ralstonia pseudosolanacearum, is a devastating disease that affects tomato production worldwide [93]. Ralstonia solanacearum is a highly heterogeneous bacterium that can metabolize sugar alcohols and disaccharides [94]. The bacterium enters the roots through wounds made by insects, transplanting, and cultivation. Endophytic Bacillus species have previously been used in in vitro studies to control tomato bacterial wilt via foliar spray application. Fewer pathogens were detected on plants treated with BCA, implying that the induction of jasmonic acid, salicylic acid, and ethylene-dependent defenses was involved in the protective effects, as observed using the real-time polymerase chain reaction (PCR) method [95]. Pseudomonas fluorescens and P. aeruginosa can control bacterial wilt in tomatoes by reducing disease severity by more than 50% [96]. Evidence has shown that Bacillus and Pseudomonas species used as BCAs are promising for eradicating bacterial wilt.
Botrytis, also known as gray mold disease, is caused by Ascomycota Botrytis cinerea, a necrotrophic pathogenic fungus that causes substantial losses in chili peppers, tomatoes, and potatoes worldwide [97]. The disease shows various symptoms, ranging from the soft rotting of plant parts to the development of brown lesions, in addition to the production of fuzzy gray-brown mold [98]. Botrytis cinerea can be controlled by colonizing the pathogen with Beauveria bassiana, which is an antagonist that has a significant antifungal effect [77].

4. Mode of Action of Antagonistic Microbes for the Management of Plant Diseases

The perception about the mechanism of action of antagonists is a vital key factor for the effective prevention of phytopathogens from their hosts [99]. The mechanism of action related to how the biological control system occurs involves activities that include competition for nutrients and space, mycoparasitism, the secretion of antifungal antibiotics and volatile metabolites, and the induction of host resistance (Figure 2). The mechanism of action of BCA from the genus Bacillus is predicted by either the production of cyclic lipopeptides (LPs), such as fengycin, plipastatin, mycosubtilin, iturin, bacillomycin, and surfactin, or through the production of lytic enzymes, such as chitinase, cellulase, endoglucanase, or hemicellulase, which suppress the growth of pathogens [100]. However, in Trichoderma, the soluble secretome plays a significant role in modulating the mycoparasitic and antibiosis activity and in the attachment, penetration, and colonization of plant roots [101].

4.1. Competition for Nutrients and Space

The rhizosphere is a complex environment that harbors diverse microorganisms that interact with their host (host–microbe) or among themselves (microbe–microbe) [102]. The main strategy adopted by most microbial antagonists against phytopathogens is competition for nutrients such as carbohydrates, nitrogen, oxygen, amino acids, vitamins, and minerals, as well as space [25]. For a strain to be an effective BCA, it must be able to colonize plant surfaces in nutrient-deficient conditions to produce a beneficial effect. Therefore, for greater effectiveness, microbial antagonists can rapidly colonize the fruit wounds prior to colonization by the pathogen [103] by assimilating the carbon sources for survival and proliferation, thereby depleting carbohydrates and starving the competing pathogens [104]. Understanding the mechanism used by BCAs to compete and interact with other microbes within the rhizosphere is crucial for their effective colonization. This intrinsic mechanism has been described in several biological control studies on antagonists such as Serratia plymuthica and Pseudomonas agglomerans [105]. A saprophytic fungus, Trichoderma spp., which is known for its fast mycelial growth, controls the invasion of pathogenic fungi in the root of a plant by rapidly absorbing the nutrients required for the growth of the pathogen fungi, resulting in nutrient deficiency and inhibiting the growth and reproduction of the pathogen fungi [106]. The growth rate of Trichoderma is much faster than that of B. cinerea, Fusarium solani, and other pathogenic fungi [107]. Consequently, it can capture water and nutrients, occupy space, and consume oxygen faster to weaken and exclude pathogens in the same habitat [73].

4.2. Mycoparasitism

Mycoparasitism is a common form of antagonism that involves the direct physical contact of the mycoparasite with the host hyphae. The mycoparasite often coils around the hyphae, penetrates the host, absorbs nutrients, and, finally, disintegrates the cells of the host to produce extracellular cell wall lytic enzymes. [56]. The produced extracellular lytic enzymes include cellulases, lipases, proteases, chitinases, and glucanases [108]. Chitinases are glycosyl hydrolases that directly degrade chitin to low-molecular weight chitooligomers. Chitin is the second most abundant polysaccharide after cellulose [109]. Trichoderma spp. can parasitize Sclerotinia sclerotiorum, Rhizoctonia, Pythium, Peronospora, and Phytophthora by directly invading the mycelium, causing the pathogen cells to expand, deform, and shorten, while shrinking the protoplasm and breaking the cell wall [110].

4.3. Antibiosis

Antibiosis refers to the interaction between two organisms, whereby the growth and activity of one organism are inhibited by the other organism through the production of chemical compounds [111]. Streptomyces sp. produces antibiotics, enzymes, and other antimicrobial compounds that directly suppress pathogens [67]. Bacillus sp. also suppresses the growth of pathogens via an antibiosis mechanism [112]. Similarly, Trichoderma sp. inhibits the growth of the nematode Meloidogyne incognita by producing secondary metabolites, including terpenes, polyketones [113], trichomycin, gliotoxin, viridin, antibacterial peptide [114], chitinase, butyrolactones, and some volatile substances (esters, terpenoids, furans, aldehydes, alkanes, olefins, and heterocyclic compounds [115]. Other bacterial genera that suppress postharvest microbial pathogen growth by producing antibiotics include Burkholderia, Pseudomonas, Enterobacter, and Lysobacter [116].

4.4. Induced Systemic Resistance

Induced systemic resistance (ISR) is a mechanism by which selected plant growth–promoting bacteria and fungi in the rhizosphere prime the whole plant body for enhanced defense against various pathogens and insects [117]. Beneficial microorganisms need to recognize the presence of pathogens to avoid forming symbiotic relationships [80]. Beneficial bacteria, such as Pseudomonas spp. and Bacillus spp., stimulate defense responses and help plants obtain broad-spectrum disease resistance [83], while beneficial fungi, such as arbuscular mycorrhizal fungi (AMFs) and Trichoderma spp., induce systemic resistance and defense against Phytophthora parasitica in tomatoes and Botrytis cinerea, respectively [74].

5. Difficulties Encountered During the Commercialization of Biological Control Agents

The commercialization of BCAs begins in the field with identifying the target crop and the pathogen, understanding current disease-control strategies, isolating potential microbial strains [118], and taxonomic classification using 16S rRNA gene sequencing in the lab [119]. The screening process is a crucial, time-consuming process that is followed by bioassay tests to determine its efficacy on a laboratory scale in a controlled environment. For example, to screen BCAs to address the postharvest diseases, microbes must be screened from the surface of the fruit/vegetable, instead of screening for microbes that compete for soil colonization. The efficacy of a potential BCA must be tested later at different geographical locations, under different climatic conditions, and on different crops against a range of pathogens to evaluate their potential for broad-spectrum activity. However, the consistency of the BCAs is not maintained in an uncontrolled environment because of their modes of action [120].
Several commercial BCAs have been jointly developed by researchers working with commercial companies (Table 2) [121]. As measured by their widespread acceptance and use, the potential commercial biological control products have produced low success rates because of inconsistent performance under commercial conditions. The efficacy of these products must be similar to that achieved by agrochemicals, which is in the range of 98–100% disease control in the field [122]. However, a greater success rate has been observed under greenhouse conditions, contributing to a higher number of biological control products being produced. To date, 390 microbial biological control agents (MBCAs) have been approved by the Environmental Protection Agency (EPA) [104]. Similarly to synthetic pesticides, BCAs are subjected to risk evaluations according to the European Regulation (EC) No. 1107/2009 procedures for plant protection product marketing before they can be licensed [102].

6. Future Directions and Challenges

Utilizing microbial antagonists to control postharvest diseases is a viable strategy for reducing the need for agrochemicals and mitigating the detrimental effects of phytopathogens on crop productivity. However, there are still several challenges that need to be addressed to fully utilize these BCAs effectively and sustainably. The challenges are as follows: BCAs might not be as effective as well-established pesticides, environmental factors such as temperature can be a factor because some of the bacterial strains function better at optimal temperatures, and the cost of manufacturing might be too high to allow for profitability, making BCAs inaccessible to most farmers. Most developing countries continue to produce and use BCAs without registration to avoid the high registration costs, while some companies register BCAs as biofertilizer, not as BCAs, for general use in all agricultural crops.
Since BCAs impact the natural environment, one must preferably predict any possible risks that could result from their implementation because their mechanisms of action for suppressing pathogens are not always known. Therefore, a comprehensive analysis of their advantages and hazards should be conducted to give stakeholders the knowledge they need for effective, secure, and long-term pest control and production and to eliminate the fear of the unknown. Knowing the molecular mechanisms behind these interactions is a crucial part of understanding how the plant host reacts to this interaction, as well as how phytopathogens react to BCAs, or vice versa. Furthermore, the method by which plants distinguish between beneficial and harmful bacteria is still unknown. However, it has been proposed that plants can adjust their microbiomes by releasing certain nutrients to increase competitiveness. Nevertheless, with all the proper isolation, screening, and field trials needed to scale up the potential microbes from the lab to the agricultural field, there is always a delay in the regulatory approval, registration process, and marketing of products. However, diverse effective BCAs are available commercially. By addressing most of these challenges, potential BCAs might contribute to the sustainability and effectiveness of disease management while promoting a more environmentally friendly agricultural system.

7. Concluding Remarks

Microbial antagonists have long-term potential in improving sustainable agriculture, with more than 440 currently available species that act as control agents for various pests and pathogens, from the most widely researched rhizobacteria, Bacillus, to Paenibacillus, which is the least researched after Serrati because it was reclassified as a separate genus. These microbial antagonists are involved in a variety of mechanisms, including competition for nutrients and space, antibiosis, and the induction of systemic resistance, that inhibit some plant diseases and, hence, reduce the need for agrochemical pesticides. By unraveling these mechanisms, researchers can develop targeted strategies for enhancing the colonization efficiency and overall effectiveness of biological control bacteria, leading to more sustainability and resilience. Solanaceae crops, such as Solanum tuberosum, Solanum lycopersicum, Capsicum annuum, and Solanum melongena, are globally significant and are known to be susceptible to a wide range of bacterial and fungal pathogens, resulting in substantial economic losses. This susceptibility makes them an ideal target for researchers to develop BCAs to reduce reliance on fungicides and pesticides to fight pathogens and to ensure food security and economic stability. Although microbial formulations for commercialized BCAs, such as liquid and solid formulations, exist, a major bridge between fermentation and field application still exists because of factors such as production at a large scale, stabilizing the BCAs during shelf life, the handling and use of the product, and ensuring the viability efficacy at the target site. Nevertheless, we can positively conclude that the prospects of BCAs are promising and that they will benefit the environment in controlling crop diseases.

Author Contributions

T.W.M.: writing—original draft, conceptualization, figures, review and editing, and visualization; P.S.: project administration, investigation, review and editing, supervision, and visualization. All authors contributed to editorial changes in the manuscript. All authors have read and agreed to the published version of the manuscript.

Funding

This research received no external funding.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

No new data were created or analyzed in this study.

Conflicts of Interest

The authors declare no conflicts of interest.

Abbreviations

The following abbreviations are used in this manuscript:
BCABiological control agents
GDPGross domestic product
LPLipopeptides
EPAEnvironmental Protection Agency
EREuropean Regulation

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Figure 1. Bibliometric analysis of 6218 articles published on biological control according to the Scopus database using specific keywords, such as “Biological control agents” AND “Plants” (a), which revealed the network relationship between keywords found on Solanaceae (b) and showed a comprehensive perspective of the current research of this area worldwide (c). Network overlay visualisation map showing biological control agents related to the research areas for the period of 2015–2025.The bigger the size of the circle, the higher the emphasis is on that research area. The keywords reveal that South Africa focuses on the use of biological agents as natural enemies to control invasive weeds. They also show that Solanaceae is the most investigated family, including Capsicum annuum, Solanum tuberosum, Solanum melongena, Solanum mauritianum, and Lycopersicon esculentum.
Figure 1. Bibliometric analysis of 6218 articles published on biological control according to the Scopus database using specific keywords, such as “Biological control agents” AND “Plants” (a), which revealed the network relationship between keywords found on Solanaceae (b) and showed a comprehensive perspective of the current research of this area worldwide (c). Network overlay visualisation map showing biological control agents related to the research areas for the period of 2015–2025.The bigger the size of the circle, the higher the emphasis is on that research area. The keywords reveal that South Africa focuses on the use of biological agents as natural enemies to control invasive weeds. They also show that Solanaceae is the most investigated family, including Capsicum annuum, Solanum tuberosum, Solanum melongena, Solanum mauritianum, and Lycopersicon esculentum.
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Figure 2. Key mechanisms of action involved in the biological control of potato late blight disease by microbial antagonists. The mechanism of action of biocontrol agents (BCAs) is an intricate process that consists of microbial antagonists, pathogens, and the host plant. BCAs compete with the pathogen for nutrients and space, produce various types of phytohormones and siderophores, and cause nitrogen fixation and solubilization through induced systemic resistance and mycoparasitism (where one fungus parasitizes another), resulting in improved plant growth and, hence, the control of plant disease. However, in the absence of BCAs, a pathogenic fungus can infect a potato plant, causing potato late blight disease, resulting in the production of toxic metabolites. Compound ID represents toxic metabolites: 1-atropine, 2-hyoscyamine, 3-scopolamine, 4-pyrrolic alkaloids, and 5-pyrrodine. This figure was created using Biorender.com.
Figure 2. Key mechanisms of action involved in the biological control of potato late blight disease by microbial antagonists. The mechanism of action of biocontrol agents (BCAs) is an intricate process that consists of microbial antagonists, pathogens, and the host plant. BCAs compete with the pathogen for nutrients and space, produce various types of phytohormones and siderophores, and cause nitrogen fixation and solubilization through induced systemic resistance and mycoparasitism (where one fungus parasitizes another), resulting in improved plant growth and, hence, the control of plant disease. However, in the absence of BCAs, a pathogenic fungus can infect a potato plant, causing potato late blight disease, resulting in the production of toxic metabolites. Compound ID represents toxic metabolites: 1-atropine, 2-hyoscyamine, 3-scopolamine, 4-pyrrolic alkaloids, and 5-pyrrodine. This figure was created using Biorender.com.
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Table 1. The most common bacterial and fungal biological control agents used in Solanaceae crops.
Table 1. The most common bacterial and fungal biological control agents used in Solanaceae crops.
Biological Control AgentsPathogensMode of ActionPlant CropReference
Acinetobacter rhizosphaereRalstonia solanacearumEnhances salt stress, produces plant growth hormones (auxin), and degrades organophosphorus pesticides by producing indole-3-acetic acidPotato[39]
Aspergillus flavus (ON146363)Meloidogyne incognitaReduces nematode propagation by producing various nematicidal secondary metabolites: gadoleic acid, oleic acid, and palmitic acid.Potato[40]
Azospirillum brasilensePseudomonas syringaePhytohormone production, induced systemic resistance (ISR), and induced systemic tolerance (IST)Tomato, potato[41]
Azotobacter chroococcumRhizoctonia solani and Fusarium oxysporumNutrient solubilizationTomato[42]
Bacillus amyloliquefaciens HTRhizoctonia solaniSecretes various extracellular enzymes (protease, amylase, and cellulase)Potato[43]
Bacillus circulans CB7Dematophora necatrixP-solubilization and 1-aminocyclopropane-1-carboxylate deaminase activityTomato[44]
Bacillus pumilusFusarium oxysporumActivates plant defence responses under adverse conditions.Tomato[45]
Bacillus subtilis FJ3Fusarium oxysporum, Aspergillus flavus, Aspergillus niger, and Rhizopus oryzaeProduces hydrolytic enzymes, siderophores, indole acetic acid, biofilm formation, and phosphate solubilizationTomato[44]
Bacillus thuriengiensisFusarium oxysporumProduces multiple crystal proteins (δ-endotoxins)Tomato[45]
Bacillus velezensis DMW1Phytophthora sojae and Ralstonia solanacearumAntimicrobial metabolites (fengycin, iturin, and bacillomycin) demonstrated antagonistic activity in vitro and in pot experimentsTomato[46]
Enterobacter cloacaeFusarium oxysporumInduces systemic acquired resistance and produces antifungal compoundsTomato, potato, and eggplant[47]
Paenibacillus polymyxa YFRhizoctonia solaniAntimicrobial lipopeptides, including fenB, ituC, and srfAA, which are associated with surfactin, iturin, and fengycin synthesisPotato, eggplant[48]
Pseudomonas aeruginosa CQ-40Botrytis cinereaSolubilizes phosphorus, fixes nitrogen, and produces cellulase, protease, and ferrophilin, but it does not produce glucanase or hydrocyanic acidTomato[49]
Pseudomonas putida PCL1760Fusarium oxysporumCompetition for nutrients and nichesTomato[50,51]
Ralstonia pickettii QL-A6Ralstonia solanacearumInduces plants to up-regulate four disease-resistant defence enzymes: phenylalanine ammonia lyase (PAL), polyphenol oxidase (PPO), peroxidase (POD), and superoxide dismutase (SOD)Tomato[52]
Serratia marcescensFusarium oxysporum, Ralstonia solanacearum, and Sclerotinia sclerotiorumProduces antimicrobial compounds like antibiotics (e.g., prodigiosin)Bell peppers (Capsicum)[53,54]
Table 2. List of approved commercially available biological control agents and their target pathogens.
Table 2. List of approved commercially available biological control agents and their target pathogens.
BCACommercial NameTarget Pathogens/Disease
Bacillus amyloliquefaciens strain MBI 600SERIFEL®Botrytis cinerea, Sclerotinia spp.
Bacillus amyloliquefaciens strain FZB24TAEAGRO®Powdery mildew diseases, Botrytis sp.
Bacillus amyloliquefaciens subsp. plantarum strain D747AMYLO-X®Botrytis cinerea, Monilinia spp., Sclerotinia spp.
Bacillus pumilus strain QST 2808SONATA®Powdery mildew diseases
Pseudomonas chlororaphis strain MA342PRORADIX®Rhizoctonia spp., Helmintosporium solani, Fusarium spp.
Pseudomonas chlororaphis strain 63-28AtEze®Pythium spp., Rhizoctonia solani, and Fusarium oxysporum
Streptomyces lydicus strain WYEC 108ACTINOVATE® AGRhizoctonia spp., Verticillium spp., Phytophthora spp., Fusarium spp., Alternaria spp., Botrytis spp.
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Maake, T.W.; Sibisi, P. Microbial Antagonists for the Control of Plant Diseases in Solanaceae Crops: Current Status, Challenges, and Global Perspectives. Bacteria 2025, 4, 29. https://doi.org/10.3390/bacteria4030029

AMA Style

Maake TW, Sibisi P. Microbial Antagonists for the Control of Plant Diseases in Solanaceae Crops: Current Status, Challenges, and Global Perspectives. Bacteria. 2025; 4(3):29. https://doi.org/10.3390/bacteria4030029

Chicago/Turabian Style

Maake, Takalani Whitney, and Phumzile Sibisi. 2025. "Microbial Antagonists for the Control of Plant Diseases in Solanaceae Crops: Current Status, Challenges, and Global Perspectives" Bacteria 4, no. 3: 29. https://doi.org/10.3390/bacteria4030029

APA Style

Maake, T. W., & Sibisi, P. (2025). Microbial Antagonists for the Control of Plant Diseases in Solanaceae Crops: Current Status, Challenges, and Global Perspectives. Bacteria, 4(3), 29. https://doi.org/10.3390/bacteria4030029

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