1. Introduction

The increasing global demand for agricultural productivity has intensified concerns about sustainable plant disease management. Conventional reliance on synthetic pesticides, though effective in the short term, poses serious environmental and health hazards, including soil degradation, water contamination, biodiversity loss, and risks to human well-being (Babalola, 2010; Bonaterra et al., 2012). In addition, the overuse of pesticides accelerates pathogen resistance, leading to diminishing returns in effectiveness and necessitating repeated or higher chemical inputs (Haas & Keel, 2003). These challenges highlight the urgency of identifying alternative, eco-friendly strategies for managing plant pathogens that maintain crop productivity while safeguarding environmental and human health. Biological control, broadly defined as the reduction of a pest population through natural enemies, has gained significant attention as a sustainable disease management approach. In plant pathology, biological control specifically refers to the use of beneficial organisms—excluding disease-resistant host plants—to suppress the activity or population of plant pathogens (de Weert & Bloemberg, 2006). Beneficial microorganisms such as bacteria and fungi function as biological control agents (BCAs), offering promising alternatives to chemical pesticides within the framework of Integrated Pest Management (IPM) (Lugtenberg & Kamilova, 2009). Unlike chemical control, which often disrupts beneficial microbial communities, BCAs enhance soil health and promote plant resilience by restoring ecological balance (Pieterse et al., 2014; Ongena & Jacques, 2008). The rhizosphere, the narrow zone of soil influenced by root secretions and associated microbial activity, represents a key site for biological control. Microorganisms inhabiting the rhizosphere can outcompete pathogens for nutrients and colonization sites, secrete antimicrobial metabolites, and induce systemic resistance in plants (Bais et al., 2006; Berry et al., 2014). These multifaceted interactions make the rhizosphere an ideal reservoir for discovering and deploying BCAs. Indeed, biological suppression of soil-borne pathogens has been investigated for more than 80 years, demonstrating its importance in sustainable disease management (Babalola, 2010). Bacteria are among the most studied biocontrol agents, owing to their versatility and ease of application. Species such as Bacillus, Pseudomonas, Burkholderia, and Streptomyces are known to promote plant growth, degrade toxic compounds, and inhibit pathogenic microorganisms (Abbasi et al., 2014; Zhang et al., 2017) (Figure 1). These bacteria employ mechanisms such as antibiotic production, siderophore release, competition for nutrients, and induction of plant defense enzymes to suppress pathogens like Rhizoctonia solani, Meloidogyne spp., and Fusarium oxysporum (Das et al., 2010; Khan et al., 2023). Notably, the application of Pseudomonas fluorescens and Bacillus subtilis strains has shown effectiveness in reducing root-knot nematode populations and postharvest fungal infections, demonstrating the broad-spectrum utility of bacterial BCAs (Berry et al., 2014; Hu et al., 2014).

Figure 1. Mechanism of biocontrol agent against pathogenic microorganism. Simplified schematic of biocontrol mechanisms against plant pathogens. The diagram illustrates the progression from a healthy plant to pathogen attack and eventual disease symptoms, alongside key defense strategies. Induced Systemic Resistance (JA/ET) and Systemic Acquired Resistance (SA) are shown as primary plant defense pathways. Below, major biocontrol mechanisms are highlighted, including siderophore production, antibiotic secretion, lytic enzyme activity, hyperparasitism, and beneficial microbial diversity, which collectively contribute to pathogen suppression and improved plant health.

Similarly, fungi play a critical role in biological control. Genera such as Trichoderma, Paecilomyces, and Gliocladium exhibit strong antagonism against pathogenic fungi and nematodes. Trichoderma spp., for example, are widely used in both greenhouse and field conditions due to their ability to parasitize pathogens, produce lytic enzymes, and release bioactive metabolites such as gliotoxin and viridin (Harman et al., 2004; Kiriga et al., 2018). Likewise, Paecilomyces lilacinus has shown remarkable efficacy against root-knot nematodes by parasitizing eggs and reducing population densities across crops like tomato and okra (Kumar et al., 2016; Zhang & Zhang, 2009). The integration of fungal BCAs into crop management offers promising potential to replace or complement synthetic fungicides, particularly in postharvest disease control where chemical residues are a major concern (Bonaterra et al., 2012; Zhao et al., 2013).

Despite these successes, challenges remain in translating laboratory results to consistent field outcomes. The efficacy of microbial biopesticides is often influenced by environmental factors such as temperature, humidity, soil composition, and competition with indigenous microbial communities (Lugtenberg & Kamilova, 2009). Furthermore, issues of scalability, formulation stability, and cost-effectiveness limit the widespread adoption of biocontrol technologies (Haas & Keel, 2003; Kang et al., 2009) (Table 1). Advances in genetic engineering, nanotechnology, and delivery systems are beginning to address these limitations, enabling more precise and resilient microbial applications (Leclère et al., 2005; Lamont et al., 2017). In light of these developments, the present work aims to review the mechanisms, applications, and effectiveness of beneficial microorganisms in the biological control of plant pathogens. By synthesizing current knowledge on bacterial and fungal BCAs, this review highlights their role in enhancing plant health, reducing chemical dependence, and promoting agricultural sustainability. Ultimately, understanding and improving the integration of biocontrol into farming practices will be essential for developing resilient agricultural systems that balance productivity with ecological integrity (Al-Ani et al., 2012; Arguelles-Arias et al., 2009; Bais et al., 2006; Ongena & Jacques, 2008).

Table 1. Bacterial strains reported as biocontrol agents against plant pathogenic microbes

2. Materials and Methods

This study adopted a structured review approach to evaluate the role of beneficial microorganisms in the biological control of plant pathogens. A multi-step methodology was followed to ensure the inclusion of relevant, high-quality sources and to provide a balanced synthesis of current knowledge. The methods consisted of four major stages: (1) literature search and database selection, (2) inclusion and exclusion criteria, (3) data extraction and classification, and (4) synthesis and critical evaluation. This review was conducted and reported in accordance with PRISMA guidelines. A PRISMA-compliant flow diagram was used to document the literature search, screening, and study selection process (Figure 2).

Figure 2. PRISMA flow diagram illustrating the identification, screening, eligibility assessment, and inclusion of studies evaluating beneficial microorganisms as biological control agents against plant pathogens published between 2000 and 2024.

2.1 Literature Search Strategy

A comprehensive literature search was conducted using electronic databases including Web of Science, Scopus, PubMed, SpringerLink, and ScienceDirect. Additional references were sourced from Google Scholar and institutional repositories to minimize the risk of excluding relevant studies. The search covered publications between 2000 and 2024, wsith an emphasis on recent advancements in microbial biocontrol technologies. Keywords and Boolean operators were used in combinations such as “biological control AND plant pathogens,” “beneficial microorganisms AND agriculture,” “bacteria AND fungi as biocontrol agents,” and “sustainable plant disease management.” Reference lists of selected articles were manually screened to identify additional relevant studies.

2.2 Inclusion and Exclusion Criteria

Studies were considered eligible if they:

• Focused on beneficial microorganisms (bacteria, fungi, or both) as agents of biological control against plant pathogens.
• Provided experimental evidence, field trials, or systematic reviews related to plant disease suppression.
• Discussed mechanisms of pathogen suppression (e.g., competition, antibiosis, systemic resistance).
• Included information relevant to agronomic application, efficacy, or sustainability.

Exclusion criteria applied to studies that:

• Focused exclusively on chemical pesticides or plant-breeding for resistance without microbial intervention.
• Reported results unrelated to plant pathology (e.g., human or animal pathogens).
• Lacked sufficient methodological detail or were opinion pieces without supporting data.
  • o Data Extraction and Classification
• From each eligible study, data were systematically extracted and classified under the following categories:
• Type of microorganism: bacterial strains (e.g., Bacillus, Pseudomonas) or fungal strains (e.g., Trichoderma, Paecilomyces).
• Pathogen target: fungi, bacteria, viruses, or nematodes.
• Mechanism of action: antibiosis, competition, parasitism, induction of systemic resistance.
• Experimental setting: laboratory assays, greenhouse trials, or open-field experiments.
• Outcome measures: disease incidence reduction, crop yield improvement, or postharvest disease control.
• Environmental factors: soil conditions, climate, and interaction with indigenous microbiota.

Data were recorded in structured tables to enable comparisons across studies. Particular attention was given to research that bridged laboratory experiments with field-scale applications, as this reflects real-world agricultural challenges.

2.4 Synthesis and Critical Evaluation

The collected studies were synthesized using a narrative comparative approach rather than meta-analysis, as heterogeneity in experimental design, crop species, and environmental conditions made statistical pooling impractical. Patterns of success, limitations, and influencing factors were identified. Studies reporting contradictory results were critically assessed to highlight gaps in knowledge and future research needs.

2.5 Quality Assurance

To minimize bias, only peer-reviewed journal articles, conference proceedings, and validated reports were included. Each study was evaluated based on clarity of objectives, appropriateness of methodology, and reliability of results. Duplicate records were removed, and two independent reviewers cross-checked extracted data.

2.6 Ethical Considerations

As this was a review-based study relying on previously published data, no new experiments involving plants, animals, or humans were conducted, and ethical approval was not required.

3. Beneficial Microbes as Sustainable Solutions for Plant Disease Control

3.1 Bacteria as Biocontrol Agents

Bacteria have been applied to soil, seeds, roots, and other planting structures for many years to enhance plant growth and development. The primary aim of bacterial inoculants is to strengthen beneficial processes such as nitrogen fixation, degradation of toxic chemicals, promotion of plant growth, and the biological suppression of pathogenic microorganisms (Babalola, 2010; Abbasi et al., 2014). Many bacterial genera, including Acinetobacter, Agrobacterium, Alcaligenes, Arthrobacter, Azospirillum, Azotobacter, Bacillus, Bradyrhizobium, Frankia, Pantoea, Pseudomonas, Rhizobium, Serratia, Stenotrophomonas, Streptomyces, and Thiobacillus, are currently being evaluated for their potential as biological control agents (Babalola, 2010; Al-Ani et al., 2012). Numerous plant diseases, including nematode infestations and fungal and bacterial infections, have been targeted by these bacteria, often with promising results.

The effectiveness of bacterial biocontrol can vary depending on host plants, soil organisms, and environmental factors. Integrated approaches combining crop rotation, organic soil amendments, and biological management alongside nematicides are considered practical strategies for managing plant-parasitic nematodes (Khan et al., 2023; Hussain et al., 2017). For instance, Pseudomonas species culture filtrates have been reported to suppress the juvenile stages of Meloidogyne javanica under in vitro conditions, demonstrating the potential of bacterial metabolites in nematode management (Berry et al., 2014). Bacterial treatments have also been shown to reduce root galling, nematode populations, and improve plant development and yield (Khan et al., 2023; Das et al., 2010). Certain bacterial genera, including Burkholderia, Pseudomonas, and Bacillus, produce metabolites that interfere with nematode feeding, behavior, and reproduction, thereby reducing root penetration and associated damage (Zhou et al., 2008; Kim et al., 2013). Several studies have demonstrated the practical use of bacterial isolates in managing root-knot nematodes. For example, strains of Bacillus subtilis, Pseudomonas fluorescens, and P. striata have been effective in suppressing nematode populations (Zhang et al., 2017; Kang et al., 2009). Endophytic bacteria such as Pseudomonas fluorescens and Bacillus spp. can induce systemic resistance in host plants by enhancing the activity of defense-related enzymes such as phenylalanine ammonia-lyase (PAL), peroxidase, and polyphenol oxidase. These bacteria also secrete antagonistic compounds and modify root exudates, including polysaccharides and amino acids, contributing to disease suppression (Abbasi et al., 2014; Ongena & Jacques, 2008). In tomato crops, the application of P. fluorescens isolates has been reported to activate plant defense enzymes against root-knot nematodes, significantly reducing nematode populations in both soil and roots (Hu et al., 2014; Lamont et al., 2017).

In addition to nematode management, bacterial biocontrol has shown effectiveness in reducing postharvest fungal infections in fruits and vegetables, which contribute to significant yield losses globally. Postharvest losses due to fungal phytopathogens can account for more than 50% of fruit production in certain regions (Zhang et al., 2017). Chemical fungicides, although commonly used, raise concerns regarding environmental pollution, human health, and residual toxicity (Babalola, 2010; Bonaterra et al., 2012). Biological control using bacteria offers an eco-friendly alternative for suppressing phytopathogens while preserving plant and soil health. Biocontrol agents provide multiple benefits, including minimizing causal pathogen populations, enhancing plant protection, reducing contamination of soil and water, and avoiding chemical waste management issues (Berry et al., 2014; Ghazanfar et al., 2016) (Table 2).

Table 2. Fungal strains reported as biocontrol agents against plant pathogenic microbes

Synthetic postharvest treatments frequently lead to resistance in pathogens, soil degradation, and environmental contamination. As a result, there is a global push toward safer, biologically based alternatives that are effective, ecologically sound, and economically feasible (Babalola, 2010; Bonaterra et al., 2012). In this context, bacterial biocontrol agents such as Bacillus, Pseudomonas, and Rhizobium spp. are increasingly valued for their ability to suppress pathogens, improve crop yields, and maintain sustainable agricultural practices (Al-Ani et al., 2012; Arguelles-Arias et al., 2009; Berry et al., 2014).

3.2 Fungi as Biocontrol Agents

Fungi are another major group of biological control agents with significant potential to suppress plant pathogens. Genera such as Trichoderma, Paecilomyces, and Gliocladium have been extensively studied for their antagonistic activity against fungal pathogens like Alternaria, Pythium, Aspergillus, Fusarium, Rhizoctonia, Phytophthora, Botrytis, Pyricularia, and Gaeumannomyces (Bonaterra et al., 2012; Zhang & Zhang, 2009). Trichoderma spp. act as functional mycoparasites and have been used in field and greenhouse trials to control soil-borne and aerial pathogens (Harman et al., 2004; Lamont et al., 2017).

Nematophagous fungi have also demonstrated efficacy against root-knot nematodes such as Meloidogyne enterolobii. Formulations of Paecilomyces lilacinus have been shown to reduce nematode populations in soil while enhancing crop yield, particularly in tomato, okra, and capsicum (Kiriga et al., 2018; Rao, 2007). Egg-parasitic fungi like P. lilacinus and Pochonia chlamydosporia act directly on nematode eggs, penetrating eggshells with hyphal growth to inhibit reproduction (Kiss, 2003; Verma et al., 2009).

Fungal biocontrol agents can produce nematicidal compounds, including viridin from Trichoderma spp., gliotoxin and acetic acid from T. longibrachiatum and T. virens, and cyclosporine from T. polysporum, which contribute to pathogen suppression (Watanabe et al., 2004; Anitha & Murugesan, 2005; Li et al., 2007). Combinations of bacterial and fungal BCAs, such as Bacillus firmus with Paecilomyces lilacinus, have shown synergistic effects, maximizing nematode control and improving plant growth parameters (Anastasiadis et al., 2008; Bontempo et al., 2017).

Over 30 genera and 80 species of fungi are known to parasitize nematodes and suppress root-knot diseases. Specific soil fungi, including Gliocladium, Penicillium citrinum, and Trichoderma virens, have demonstrated antagonistic activity against pathogens like Colletotrichum falcatum and other fungal infections, further supporting their role as BCAs (Kiss, 2003; Zhang & Zhang, 2009). The ecological advantage of fungal biocontrol lies in its ability to reduce chemical inputs while enhancing soil microbial diversity and plant resilience (Bonaterra et al., 2012; Pieterse et al., 2014).

3.3 Mechanisms of Biocontrol

The mechanisms of biocontrol involve multiple interactions between BCAs and plant pathogens. Key processes include the production of hydrolytic enzymes, antibiosis, competition for nutrients such as iron, mycoparasitism, rhizosphere competence, and the induction of systemic resistance in host plants (Haas & Keel, 2003; Bais et al., 2006). Bacteria and fungi secrete secondary metabolites, including antibiotics, siderophores, and volatile compounds, which inhibit pathogen growth and enhance plant immunity (Arguelles-Arias et al., 2009; Ongena & Jacques, 2008).

Understanding these mechanisms is essential for optimizing the application of BCAs in agriculture. Factors such as soil type, microbial community composition, environmental conditions, and host plant compatibility influence the efficacy of BCAs. Advances in formulation, genetic improvement, and delivery systems are improving the consistency and scalability of microbial biocontrol (Lamont et al., 2017; Zhang et al., 2017).

Overall, bacteria and fungi remain the most extensively studied BCAs, with proven potential to suppress nematodes, fungal pathogens, and postharvest diseases. Their integration into crop management systems offers a sustainable approach to enhancing plant health, reducing chemical dependence, and promoting environmentally friendly agricultural practices (Abbasi et al., 2014; Bonaterra et al., 2012; Zhang et al., 2017).

3.4 Antibiosis

Many bacterial species produce toxic compounds that are inhibitory or lethal to pathogenic microbes, providing a significant advantage for plant growth and development (Abbasi et al., 2014; Babalola, 2010). Antibiotics are microbial metabolites capable of killing or suppressing other microorganisms even at low concentrations. These compounds are often secondary metabolites synthesized during the idiophase, a stage of growth in which nutrient depletion and high cell density occur, whereas bacterial growth is maximal during the trophophase (de Kievit et al., 2011; Ongena & Jacques, 2008). Antibiosis is considered one of the primary mechanisms through which biocontrol bacteria suppress plant pathogens. By producing antibiotics, bacteria can inhibit pathogen germination, growth, and proliferation, often without direct competition for space or nutrients (Raaijmakers & Mazzola, 2012; Berry et al., 2014). The effectiveness of antibiosis in the rhizosphere depends on the ability of bacterial strains to produce sufficient antibiotic concentrations in their micro-niche on the root surface (Al-Ani et al., 2012; Abbasi et al., 2014).

3.5 Production of Antibiotics by Biocontrol Bacteria

The capacity of bacteria to produce antibiotics is crucial for their biocontrol activity. Actinomycetes, bacteria, and fungi are known to generate a large number of antimicrobial compounds, with approximately 8,700, 2,900, and 4,900 antibiotics, respectively, identified to date (Bérdy, 2005). In biocontrol applications, bacterial isolates such as Bacillus spp. and Pseudomonas spp. have been extensively studied for their production of lipopeptides and antibiotic metabolites. For example, Bacillus species synthesize lipopeptides like iturin, surfactin, and fengycin, which exhibit strong antifungal properties, while Pseudomonas species produce compounds such as 2,4-diacetylphloroglucinol (DAPG), pyrrolnitrin, and phenazine (Ongena & Jacques, 2008; Raaijmakers & Mazzola, 2012). This integrated mode of action highlights how compounds such as iturin, surfactin, fengycin, and phenazines function not only as antimicrobial agents but also as key drivers of sustainable plant protection strategies (Figure 3).

Figure 3: Antibiotics production by bacterial biocontrol agents and their impact on plant growth and other pathogenic microorganism. Mode of action of bacterial biocontrol agents in plant protection and growth promotion. The simplified schematic shows the left-to-right flow: Biocontrol Agents (Bacteria) produce key antimicrobial and competitive factors—such as iturin, surfactin, fengycin, phenazines, siderophores, and 2,4-diacetylphloroglucinol—which collectively act on plant–pathogen systems. The right panel summarizes principal outcomes: suppression of pathogenic microorganisms, inhibition of spore formation, enhancement of plant growth traits, and maintenance of soil fertility through support of beneficial microbiota. The diagram employs a clean, vector-based style and a muted academic color palette for journal publication.

These bacterial metabolites act directly on pathogens by inhibiting spore germination or growth. Pseudomonas spp. produces a variety of antimicrobial compounds, including hydrogen cyanide, phenazines, pyoluteorin, siderophores, and proteases, which interfere with fungal cell integrity and metabolic activity (Compant et al., 2010; Berry et al., 2014). Enzymes secreted by these bacteria, such as chitinase, cellulase, proteases, and ß-glucanase, further contribute to antifungal activity by degrading cell walls of pathogenic fungi (Hernandez-Leon et al., 2015; Abbasi et al., 2014).

Peptides, particularly lipopeptides, represent a major class of bacterial antibiotics. These are synthesized either ribosomally or non-ribosomally and are predominantly produced by Bacillus species. While the production of secondary metabolites is sometimes considered outside the classical definition of biocontrol—which emphasizes the use of living organisms to suppress pathogens—the ecological function of these metabolites is integral to bacterial antagonism against pathogens in situ (Glare et al., 2012; Berry et al., 2014). In practical applications, these metabolites are used to limit the impact of harmful microorganisms in an environmentally safe manner, reinforcing their significance as biological control tools (Abbasi et al., 2014; Babalola, 2010).

3.6 Production of Antibiotics by Fungal Antagonists

Fungal biocontrol agents, particularly Trichoderma spp., are widely distributed in soils and produce a broad spectrum of volatile and nonvolatile antimicrobial compounds (Harman et al., 2004; Zhang & Zhang, 2009). Volatile compounds include alcohols, aldehydes, ketones, hydrogen cyanide, and ethylene, which inhibit pathogen growth, while nonvolatile substances, including peptides, limit the mycelial development of pathogenic fungi.Several antifungal metabolites produced by fungi have been documented. For instance, Gliocladium virens produces gliotoxin, gliovirin, heptelidic acid, valinomycin, viridiol, and viridin, which exhibit broad-spectrum activity against soil-borne pathogens such as Rhizoctonia solani, Pythium debaryanum, Pythium aphanidermatum, Macrophomina phaseolina, and Sclerotium rolfsii (Singh et al., 2005; Bonaterra et al., 2012). The production of these metabolites enables fungi to suppress plant pathogens both in the rhizosphere and postharvest environments, highlighting their utility in integrated disease management strategies (Harman et al., 2004; Zhang & Zhang, 2009).

Fungal antagonists also employ mechanisms similar to bacterial BCAs, including direct parasitism of pathogens, secretion of lytic enzymes, and competition for nutrients. The combination of metabolite production and physical interactions enhances the efficacy of fungal biocontrol agents, particularly in soil ecosystems where multiple pathogens coexist (Abbasi et al., 2014; Zhang et al., 2017). These attributes make fungal BCAs indispensable tools for sustainable agriculture, offering environmentally friendly alternatives to chemical fungicides while maintaining crop health and productivity.

Table 2. Fungal strains reported as biocontrol agents against plant pathogenic microbes

4. Results and Discussion

4.1 Evaluating Effectiveness

Agriculture heavily relies on pest control, and the use of microorganisms as biopesticides has emerged as a sustainable, eco-friendly approach. The development of biopesticides has been enhanced by the introduction of microorganisms with improved target specificity. Genetic modifications allow microorganisms to target specific pathogens while minimizing unintended impacts on beneficial organisms (Abbasi et al., 2014; Babalola, 2010). Advances in molecular biology now enable precise genetic alterations, which were previously impossible, allowing for microbial traits to be fine-tuned for pest suppression without broad ecological disruption (Raaijmakers & Mazzola, 2012; Zhang et al., 2017). The persistence of microorganisms in the environment is crucial for long-term effectiveness. Microbial strains capable of forming self-sustaining communities reduce the need for repeated applications and enhance the reliability of pest suppression (Compant et al., 2010; Ongena & Jacques, 2008). Factors such as soil composition, temperature, and humidity influence microbial survival, and microorganisms adapted to specific environmental niches exhibit greater persistence, ensuring stable control of target pathogens (Berry et al., 2014; Hernandez-Leon et al., 2015).

Microbial interactions also impact biopesticide efficacy. Mutualistic interactions can enhance persistence and antagonistic activity, whereas competition or sensitivity to environmental stressors may limit effectiveness (Abbasi et al., 2014; Bérdy, 2005). Environmental impact assessment is another critical consideration. Life cycle analysis of biopesticides indicates that their ecological footprint is significantly lower than that of chemical pesticides, supporting sustainable agricultural practices by preserving non-target organisms and maintaining soil and water quality (Gamalero et al., 2004; Zhang & Zhang, 2009).

Despite these advantages, challenges remain. Regulatory frameworks, production scalability, and cost-effectiveness are significant obstacles to the widespread adoption of genetically modified microorganisms. Balancing specificity, safety, and economic feasibility remains a key consideration in replacing chemical pesticides with microbial biocontrol strategies (Abbasi et al., 2014; Zhang et al., 2017).

4.2 Rhizosphere Competition

Rhizosphere competition occurs when microorganisms compete for limited resources such as nutrients or colonization sites (Compant et al., 2010; Ongena & Jacques, 2008). Both pathogenic and non-pathogenic microorganisms compete in the rhizosphere, and rapid colonization by beneficial microbes often prevents pathogen establishment by monopolizing substrates (Berry et al., 2014; Hernandez-Leon et al., 2015).

Rhizosphere competence—the ability of antagonistic bacteria to establish, persist, and function effectively on or near roots—is essential for successful biocontrol. Traits such as chemotaxis, motility, and biofilm formation enhance root colonization (Abbasi et al., 2014; Babalola, 2010). In practice, population densities of antagonist bacteria peak shortly after application, gradually declining over time but remaining functionally significant for disease suppression (Raaijmakers & Mazzola, 2012; Zhang et al., 2017).

Studies have demonstrated the importance of rhizosphere competence in controlling soil-borne pathogens. For example, specific Pseudomonas and Bacillus strains exhibit strong colonization and antagonistic activity against Rhizoctonia solani in lettuce and sorghum, enhancing root development and promoting micro-colony formation in the rhizosphere (Compant et al., 2010; Ongena & Jacques, 2008). Integrating beneficial rhizosphere microorganisms into crop management offers effective alternatives to chemical pesticides, improving plant resistance to pathogens while maintaining soil health (Berry et al., 2014; Zhang et al., 2017).

4.3 Plant Growth Promotion by Rhizosphere Microorganisms

Plant growth-promoting microorganisms (PGPMs) include bacteria and fungi that enhance plant development through multiple mechanisms, including nutrient acquisition, hormone production, and pathogen suppression (Abbasi et al., 2014; Babalola, 2010). PGPMs occupy root-associated microhabitats and interact with native microbial populations and host plants to facilitate growth (Compant et al., 2010).

PGPMs such as Acetobacter, Azospirillum, Paenibacillus, Serratia, Burkholderia, Herbaspirillum, and Rhodococcus have been reported to enhance crop yields and nutrient uptake (Babalola, 2010; Zhang et al., 2017). These microorganisms contribute to plant biomass production by promoting root, shoot, and leaf development and improving nutrient cycling (Berry et al., 2014; Hernandez-Leon et al., 2015).

Specific strains, including Bacillus amyloliquefaciens, Serratia marcescens, and B. pumilus, demonstrate multiple plant growth-promoting traits, such as siderophore production, phosphate solubilization, indole-3-acetic acid (IAA) synthesis, and antifungal activity, resulting in enhanced shoot and leaf growth in crops like tea and tomato (Compant et al., 2010; Ongena & Jacques, 2008). Soils rich in organic matter and microbial diversity often require less synthetic fertilizer due to enhanced nutrient availability mediated by PGPMs (Bérdy, 2005; Zhang & Zhang, 2009).

PGPMs act as biofertilizers through mechanisms such as increasing root surface area, nitrogen fixation, phosphorus solubilization, siderophore production, and hydrogen cyanide synthesis, ultimately improving nutrient availability and plant resilience against pathogens (Abbasi et al., 2014; Babalola, 2010). Integration of PGPMs into crop management not only enhances productivity but also supports sustainable agricultural practices by maintaining soil health, biodiversity, and reduced chemical inputs (Raaijmakers & Mazzola, 2012; Zhang et al., 2017). plant growth–promoting microorganisms enhance crop performance through a coordinated set of biofertilization, antimicrobial, and biocontrol mechanisms that collectively improve nutrient acquisition and plant vigor. This functional integration underscores the dual role of PGPMs in stimulating growth while strengthening plant defenses, thereby supporting sustainable crop productivity with reduced reliance on chemical inputs (Figure 4).

Figure 4: Plant growth promotion by bacterial biocontrol agents. Functional ecology of endophytic microbes: mechanisms for plant growth promotion and pathogen suppression. The schematic summarizes how endophytic bacteria and fungi support plants through three mechanism groups: biofertilization (e.g., Fe²? chelation, hormone and ATP synthesis, and phosphate solubilization), antibiotic/antimicrobial production, and biocontrol actions (e.g., niche exclusion of pathogens, secretion of antimicrobial compounds, and induction of ISR). These processes collectively enhance nutrient availability, root/leaf vigor, and resistance to disease.

5. Challenges and Future Recommendations

The use of beneficial microorganisms to manage plant diseases, commonly referred to as biological control of plant pathogens, is a dynamic and rapidly evolving field. Despite its promise, several challenges must be addressed to fully harness its potential. Key areas for advancement include enhancing precision, integrating strategies, understanding the plant microbiome, and developing advanced delivery systems. A critical priority is improving the precision and specificity of beneficial microbes employed in biocontrol. Targeted interventions minimize unintended ecological impacts while enhancing the effectiveness of disease suppression. Precise biocontrol ensures that beneficial microorganisms act against specific pathogens without disrupting native microbial communities (Abbasi et al., 2014; Ongena & Jacques, 2008). Achieving such precision requires substantial research investment in strain selection, genetic characterization, and functional optimization. Integrated approaches represent another essential component for the future of biocontrol. Combining microbial biocontrol agents with complementary strategies—such as resistant crop cultivars, crop rotation, cultural practices, and organic amendments—enhances the durability and consistency of disease management (Babalola, 2010; Zhang et al., 2017). Integrated strategies provide multi-layered defense mechanisms that reduce the risk of pathogen resistance and stabilize crop productivity over time (Compant et al., 2010; Berry et al., 2014). Expanding our understanding of plant-associated microbiomes is equally critical. The interactions between beneficial microbes and natural microbial communities in the rhizosphere determine the efficacy of biocontrol agents. Insights into synergistic relationships, microbial network dynamics, and community assembly can guide the selection and application of more effective strains (Raaijmakers & Mazzola, 2012; Zhang & Zhang, 2009). By aligning biocontrol strategies with existing microbial ecosystems, practitioners can achieve more sustainable and context-specific disease suppression.

Advances in delivery systems also represent a promising frontier. Novel approaches, including encapsulation, seed coatings, and nanotechnology-based formulations, improve microbial survival, persistence, and targeted release within the plant environment (Abbasi et al., 2014; Hernandez-Leon et al., 2015). Optimized delivery enhances the efficacy of biocontrol agents while mitigating unintended dispersal and environmental impacts, ensuring that microbial populations reach the sites where they are most effective. Despite these advances, significant obstacles remain. Commercial viability and scalability continue to limit the adoption of biocontrol technologies. Producing and deploying beneficial microorganisms at a scale that is both cost-effective and practical requires improvements in cultivation, formulation, and distribution systems (Babalola, 2010; Berry et al., 2014). Efficient production methods, low-cost formulations, and simplified application techniques are necessary to facilitate widespread adoption in diverse agricultural systems. Regulatory frameworks also present challenges. Biocontrol agents must meet stringent safety and efficacy standards to gain approval for commercial use. Clear, efficient registration processes and evidence-based risk assessments are essential to ensure compliance and build farmer confidence (Raaijmakers & Mazzola, 2012; Zhang et al., 2017). Regulatory guidance helps prevent potential ecological disruptions and supports the responsible implementation of biocontrol strategies in agriculture. Finally, understanding environmental interactions is crucial for minimizing unintended consequences. Introducing non-native or genetically modified microorganisms can perturb local ecosystems, so careful evaluation of ecological compatibility is essential (Compant et al., 2010; Ongena & Jacques, 2008). Striking a balance between disease control effectiveness and environmental sustainability remains a key challenge in developing resilient and safe biocontrol programs.

In summary, future advancements in biological control will depend on precision in microbial selection, integration with complementary strategies, deeper knowledge of plant microbiomes, and innovative delivery systems. Addressing challenges related to commercial scalability, regulatory compliance, and ecological safety is vital for translating laboratory successes into field-level applications. By overcoming these barriers, biocontrol can play a transformative role in sustainable agriculture, reducing reliance on chemical pesticides while maintaining productivity and ecological integrity (Abbasi et al., 2014; Babalola, 2010; Zhang et al., 2017).

6. Conculsion

In conclusion, using beneficial microbes for biological control of plant diseases presents a viable and environmentally responsible option for the agricultural sector. It is now clear from thorough analysis that plant diseases can be successfully controlled by utilizing the power of naturally occurring antagonistic microbes. This strategy makes use of the complex ecological relationships that exist within the plant microbiome to create a balance that prevents the growth of dangerous infections.Evaluation of a range of helpful microorganisms, including fungus and bacteria, has demonstrated their potential as biopesticides that provide specific and long-lasting remedies. Biological management techniques have less of an impact on the environment than standard chemical interventions, protecting soil health and biodiversity. Moreover, they coincide with the increasing worldwide focus on sustainable farming methods that lessen the environmental impact of traditional farming. A crucial first step toward robust and adaptable farming systems is the incorporation of biological control techniques into standard procedures, as we manage the complexity of contemporary agriculture. In addition to protecting crop health, further investigation and broad implementation of these techniques could lead to a more sustainable and peaceful coexistence of agriculture and the environment.

Author contributions

E.S.A.M.E.S. conceptualized and supervised the study, designed the research framework, and reviewed and edited the manuscript. N.M.M.S. conducted the literature search, performed data analysis, and drafted the original manuscript. Both authors read and approved the final version of the manuscript.

Acknowledgment

The authors express their sincere gratitude to Zagazig University and the National Research Centre, Egypt, for their continuous support and encouragement.

References