1 Introduction
Global agriculture stands at a critical juncture, facing the dual pressures of rising food demand and persistent pathogen threats. Current farming methods are not adequate to meet the need to sustain high productivity while minimizing the environmental and health risks associated with conventional agrochemical use. Among the most serious threats to crop performance are plant diseases caused by fungal pathogens, with mycotoxigenic species posing the greatest risk to consumers. Current agrochemical methods are insufficient in addressing the dangers posed by mycotoxigenic fungi, leaving the future of food safety and security compromised. These limitations highlight the shortcomings of chemical-based disease management strategies and the need for effective solutions.
In response, biologically based alternatives are gaining attention for their ability to promote plant health and yield while aligning with ecological and regulatory goals. Beneficial microbes, particularly bacterial endophytes have developed as promising tools capable of suppressing pathogens, enhancing stress tolerance and contributing to plant defense through both direct and indirect mechanisms. Their integration into disease management strategies represents a shift toward more sustainable and holistic approaches to crop protection.
This review examines the global impact of plant pathogens and mycotoxins, fungal infection biology and plant defense mechanisms. It examines established and emerging disease management practices, with an emphasis on plant microbiome and beneficial microbes, particularly endophytic bacteria as effective biological tools for crop enhancement and fungal control. Additionally, advances in nanotechnology and formulation science are appraised for their potential to improve field performance of microbial formulations. Finally, the review seeks to provide insights for key challenges limiting broader adoption and outlines future directions for integrating these microbial tools into sustainable and regenerative agricultural systems.
1.1 Plant pathogen impact and yield losses
Plant diseases caused by certain fungi, bacteria, viruses, nematodes and protozoa result in major production and economic losses. Globally, direct crop losses due to plant pests and pathogens are estimated at 20% to 40% of total production, amounting to about 220 billion USD annually
[1,
2]. However, these estimates do not account for the short- and long-term effects as well as the indirect impact on food security, public health, economies and the environment
[1,
2]. Around 83% of plant diseases are caused by fungi with the rest being due to viruses, phytoplasmas and bacteria
[3]. Also, fungal pathogens alone destroy 30% of crops, impacting food availability for about 600 million people worldwide, and postharvest losses amount to an additional 10% due to quality reduction
[4–
6]. Also, filamentous fungi can threaten produce both pre- and postharvest as they pose significant health risks due to toxin production. These findings highlight the shortcomings of current disease management strategies and emphasize the need for effective approaches, particularly against fungal pathogens in order to meet the growing demands for quality assured food production.
1.2 Mycotoxin presence and management
Food contamination by harmful microorganisms and their metabolites is a significant global health concern that is intensified by the complexity of the food supply chain and the increased exposure to contaminants. A major challenge in food safety is the increasing prevalence of plant diseases caused by toxigenic filamentous fungi that produce stable and harmful secondary metabolites known as mycotoxins
[7]. Global agricultural crop contamination by mycotoxins was estimated at 25% in 1999 by the UN Food and Agriculture Organization, with cereals, maize, nuts, and rice most affected
[8,
9]. However, recent estimates place contamination levels at 60% to 80% due to increased production, climate change, and the availability of analytical methods with improved sensitivity
[8].
Estimated annual losses attributed to mycotoxins in human food, animal feed and products, and soils total to billions of US dollars
[10]. The health implications are a significant challenge, with over 400 mycotoxins currently recognized as harmful
[11]. Mycotoxicosis can cause a wide range of adverse effects, from acute symptoms, such as vomiting and abdominal pain, to severe or chronic issues, such as immunosuppression, impaired growth, tumors, coma and even death
[12,
13]. To minimize these risks, postharvest management focuses on reducing food contamination levels through various decontamination strategies, such as heat treatment, irradiation, cold plasma, mycotoxin binders and chemical treatments
[14]. These methods exhibit varied effectiveness dependent on several factors, such as the type of mycotoxin, concentration, particle size and moisture content. Also, the impact of food processing on mycotoxin transformation is not fully understood, and current treatments do not guarantee complete detoxification, as transformed toxins may remain harmful and escape detection
[15]. Additionally, impacts of decontamination treatments on food texture, flavor and nutritional content need to be considered. Therefore, prevention through preharvest strategies is likely a more effective approach. This includes using host genetic resistance, agricultural practices and crop protection tactics, including fungicide application, biological control and pest management.
1.3 Need for sustainable management approaches
Pesticides have long been central to disease management and represent the second largest group of synthetic chemicals after mineral fertilizers
[16]. However, despite their effectiveness, excessive and unregulated use has raised significant health, agricultural and environmental concerns. Bernardes et al.
[17] reported that only 1% of applied pesticides effectively target intended pests, with the remaining impacting non-target organisms including beneficial insects, humans and wildlife. Compounding these risks is the widespread occurrence of multiple pesticide residues in food: a recent EU report found that 44.3% of the tested food samples contained more than one pesticide, while the US Pesticide Data Program reported a similar figure of 57.5%
[18]. These findings are particularly troubling given the several health concerns associated with pesticide exposure, including increased risk of diabetes among farmers, respiratory issues, endocrine disruption, and potential mutagenic, carcinogenic, embryotoxic, immunotoxic and neurotoxic effects
[19–
22]. Similarly, environmental persistence in agricultural soils and groundwater, along with their mobility through leaching, volatilization and runoff, amplifies the ecological risks. These properties contribute to bioaccumulation in non-target organisms, biomagnification through food chains and long-term environmental pollution.
Beyond health and ecological risks, pesticides impose substantial financial burdens that are often overlooked. These include regulatory fees, costs associated with environmental degradation, healthcare expenses and defensive costs, such as increased demand for organic produce. In the USA alone, these hidden costs have been estimated at nearly 40 billion USD annually, potentially outweighing the benefits of pesticide use
[23]. Given these concerns, there is a growing emphasis on stricter regulations and the adoption of sustainable solutions that minimize health and environmental risks while maintaining agricultural productivity.
Biological pesticides (biopesticides) have emerged as promising alternatives, now comprise about 10% of the global pesticide market
[24]. Their market value is expected to grow from 5 to 15 billion USD by 2029, with a compound annual growth rate of almost 14%
[25]. With rapid growth in this sector, their market is projected to match that of synthetic pesticides by the late 2040s or the early 2050s
[26]. This is largely attributed to their cost-effectiveness in the long run. For example, integrating bacterial biopesticides into navel orangeworm control programs in almond orchards, improved control from 50% to over 90%, resulting in an estimated 20-fold return on investment
[27]. Biopesticides are also significantly cheaper and faster to develop, typically requiring under four years and 3 to 7 million USD, compared to over a decade and about 300 million USD of synthetic pesticides
[28].
Despite this promising trajectory, research on biopesticides still lags significantly behind that on synthetic pesticides. For example, between 1985 and 2021, fewer than 5000 scientific publications referenced the term
biopesticide in the Web Science database, compared to over 130,000 for
pesticide[29]. Although scholarly interest in biological alternatives is rising, these natural pest control strategies remain inadequately investigated. This underscores both the growing potential of biopesticides and the need for stronger scientific engagement.
2 Fungal infections in plants
2.1 Host penetration
Most pathogenic bacteria, viruses and a few fungal species infect the plant through plant wounds and natural openings, such as stomata and hydathodes
[30]. In contrast, many pathogenic fungi can actively breach the plant surface, using both enzymatic and mechanical strategies. These fungi produce a variety of hydrolytic enzymes, primarily pectinases but also cutinases and cellulases, which degrade or modify plant cell wall, thereby facilitating infection
[31]. This enzymatic activity softens structural barriers, allowing fungal hyphae to advance through the plant epidermis. In addition to enzymatic degradation, many fungi form specialized infection structures known as the appressoria at the tip of their germ tubes. These structures adhere tightly to the plant surface and generate high turgor pressure, which is used to drive an infection peg through the cuticle and cell wall. The peg, supported by the action of hydrolytic enzymes, breaches the host surface and initiates colonization (Fig. 1)
[32]. This dual strategy is especially prominent among biotrophic and hemibiotrophic fungi. However, necrotrophic fungi often use extensive enzymatic degradation and toxin secretion.
2.2 Colonization and infection
To improve their chance of survival within the host, fungal pathogens alter the host physiology and functions through the secretion of phytotoxins. These compounds may kill host cells to serve as a source of nutrients or to appropriate the cellular machinery
[32]. For example,
Fusicoccum amygdali, the causal agent of peach and almond canker, produces the phytotoxic metabolite, fusicoccin, which induces irreversible stomatal opening, stimulates the activity of the plant plasma membrane H
+-ATPase, and results in increased cation uptake, elevated transpiration, uncontrolled water loss and wilting
[32–
34]. Likewise,
Alternaria alternata produces a cyclic tetrapeptide tentoxin, which inhibits chloroplast development. It does so by blocking energy transfer of the chloroplast-localized CF
1 ATPase and disrupting the transport of nuclear-coded enzyme polyphenol oxidase, ultimately leading to chlorosis and necrosis
[32].
During host infection, pathogen-derived low molecular weight compounds, known as exogenous elicitors, are released. These include proteins, carbohydrates, lipids, cell wall fragments or other molecules, all of which can trigger immune responses by binding to plant receptors, thereby activating defense signaling and inducing necrosis
[35]. However, some fungal pathogens, such as the pea pathogen
Mycosphaerella pinodes, can avoid triggering elicitor-induced responses through the secretion of suppressor proteins, such as supprescin A and B, which occupy recognition sites, thus disrupt signal transduction, and interfere with defense gene activation
[36,
37].
2.3 Fungal avirulence genes
Plant pathogen interactions are often described by the widely accepted gene-for-gene model, which posits that host resistance (R) genes recognize specific pathogen avirulence genes
[38]. R genes encode proteins that recognize avirulence gene products whereas avirulence genes encode effector proteins that may be recognized by the host receptors
[39]. Incompatible interactions occur when the avirulence gene is present, triggering host defense responses, such as hypersensitive responses, whereas compatible interactions result when the avirulence gene is absent or mutated, allowing the pathogen to infect and cause disease
[40].
Additionally, avirulence genes can also be classified by their specificity to host R genes, cultivar-specific genes interact with R genes in specific cultivars whereas species-specific genes interact with R genes across a species or multiple species. The extracellular nature of avirulence proteins and the cytoplasmic localization of R gene products indicates that fungal elicitors might enter plant cells through the haustorial membrane (Fig. 1)
[41]. Also, the structural features of avirulence proteins, such as their cysteine content, are closely linked to their secretion pathways and localization patterns. Cysteine-rich avirulence proteins are typically found in the plant apoplast or xylem, while cysteine-poor avirulence proteins are more commonly associated with haustoria-forming pathogens
[42].
3 Plant defense systems
Despite the abundance of fungal pathogens, only a minority succeed in establishing infections since disease development requires the simultaneous presence of a susceptible host, a virulent pathogen and favorable environmental conditions. The interactions between plants and pathogens are dynamic contests of attack and counterattack between the complex defense mechanisms of the plant and invasive strategies of the pathogen as both have evolved genetic components to navigate and counteract each other
[43]. The plants first layer of defense are the outer tissues acting as a physical barrier, while the advanced response, known as induced resistance, involves two main forms: systemic acquired resistance (SAR) and induced systemic resistance (ISR), both of which involve several pathways and defense-related compounds that act locally and systemically throughout the plant.
3.1 Systemic acquired resistance
SAR is a slow but long-lasting plant defense response that is activated upon microbial infection or their chemical stimuli, such as chitosan and salicylic acid (SA)
[44]. It is initiated upon the recognition of pathogen-associated molecular patterns, microbe-associated molecular patterns, damage-associated molecular patterns or pathogen effector molecules, such as proteins, enzymes, and toxins by pattern recognition receptors present on plant cells. Thus, triggering systemic defense responses such as the production of antimicrobial compounds, reinforcement of cell walls, and the induction of pathogenesis-related (PR) proteins. SAR involves multiple PR genes that control the potential of the plant to activate defenses, however the non-expresser of pathogenesis-related genes 1 has a crucial regulatory role by modulating the expression of PR genes and coordinating the defense response
[44,
45].
SAR operates through two branches: during pathogen-associated molecular pattern-triggered immunity, a basal defense response that helps plants resist a wide range of pathogens
[44]. This is initiated by the recognition of pathogen-associated molecular patterns by pattern recognition receptors and the initiation of a signaling cascade involving mitogen-activated protein kinase. This kinase phosphorylate transcription factors and regulatory proteins, leading to altered gene expression and enhanced defense responses in plants against pathogens
[45,
46]. During effector-triggered immunity, a rapid defense response that is activated when pathogen effector molecules are detected by nucleotide binding site and leucine-rich repeat protein, leading to a hypersensitive response
[45,
47]. This response leads to the production and accumulation of reactive oxygen species which can either serve as signaling molecules to amplify defense-related gene expression, reinforce cell wall barriers by lignin and callose deposition, or lead to cell death by oxidative damage to cellular components
[44]. The SA pathway is a central component of SAR, with SA acting as the primary signaling molecule that directly contributes to plant defense and activates other metabolites.
3.2 Induced systemic resistance
ISR is a plant defense mechanism that is activated by chemical or biological signals and regulated by a complex hormone signaling networks. It provides a rapid and temporary response both at the site of infection and in unaffected regions
[44]. ISR is triggered by beneficial microbes, their byproducts, as well as certain chemicals that stimulate the defense responses, leading to the production of signaling compounds, such as jasmonic acid (JA) and ethylene (ET). Additionally, bacterial volatiles can induce ISR through an ethylene-dependent pathway, while siderophores and cyclic lipopeptide antibiotics can also trigger ISR
[48].
JA and ET are key regulators in SA-independent ISR, often stimulated by beneficial soil microbes such as
Bacillus spp.,
Pseudomonas spp.,
Trichoderma spp. and other rhizobacteria. ISR effectively combats necrotrophic pathogens and insect herbivores sensitive to JA and ET
[45]. Unlike SAR, ISR does not rely on the presence of PR and instead primes the immune system of the plant through the expression of JA and ET-responsive genes, leading to faster and enhanced defense responses upon subsequent attacks
[49]. Although ISR responses may not directly kill pathogens, it strengthens the overall resistance of the plant to disease by activating systemic defense pathways. Also, beneficial microbe-mediated ISR primarily operates through SA-independent mechanisms. However, some microbial species, such as
Pseudomonas spp. and
Paenibacillus spp., can induce SA-dependent ISR, where reactive oxygen species accumulating at the site of colonization act as main elicitors.
3.3 Microbiome-mediated protection
Earlier perspectives portrayed disease incidence as being mainly dictated by plant susceptibility and pathogen virulence. However, current scientific paradigms place more emphasis on crop environment, particularly the plant microbiome which is now considered to be an extension of the plant immune system and a key factor influencing disease outcomes. This microbial ecosystem refers to plant-associated microorganisms that can be found in seeds, on plant surfaces (phyllosphere), inside plant tissues (endosphere), and surrounding the roots (rhizosphere). The composition and activity of these microbial communities can significantly influence crop health and susceptibility to both biotic and abiotic stresses. Among these, rhizospheric communities are crucial for disease suppression, with the presence of certain taxa reducing disease incidence. Soils known to be disease-suppressive often harbor specific microbial groups such communities, such as Actinobacteria, Firmicutes and Proteobacteria. Also, plants are capable of selectively recruiting beneficial microbes during pathogen attacks by releasing root exudates that preferentially enhance microbial chemotaxis, swarming, and biofilm formation, thus promoting their activity in a phenomenon referred to as a cry-for-help
[50]. These beneficial microbes mitigate disease through various mechanisms that reduce pathogen growth or metabolic activity, including antimicrobial production, resource competition, and induction of plant immune responses, as previously described. In contrast, disease-conductive soils contain harmful microbes that are either directly pathogenic or can increase disease susceptibility by suppressing plant immune functions. While the plant microbiome in all its forms (endosphere, phyllosphere and rhizosphere) may not always be the primary determinant of diseases, it is critical for modulating disease incidence and severity through dynamic interactions with both the plant host and its pathogens. A greenhouse study on
Pythium aphanidermatum, the causal agent of tomato root rot, confirmed the ability of two
Streptomyces spp. isolates obtained from soil to effectively suppress disease incidence and improve overall plant health
[51]. These mechanisms and their implications will be discussed in detail in later sections.
4 Disease management strategies
4.1 Plant breeding
Modern plant breeding focuses on enhancing desirable crop traits, such as durable biotic and abiotic stress resistance and high productivity, through molecular techniques, such as marker-assisted selection gene pyramiding and gene editing which in the presence of fully sequenced genomes, to enable the better manipulation of plant genetics
[52,
53]. Marker-assisted selection-based gene pyramiding allows the efficient selection of multiple R genes or quantitative trait loci that can be stacked to enhance resistance degree and durability
[54,
55]. For example, pyramiding lines based on different combinations of quantitative trait loci and broad-spectrum R genes resulted in varying resistance level and frequency (PPL
Piz/Pi33 RF = 15.2% and PPL
Pigm/Pi1 RF = 97.7%) to the fungal pathogen,
Magnaporthe oryzae, causing seedling blast and panicle blast in Mushk Budji rice
[55].
Meanwhile, CRISPR/Cas9 systems allow the targeted modification of defense-related genes and the cleavage of viral genomes. Several susceptibility genes have been identified and successfully removed to produce resistant lines against various pathogens. For example, targeting
OsSWEET13 gene enhanced resistance to bacterial pathogen
Xanthomonas oryzae in
Oryza sativa, and
DIPM-1, DIPM-2 and
DIPM-4 to bacterial pathogen
Erwinia amylovora in
Malus domestica[56,
57]. Additionally,
CP,
Rep and
IR genes to bean yellow dwarf virus in
Nicotiana benthamiana and
Arabidopsis thaliana[58].
4.2 Chemical control
Fungicides combat fungal pathogens through various modes of action classified by the Fungicide Resistance Action Committee, an inter-corporate specialist group that was established in 1981 to provide guidelines for effective fungicide use, resistance management and collaboration with agricultural stakeholders and governmental bodies
[59,
60]. Generally, preventive fungicides also referred to as contact fungicides remain on the plant surface and directly inhibit or kill fungi and fungal spores. These include copper-based, sulfur-based, phthalimides and other classes, and are considered safer since they can be washed of crop surfaces
[61]. Curative fungicides or systemic fungicides are a greater health concern since they can penetrate the surface and move within the plant tissues to control fungal infections. Among the most used are strobilurins, such as azoxystrobin, which inhibit fungal respiration, and sterol biosynthesis inhibitors, which block ergosterol production, a major component of fungal cell membranes
[62].
Synthetic fungicides are fast acting and exhibit high effectiveness. For example, strobilurin and triazole application resulted in 95% to 99% and 33% to 65% control of beet rust under greenhouse and field conditions, respectively
[63]. Despite their ability to control pests, these chemicals present several health risks. Human serum samples tested for multiple pesticides revealed the presence of several agrochemicals, with fungicides showing the highest prevalence, concentrations, estimated daily intake levels and exposure risks compared to triazine herbicides and neonicotinoid insecticides
[64]. In addition, stable chemicals, such as strobilurins, are problematic due to long-term risks of bioaccumulation and biomagnification. The excessive use of agrochemicals has led to the development of several resistant pathogen biotypes, such as
Botrytis cinerea resistant to benzimidazoles, dicarboximides and fluazinam fungicides
[65]. Similarly,
Venturia inaequalis resistance to benzimidazoles, quinone outside inhibitors and succinate dehydrogenase inhibitors
[66]. These findings have driven the search for safer pesticide alternatives.
4.3 Integrated pest management
Integrated pest management (IPM) is a multifaceted approach that focuses on long-term prevention of crop pests by incorporating different strategies, such as cultural practices, resistant cultivars, biological control and forecasting to minimize chemical resistance
[67]. IPM promotes natural pest control and minimizes use of disruptive intervention strategies by establishing pest thresholds and economically significant thresholds
[68]. Research across nine European countries demonstrated that IPM, supported by decision systems for fungicide applications, effectively helped manage wheat rust diseases, reducing infection rates and fungicide use, while maintaining stable yields with resistant cultivars
[69]. Also, IPM is highly adaptable and capable of accommodating new innovations, leading to improvements in yield and quality, and reduction in the use of agrochemicals through the judicious use of synthetic chemicals and the adoption of environmentally safer alternatives, such as microbial inoculants.
4.4 Biological control
The challenges posed by the health and environmental impacts of synthetic pesticides, together with the inherent limitations in plant breeding such as the complexity of trait development and the long time frame involved, have renewed interest in biological control strategies. These methods leverage naturally occurring substances, plant derived products and beneficial organisms to manage plant pathogens with minimal ecological disruption. With the growing urgency for effective and sustainable disease management strategies, beneficial microbial populations have received increasing attention. This is due to their ability to influence plants, plant microbiomes and phytopathogens through direct and indirect mechanisms, ultimately suppressing diseases and improving plant health. Among biocontrol agents, bacterial endophytes are distinctive due to their unique ecological niche within the plant tissues, which allows them to act as both protectors and promoters of plant health. Their close association with the plant host enables them to boost overall crop fitness, prime plant immunity and support resilience to biotic and abiotic stresses. The following sections review the classification, mechanisms and practical applications of biocontrol agents, leading to a more detailed examination of endophytic bacteria as key contributors to disease management and sustainable agriculture.
4.4.1 Definition and classification
Biological control or biocontrol is defined as the direct or indirect reduction or suppression of diseases, causal pathogens or their activity using an antagonistic organism or group of organisms
[70,
71]. More recent definitions have expanded this concept to include not only the organisms themselves but also their genes, metabolites and natural products with bioactive properties
[72]. This broader understanding of biocontrol provides the foundation for biopesticides, which are pest control products derived from living microorganisms or their byproducts. According to the EPA, biopesticides are categorized into three main groups: microbial pesticides, biochemical pesticides and plant-incorporated protectants
[73]. Microbial pesticides, comprising nearly 90% of biopesticides products, are commonly based on microorganisms, such as
Bacillus thuringiensis[74]. Biochemical pesticides include naturally occurring substances (e.g., kaolin clay) and plant-derived substances (e.g., azadirachtin, pyrethrins and nicotine) as well as semiochemicals (e.g., pheromones), which interfere with pest behaviors, such as mating and aggregation. These biopesticides are generally characterized by low toxicity, minimal environmental persistence and negligible crop residues. Lastly, plant-incorporated protectants are pesticidal substances produced by genetically modified crops, through the insertion of pest-resistant genes, such as those encoding
B. thuringiensis toxins
[75].
Biopesticides have gained considerable attention as an alternative to synthetic pesticides due to their diverse and often targeted modes of action, including antifeeding activity, mating disruption, suffocation and desiccation
[73]. Their complex mechanisms make them less likely to lead to resistance in pests and pathogens as rapidly as synthetic pesticides. In addition, biopesticides are typically effective at low doses, degrade more rapidly in the environment, and pose lower risks to human health and non-target organisms. Consequently, they are usually exempt from residue tolerance requirements. Also, biopesticides have shown to produce a carbon footprint that is 60% to 90% lower than that of synthetic pesticides, an important advantage given that pesticides and fertilizers contribute significantly to agriculture’s 15% share of global greenhouse gas emissions
[25]. These attributes make biopesticides more compatible with food safety standards and sustainable agricultural practices.
For clarity in both scientific and regulatory frameworks, some research groups advocate for clear distinctions, reserving the terms biocontrol agent (BCA) for living organisms (e.g., macrobial and microbial agents) and bioprotectants for non-living substances of biological origin such as microbial metabolites
[76]. This review adopts this classification (Fig. 2).
4.4.2 Mechanisms of biocontrol agents
Building on the previous classification, this section considers the primary modes of action by which biocontrol agents exert protective effects against pests. These mechanisms include antagonism, hypovirulence and the induction of host resistance (Fig. 2).
(1) Antagonism
Antagonism involves the direct suppression of pathogens using three main strategies
[48]. (a) In exploitation, the BCA directly feeds on the host pest or parasitizes it. For example,
Ampelomyces parasitizes powdery mildew cells, causing cytoplasm degradation and inhibited sporulation
[77]. (b) During competition, the BCA outcompetes the pathogen for space and nutrients, ultimately suppressing through resource depletion. For example,
Pseudomonas fluoroscens B10 suppresses fusarium wilt by releasing siderophore pseudobactin which sequesters rhizospheric iron, an essential nutrient for fungal colonization and pathogenicity
[78]. (c) Antibiosis refers to the production inhibitory compounds or toxins by the BCA. Examples include agrocin 84, produced by
Agrobacterium to control
Agrobacterium tumefaciens, the causal agent of crown gall
[79]. Also, hydrogen cyanide produced by
Pseudomonas fluorescens strain PF1 to control
Macrophomina phaseolina, a causal agent of rot disease in many crops
[80]. Other reported antibiotic compounds include bacillomycin D, iturin A and mycosubtilin produced by
B. subtilis, and 2,4-diacetylphloroglucinol and phenazines produced by
P. fluorescens[81–
83].
(2) Hypovirulence
This mechanism refers to the reduction in pathogenicity, viability or reproduction of a virulent fungal strains following the introduction of a weakened and less virulent strain acting as a BCA
[84]. Hypovirulent strains typically carry double-stranded RNA mycoviruses that induce gene silencing through RNA interference, which involves the degradation of specific mRNA sequences. This effectively suppresses the expression of pathogenesis-related genes, ultimately reducing the virulence of the fungal pathogen
[85,
86]. For example,
Hypovirus FGHV2, which infects
Fusarium graminearum, was shown to significantly reduce both the mycelial growth rate and the synthesis of deoxynivalenol, a harmful mycotoxin produced by the pathogen
[87].
(3) Induction of host resistance
As previously discussed, this mechanism involves the activation of the host plant defenses to enhance its ability to resist pathogenic attacks. The process is initiated by the release of chemical elicitors by the BCAs, which are then perceived by the host, leading to the activation of defense-related signaling pathways, such as the JA/ET or SA pathways
[88,
89]. Certain root-colonizing microbes, such as
Pseudomonas spp. and
Trichoderma spp., along with various plant growth-promoting rhizobacteria (PGPR), have been documented as potential elicitors of host resistance
[90,
91]. For example,
Pseudomonas chlororaphis subsp.
aurantiaca (syn.
Pseudomonas aurantiaca) ST-TJ4 emits volatile organic compounds (VOCs) that trigger systemic resistance to
Verticillium dahliae, the causal agent of Verticillium wilt in cotton. This response involves the activation of SA and hydrogen peroxide signaling pathways in the host, leading to the accumulation of resistance-associated proteins (e.g., chitinases) which degrade fungal cell walls, as well as secondary metabolites (e.g., flavonoids and phenols) that exhibit antimicrobial and antioxidant activity
[92].
4.4.3 Common biocontrol agents
The implementation of BCAs in disease suppression can involve a variety of species. Prominent biocontrol agents are in the bacterial genera
Bacillus,
Lysobacter, Pantoea, Pseudomonas and
Streptomyces, as well as fungal genera, such as
Aspergillus,
Gliocladium,
Petriella,
Trichoderma and non-pathogenic
Fusarium spp.
[93,
94]. Some of these biocontrol agents, including bacteria, such as
Pseudomonas chlororaphis, and fungi, such as
Ampelomyces quisqualis,
Trichoderma polysporum and
Verticillium lecanii, have already been commercialized
[95].
For fungal diseases control, several documented cases have shown successful control using BCAs that are comparable to synthetic fungicides. For example, in a two-year field study conducted on three strawberry cultivars,
Trichoderma atroviride LU132 gave significant suppression of
B. cinerea sporulation on leaves and flowers comparable to the fungicide control fenhexamid
[96]. In a recent study, the volatile compounds and the lipopeptides extracted from
Bacillus subtilis CTXW 7-6-2 effectively inhibited the growth of
Rhizoctonia solani in tobacco. Also, treated seedlings showed improved growth parameters and upregulation of diseases resistance genes
[97]. Another study revealed that
B. subtilis JNF2 successfully suppressed the soilborne pathogen
Fusarium oxysporum on cucumber seedlings, surpassing the efficacy of the synthetic fungicide hymexazol, and promoted seedling growth through the production of antimicrobial compounds, hydrolytic enzymes, siderophores, and indoles
[98]. Similarly,
Pseudomonas rhodesiae HAI-0804 conferred protection against damping off and root rot induced by
Globisporangium ultimum (syn.
Pythium ultimum) in cucumber, with enhanced biocontrol linked to glutamate stimulated siderophore production, root colonization and biofilm formation despite the absence of direct antibiotic activity
[99].
5 Plant microbiome and beneficial bacteria
5.1 Recruitment of microbiota
Plant ecosystems and soils provide diverse environmental conditions that support the growth and development of a wide range of plant-associated microbial communities. High populations densities are primarily found in rhizospheric soils, where root exudates serve as a major source of organic carbon, making these areas aggregations for microbial activity
[100]. As result, microorganisms can establish pathogenic, neutral or beneficial relationships with the host. The plant microbiome is a product of plant-microbe coevolution and adaptation, which is further shaped through the dynamic processes of microbial filtering and recruiting
[101,
102]. Within the plant microbiome, the consistent presence of certain core microorganisms, such as
Agrobacterium, Fusarium and
Pseudomonas, in the rhizosphere, indicates preferential recruitment and adaptation to coexist with the host and participate in its functions
[103,
104]. Consequently, identifying these microorganisms and understanding their behavior within plant systems is beneficial for research aimed at leveraging beneficial microbial communities, particularly since many of these induce beneficial effects on growth, productivity and pathogen resistance.
5.2 Bacterial endophytes
According to Omomowo and Babalola
[105], endophytes are microbial communities that inhabit the internal tissues of host plants without causing symptoms. These communities competently colonize various plant tissues and organs including roots, stems, leaves, flowers, fruits and seeds, with the highest densities typically found in roots, followed by stems and leaves
[106,
107]. Their population density and distribution are influenced by factors, such as host plant variety, health and developmental stage, isolation procedures, environmental factors, soil pH, temperature and the presence of pathogens. Once established, beneficial endophytic bacteria can reside in the host plant for a part or the entirety of their life cycle, during which they can interact with the host plant both directly and indirectly, engaging in essential roles in plant systems (Fig. 2)
[108].
The ability of endophytes to colonize internal tissues and organs, and establish beneficial relationships makes them particularly advantageous since they remain protected throughout their life cycle from external stresses
[109,
110]. Notably, the beneficial effects of endophytes are not limited to their original plant hosts. Several studies have demonstrated that both native and non-native endophytes can be successfully introduced into different crops, where they confer protective and growth-promoting effects. For example, inoculating Indian long pepper (
Piper longum) with native endophytic bacteria
Actinobacter soli PlS14 and
Enterobacter hormaechei PlR15 increased root percentage by 50% in cuttings and promoted growth in plants
[111]. Meanwhile, the inoculating cucumber seedlings in a hydroponics system with the non-native
Pseudomonas sp. ALR1619 provided short- to medium-term protection against
Pythium blight, increasing survivability by 41% when the pathogen was introduced 1 day after inoculation and by 38% when introduced after 5 days, compared to the control
[112].
In addition to their roles in biocontrol, many bacterial endophytes also exhibit plant growth-promoting traits that position them as effective crop biostimulants. According to the EU Regulation 2019/1009, a plant biostimulant is defined as “a product stimulating plant nutrition processes independently of the product’s nutrient content with the sole aim of improving one or more of the following characteristics of the plant or the plant rhizosphere: (a) nutrient use efficiency; (b) tolerance to abiotic stress; (c) quality traits; (d) availability of confined nutrients in soil or rhizosphere”
[113,
114]. Many bacterial endophytes fulfill these criteria through mechanisms that enhance nutrient availability and uptake, modulate plant hormone levels or improve stress resilience.
5.2.1 Direct effects
(1) Nitrogen fixation
Nitrogen is a primary plant nutrient, being essential for development and a fundamental component in amino acids, proteins, nucleic acids and chlorophyll, contributing significantly to structural integrity and essential functions, such as photosynthesis. Despite its atmospheric abundance as a gas, it is only available for plant uptake in its reduced form, ammonia
[115,
116]. However, nitrogen fixers can induce the formation of symbiotic root structures termed nodules on host roots that fix atmospheric nitrogen using nitrogenase enzyme, ultimately leading to the production of ammonia (Fig. 3)
[115,
117]. The molecular mechanisms leading to this symbiotic relationship can be divided into two stages, nodule formation and invasion, followed by the establishment of symbiotic nitrogen fixation within nodule cells. Also, rhizobia possess the MoFe-containing variant of the nitrogenase enzyme system, enabling them to fix nitrogen
[118]. Despite the aerobic nature of rhizobia, the nitrogenase enzyme is highly susceptible to oxygen. To circumvent this, rhizobia induce the formation of nodules, specialized organs characterized by an extremely low-oxygen environment. Within these nodules, the synthesis of leghemoglobin aids in oxygen diffusion to bacteroids, allowing nitrogenase to function effectively
[118]. Numerous nitrogen-fixing bacteria, including
Achromobacter,
Azoarcus,
Azorhizobium,
Burkholderia,
Frankia,
Herbaspirillum and
Rhizobium, have been recognized
[119,
120].
(2) Phosphate-solubilization
Phosphorus is the second most important nutrient for plant growth. Its availability to plants is severely limited due to its presence in insoluble forms in the soil. Plants can only assimilate phosphorus in the form of monobasic or dibasic phosphates
[120]. Phosphate-solubilizing bacteria facilitate the availability of phosphate, thereby enabling plants to assimilate it effectively (Fig. 3)
[121]. The solubilization of organic phosphates uses enzymes, such as phytases, carbon-phosphorus lyases and phosphatases
[122]. Meanwhile, inorganic phosphate solubilization is done mainly through the production of organic acids which chelate cations and reduce surrounding soil pH, allowing the release of phosphates
[123,
124]. Documented effective PSM belong to the genera
Bacillus,
Pseudomonas and
Rhizobium along with non-symbiotic nitrogen-fixing organisms, such as
Azospirillum and
Azotobacter[125,
126].
(3) Indole-3-acetic acid production
Indole-3-acetic acid, an auxin-type hormone, is vital for cell division, elongation and tissue differentiation. IAA is crucial for nutrient uptake, root developmen, and biomass increase
[127,
128]. IAA production is recognized as an effective indicator for identifying beneficial microbes with plant growth promotion capabilities
[120,
129]. Tryptophan, a natural root exudate, serves as the primary precursor for IAA biosynthesis. Multiple pathways, such as indole-3-acetamide, indole-3-pyruvate, tryptamine, tryptophan side-chain oxidase and tryptophan-independent pathways, use tryptophan for IAA synthesis
[120,
130]. IAA production contributes to plant-bacteria communications and influences root nodulation and plant stress responses
[131]. Additionally, endophytes exhibiting high IAA production can influence transcriptional variations leading to higher nitrogenase activity in plants
[120,
132]. Endophytic bacteria, such as
B. subtilis,
B. aryabhattai,
Klebsiella pneumoniae,
Microbacterium trichotecenolyticum and
Paenibacillus kribbensis, were found to be IAA producers
[133].
(4) 1-Aminocyclopropane-1-carboxylate deaminase
Ethylene is crucial for regulating cell development, overall plant growth, and aiding in stress response
[115,
134]. When ethylene surpasses its threshold in plant tissues due to increased activity of the ACC oxidase enzyme, it leads to stress ethylene, impacting root and shoot development. Also, ethylene is primarily derived from the conversion of S-adenosyl methionine by ACC synthase, with 1-aminocyclopropane-1-carboxylate (ACC) serving as the main precursor. In stressful situations, heightened ACC synthase activity leads to an increased production of ethylene
[120,
128]. The existence of ACC deaminase producing PGPRs in the rhizospheric soil of stressed plants aids in alleviating this condition by degrading ACC, leading to a reduction in ethylene levels and promoting the restoration of normal plant development and root elongation
[120,
135].
5.2.2 Indirect effects
(1) Siderophore production
Iron is an essential micronutrient crucial for photosynthesis and as acts as a cofactor in chlorophyll synthesis. However, despite its abundance in nature as Fe
3+, this form cannot be absorbed by plants. However, certain PGPRs release siderophores such as pyoverdine with a high affinity for rhizospheric iron (Fe
3+), subsequently chelating it and converting it to an absorbable form (Fe
2+) (Fig. 3)
[120,
136]. Additionally, siderophore-producing PGPBs create an iron-limiting environment, impeding pathogen growth and reducing pathogenicity by sequestering rhizospheric iron. This dual action benefits plant health and limits pathogenic threats. Siderophores have been consistently reported to be produced by
Pseudomonas spp. and
Bacillus spp.
[137,
138].
(2) Hydrogen cyanide production
Certain PGPRs produce hydrogen cyanide, and while the low levels of HCN alone may not be highly effective, these bacteria often combine HCN production with the synthesis of antibiotics or cell wall degrading enzymes
[115,
139]. This synergism with HCN enhances the efficacy of antifungals against fungal pathogens and prevents the development of resistance. HCN producing genera include
Aeromonas, Alcaligenes, Bacillus, Pseudomonas and
Rhizobium[140,
141].
(3) Antibiotic production
PGPRs primarily counteract the harmful effects of phytopathogens by synthesizing antibiotics (Fig. 3). Antibiotic efficacy in controlling a particular pathogen may not necessarily apply to other pathogens on the same plant, and the behavior of the PGPR can vary under diverse field conditions. Bacteria from the genera
Bacillus and
Pseudomonas have been prolific sources of antibiotics with applications including antifungal, antibacterial, antiviral, phytotoxic, antioxidant and cytotoxic properties. Numerous antibiotics with diverse applications have been derived from these genera. Examples from
Pseudomonas spp. include ecomycins, 2,4-diacetyl phloroglucinol, pseudomonic acid, phenazine-1-carboxylic acid, azomycin, kanosamine and karalicin. Similarly,
Bacillus spp. contribute antibiotics such as bacilysin, fengycin, iturin, subtilin, subtilosin, surfactin and Tas A
[115,
142]. In addition, endophytes produce a variety of natural products, such as steroids, terpenoids, flavonoids and alkaloids, which are used as antibiotics, biological control agents and anticancer agents, and various other bioactive compounds
[143].
(4) Cell wall degrading enzymes production
PGPR can produce a variety of extracellular hydrolytic enzymes, which have been widely reported for their roles in controlling plant pathogens
[144]. These enzymes include a diverse group of compounds, most notably glycoside hydrolases (e.g.,
β-1,3-glucanase, chitinase and cellulase), peptidases (e.g., proteases) and oxidoreductases (e.g., catalase), among others
[145]. They function by degrading essential components of phytopathogen cell walls and membranes, including chitin, cellulose, hemicellulose, proteins and even DNA
[146]. When paired with antimicrobial metabolites, these enzymatic activities enhance their biocontrol potential, making them particularly effective against fungal spores and mycelia. Thus, PGPR act as potent extensions of the host plant defense mechanisms (Fig. 3). Beyond their role in pathogen suppression and control, hydrolytic enzymes also facilitate the colonization of plant roots by PGPR
[120,
147]. Endophytic bacteria from various genera, including
Azotobacter,
Bacillus,
Cladosporium,
Enterobacter,
Pseudomonas,
Rhizobium,
Serratia and
Streptomyces, have been reported to secrete hydrolytic enzymes that exhibit biocontrol activity against important fungal pathogens such as
F. oxysporum and
R. solani, positioning them as promising tools for biocontrol
[120,
148,
149].
(5) Volatile organic compound production
VOCs serve as signaling molecules for cellular communication and contribute to restricting the growth of pathogens (Fig. 3)
[120,
150]. To date, 346 distinct VOCs have been identified from species, such as
Bacillus,
Pseudomonas,
Erwinia and
Staphylococcus[151].
Bacillus endophytes, such as
B. subtilis, have biocontrol activity by directly protecting plants against phytopathogens or indirectly inducing plant resistance. For example,
B. subtilis strain DZSY21 inhibits the growth of the fungal pathogen
Curvularia lunata[152], while VOCs from
Bacillus velezensis strain ZSY-1 have strong antifungal activity against
Alternaria solani and
B. cinerea[150,
153]. In addition, VOCs emitted by
Bacillus spp. can modify root architecture and stimulate plant growth parameters
[154].
(6) Quorum sensing
Quorum sensing (QS) is a bacterial communication process involving the production, detection and response to extracellular signaling molecules known as autoinducers. These allow cooperation or interference (quorum quenching) between different bacterial taxa. As bacterial population density increases, autoinducers accumulate, enabling collective alterations in gene expression and controlling diverse physiologic functions such as bioluminescence, sporulation, antibiotic production, biofilm formation and virulence factor secretion
[155,
156]. In addition, QS alters several activities such as symbiosis, competence, conjugation and motility
[157]. In general, gram-negative bacteria communicate using small molecules, such as acyl-homoserine lactones, whereas gram-positive bacteria use oligo-peptides, called autoinducing peptides
[155,
158], both are crucial for bacterial gene regulation at high cell density, orchestrating complex interactions within plant microbiomes. HSLs perceived by plants can influence metabolism, immune response and root development. For example, the endophyte M6 swarms toward
F. graminearum, forming a barrier and killing the pathogen. Studies have shown that plant-associated microbiomes are enriched with HSL, with 40% to 50% of bacteria having HSL activity
[101,
159]. This high prevalence highlights the potential role of AHL-mediated communication in coordinating microbial interactions within the plant environment.
Recent studies have shown that QS in
B. subtilis shapes the fungal microbiome across citrus plant compartments, where quorum quenching mutants enrich pathogenic fungi and the wild type promote beneficial taxa, such as
Trichoderma. Hence, highlighting the role of bacterial QS in microbiome homeostasis and disease suppression
[160]. Similarly, endophytic
B. subtilis EBS9 from
Tecomella undulata exhibited quorum quenching activity via diketopiperazine production, disrupting QS in
Pectobacterium carotovorum and significantly reducing its virulence. This interference also led to improved plant growth parameters both
in vitro and
in vivo experiments, highlighting its potential as in effective biocontrol and biostimulant
[161].
While not classified as autoinducers, terpenes can modulate QS through their quorum quenching activity or antimicrobial properties, thereby indirectly influencing microbial population dynamics. Terpenes fulfill diverse ecological functions, including eliciting plant responses, such as carotenoid biosynthesis, and acting as chemical defenses against herbivores and pathogens
[162]. Notably, genes involved in terpene biosynthesis are highly represented in among plant-associated bacteria, with 49% of strains carrying a gene encoding terpene synthase, indicating a possible role in plant-microbe interactions
[101,
159].
6 Challenges of microbial formulations
Microbial formulations are increasingly recognized as efficient, eco-friendly and sustainable alternatives to the more widely-used agricultural inputs, such as pesticides and fertilizers. However, their adoption in large-scale agriculture remains limited due to several technical, biological and market-related challenges. Although generally considered low in toxicity and environmental impact, microbial pesticides face strong competition from synthetic pesticides, which are easier to produce, possess longer shelf-life and benefit from well-established industrial production systems
[163]. Consequently, synthetic pesticides tend to be significantly less expensive and readily available in global markets
[164].
A major limitation of microbial pesticides is their field instability and their generally narrow spectrum of activity. In contrast, synthetic pesticides are stable and can be used to control multiple pests with their broad activity. Also, while laboratory trials and early-stage testing are typically conducted under controlled conditions, field testing introduces several unaccounted variables
[165]. Thus, field performance can vary significantly, often requiring multiple applications and careful considerations based on crop, pest and environmental conditions, such as soil type, pH and temperature, to optimize performance
[166]. Additionally, microbial pesticides typically exhibit slower modes of action and reduced efficacy under high pest pressure, making them more effective as preventive measures or when pest populations are at low levels
[167].
Additional constraints include challenges related to dosage optimization, application timing, compatibility with existing agrochemicals or production practices, and field persistence, the effects of which remain poorly understood. Also, the potential for resistance development, lack of farmer awareness, and inadequate regulatory frameworks such as the absence of standardized quality control measures, impede their broader adoption. From a scale-up standpoint, microbial formulation are also hindered by production-related challenges such as batch-to-batch variation, risks of contamination or strain mutation, waste management issues (especially in fermentation-based formulations), and the complexity of downstream processing required for metabolite purification
[168].
Similar limitations affect microbial endophytes, which are being investigated not only for their biocontrol potential, but also for their broader roles in promoting plant growth, enhancing disease resistance and improving abiotic stress tolerance. Despite their promise, the most effective strategies for integrating endophytes in agricultural systems remain uncertain. Common application methods such as soil inoculation, foliar spraying and seed dressing, produce varying results under field conditions. Additional key obstacles include the lack of vertical transmission necessitating repeated introduction, and the unpredictability of interactions within complex soil microbiomes and the presence of pollutants that may interfere with endophyte establishment and success
[169,
170].
Although some studies indicate that reduced input rates of agrochemicals may enhance beneficial interactions with endophytes, successful field implementation will require deeper insights into their life cycles, genome plasticity and potential latent pathogenicity
[169,
171]. As with microbial pesticides, improving the consistency, predictability and robustness of endophyte performance is essential to ensure their establishment as dependable agricultural tools. This will necessitate further research especially in areas of endophyte-host and soil microbiome interactions as well as rigorous biosafety evaluations, including assessments of toxins production
[169].
The address several obstacles limiting large-scale field adoption, the development of effective and stable microbial formulations is critical. These must retain their properties throughout storage, transportation and field application. Emerging technologies, such as nanotechnology, offer promising solutions by enhancing delivery efficiency, improving stability of active compounds and enabling controlled release. Nanotechnology-based formulations can reduce application rates, minimize off-target effects and environmental contamination and lower worker exposure, contributing to safer and more sustainable pest and crop management
[172,
173].
7 Nanotechnology in agriculture
Nanotechnology is the discipline that encompasses the synthesis and applications of particles spanning between 1 and 100 nm
[174]. Consequently, they are smaller in size than bacteria, bacteriophages and viruses. Nanoscale materials have distinct properties that diverge from those of their macroscopic equivalents. In their reduced form, nanoparticles can be used in several applications due to their increased surface-to-volume ratio, reactivity and possible biochemical activity
[175]. Due to their unique properties, nanotechnology finds diverse applications in agriculture, including nanofertilizers and nanopesticides.
7.1 Nanofertilizers
Nanofertilizers encompass nanomaterials that either serve as nutrients or function as carriers or additives for the nutrients
[176]. Several types of nanofertilizers have been developed, incorporating nanoparticles, including carbon nanotubes, iron, molybdenum, silica, silver, titanium and zinc
[177]. The application of nanofertilizers has demonstrated beneficial effects on seed germination, root and shoot elongation, plant biomass and chlorophyll concentration in treated crops
[178,
179]. Nanofertilizers have enhanced mobility in their colloidal suspension state due to increased entropy, thereby enabling more efficient penetration of plant cell membranes compared to standard fertilizers
[180]. In addition, nanofertilizers minimize the losses of mobile nutrients, create slow-release fertilizers and enhance the accessibility of poorly available nutrients
[181].
7.2 Nanopesticides
The application of nanotechnology in plant protection encompasses the usage of metal nanoparticles, nano-encapsulated active substances and nanocomposites
[182]. Additionally, nanomaterials that show potential for improving pesticide effectiveness include fibers, gels, nanoemulsions and vesicles
[183]. Nanomaterials, including nanosilver, nanocopper, nanosilica and nanoformulations of synthetic pesticides, have efficacy against diverse insect pests and fungal pathogens
[184]. Silver nanoparticles have extensive antifungal efficacy against various plant pathogens, including
Alternaria spp.,
Fusarium spp. and
Rhizoctonia spp.
[185]. They can impede mycelial growth, spore germination, and compromise fungal cell membranes. Nanoformulations improve solubility, enhance their efficacy and reduce environmental impact, prolong shelf-life, and facilitate release, while the incorporation of essential oils and plant extracts further extends shelf-life without adversely affecting non-target organisms
[186]. Nanoemulsions with diminished surfactant concentrations enhance the retention and absorption of active ingredients by plants, facilitating efficient targeted delivery while reducing effects on non-target organisms
[187].
7.3 Applications for microbial agents
Microbial agents in the field are highly susceptible to degradation and diminished efficacy due to numerous biotic and abiotic factors, such as UV radiation, temperatures extremes and soil pH variations. To mitigate these effects, different nanotechnologies are being actively investigated to address issues such as stability, release profile and bioavailability.
7.3.1 Encapsulation
Microencapsulation and nanoencapsulation serve as mechanisms to address these challenges while simultaneously improving efficiency, commercial feasibility, formulation stability and minimizing losses due to volatility
[188]. Throughout this process, bioactive compounds are encapsulated by a carrier material, leading to the creation of particles or capsules at the micrometer or nanometer scale
[189]. The encapsulated substances, termed the core, fill or internal phase, are protected by the coating materials (carrier material), known as wall material, membrane, capsule, shell, matrix or external phase
[190]. In the final product, this encapsulation contributes to the improvement of bioavailability, controlled release and precision in targeting bioactive compounds
[189].
The selection of an appropriate encapsulating agent is essential for the success of the encapsulation process. In food and agriculture applications, the selected wall material must be deemed safe, function efficiently as an emulsifier, retain low viscosity at elevated concentrations, and have advantageous dissolution and network-forming characteristics
[191]. Also, it must maintain stability amidst environmental fluctuations and prevent cross-reactivity with bioactive compounds.
For example, the encapsulation of
Pseudomonas spp. using alginate beads enriched with SA and zinc oxide nanoparticles further improved its IAA production as well as its antifungal activity
[192]. In another study, the encapsulation of
B. subtilis CC-pg104 alginate enriched with humic acid resulted in increased viability and improved release even at different pH levels
[193]. Also, the encapsulation of savory essential oil with Arabic gum gelatin improved its suppressive ability as a herbicide
[194]. In a recent study, the encapsulation of
B. subtilis in chitosan gel beads prolonged its viability for up to 90 and 180 days while maintaining its antifungal activity against
Fusarium avenaceum and
R. solani[195]. Similarly, the encapsulation of
Bacillus megaterium in a poly(vinyl alcohol)-cationic starch-zinc oxide matrix via spray drying enhanced protection under extreme field-like conditions. Encapsulated cells retained viability after prolonged exposure to high temperatures, UV radiation and pesticide treatment. The formulation doubled the shelf-life to 14 months. Greenhouse application led to increased crop biomass and improved P and Zn uptake
[196]. Likewise, the microencapsulation of
B. velezensis BV9 with alginate-zedo gum improved cell viability, release profile, stability and resulted in complete suppression of
Gaeumannomyces graminis var.
tritici in wheat greenhouse experiments
[197].
These, in addition to other polymers, such as chitosan, pectin, shellac and starch, hold promise as encapsulating compounds with potential use in agricultural production, such as biofertilizers, biopesticides and seed treatment agents (Fig. 4(a))
[191].
7.3.2 Pickering emulsion
This refers to emulsions that are stabilized in two immiscible liquids using solid nanoparticles. Thus, stabilizing the system by reducing the interfacial energy
[198]. Pickering emulsions have been gaining attention for their advantages in cost, quality, and sustainability. Also, due to their ability to stabilize particles and their high loading capacity makes them attractive for many applications
[199].
Nanoemulsions can be used to give superior pesticide delivery systems characterized by enhanced kinetic stability, smaller size, low viscosity and optical transparency
[200]. Also, both nano-emulsions and microemulsions can improve the solubility and bioavailability of active ingredients.
Also, inverse Pickering emulsion (water-in-mineral oil emulsion), which consists of dispersed droplets of water stabilized in oil is effective in stabilizing live bacterial cells
[201]. This encapsulation mechanism holds promise as it can also be used to carry water soluble components of bacteria (Fig. 4(b)). In one study,
B. thuringiensis serovar aizawai cells, spores and crystals were encapsulated in water droplets and stabilized by hydrophobic silica nanoparticles. This resulted in improved pesticidal activity as compared to controls of these materials in water suspension
[202]. A more recent study has shown that the encapsulation of
B. subtilis and
Bacillus amyloquefaciens in nanosilica-based inverse Pickering emulsion enhanced their antiviral activity against groundnut bud necrosis orthotospovirus in tomato and chickpea. The formulation significantly reduced lesions, virus titer by threefold and overall disease by about 78% in tomatoes
[203].
7.3.3 Centrifugal spinning
Centrifugal spinning, a widely used nanofiber production method in the food industry, applies centrifugal force to create nanofibers. In a study by Campaña and Arias
[204], polyethylene oxide nanofibers were used as a delivery system for arbuscular mycorrhizal fungi by coating nanofibers of common bean seeds. The centrifugal spinning technique proved highly effective in producing continuous and uniform polyethylene oxide nanofibers, facilitating the creation of a fibrous mat for the application of the mycorrhizal inoculant. Additionally, the nanofibers were found to be successful in fixing the inoculant between fiber sheets and on their surfaces (Fig. 4(c)). Thus, polyethylene oxide nanofibers were found to be particularly successful as a carrier for a mycorrhizal fungal inoculant, preserving both infective capacity and beneficial properties without adverse effects
[204]. A recent study embedded
B. subtilis onto poly (3-hydroxybutyrate) fibers using simultaneous electrospinning and electrospraying with chitooligosaccharide. This resulting biohybrid material exhibited improved wettability, mechanical properties, supported bacterial proliferation and allowed effective inhibition of
Alternaria spp. and
Fusarium spp.
[205].
8 Prospects and conclusions
The earlier description of endophytes as per the first definition, focuses exclusively on culturable endophytes, which represents a very small fraction of the total endophytic community. As a result, most plant-endophytic interactions remain inadequately investigated. However, recent advances in sequencing and bioinformatic technologies, now allow for the comprehensive analysis of entire endophytic consortia, including unculturable taxa. This is particularly relevant for medicinal crops with poorly researched endophytic communities, such as Cannabis sativa, as investigation had been previously limited due to legal and regulatory barriers. Examining the endophytic communities of medicinal crops remains a promising field, especially for biocontrol purposes. For example, bacterial endophytes in cannabis plants exhibit significant chemodiversity, positioning them as promising candidates for disease biocontrol. Similarly, Chelidonium majus, a medicinal plant known for its pharmaceutical properties, offers another compelling case. However, research on C. majus has primarily focused on its extract, leaving its endophytic communities and biochemical profiles largely unexamined.
The rising demand for sustainable agricultural inputs has driven rapid growth in biopesticide market, positioning bacterial endophytes as timely and promising tools. They have demonstrated the ability to enhance plant growth, suppress pathogens and mitigate abiotic stress, indicating a role in transitioning global agriculture toward greater resilience and sustainability. However, translating these capabilities into wider field-scale success will require addressing several persistent scientific, technical and regulatory challenges.
Scaling microbial inoculants remains constrained by formulation instability, short shelf-life and inconsistent field performance across environments. Also, the use of non-native strains raises concerns around microbiome disruption, ecological imbalance and potential toxin production, which remain insufficiently studied and poorly regulated. Rather than treating microbial products as simple replacements to for synthetic agrochemicals, future research should focus on integrating them into broader regenerative systems. This includes soil health management, crop rotation and cultural control, supported by evaluation frameworks that are tailored to the dynamic nature of microbial agents rather than those designed for synthetic chemical inputs. Long-term ecological outcomes and field-based system integration should become central evaluation criteria.
Further progress also hinges on innovation in formulation technology. Technical limitations, including desiccation, UV sensitivity and viability loss, must be addressed to ensure reliable field performance. While short-term metrics, such as efficacy and availability, remain important, long-term advantages of microbial products will be reduced risk of resistance development, synergy with the host and soil microbiome, lower environmental impact, compatibility with IPM strategies and alignment with regenerative and sustainable agricultural practices. These factors are illustrated in Fig. 5.
Emerging technologies offer promising tools to overcome many of the field-related challenges. Nanotechnology, for example, may enhance microbial delivery systems, improve environmental stability and reduce application rates. Precision tools, such as nanosensors, can enable real-time monitoring of soil and plant health, thereby increasing decision-making accuracy and resource efficiency. These innovations, when aligned with ecological principles and adapted to local agricultural contexts can enhance the effectiveness and the field adoption of microbial solutions.
However, technical solutions alone are insufficient and must be accompanied by broader structural and institutional transformations. This includes the development of consistent international regulatory frameworks, expanded education and training and more equitable access to microbial technologies. Current regulatory models, which were developed primarily for chemical inputs often fail to accommodate the complex and context-dependent behavior of microbial agents. Also, the safe and effective application of emerging technologies, such as nanotechnology, will depend on regulatory standards that address biosafety, environmental compatibility and consumer trust.
Ultimately, microbial agents, such as endophytes, should not be viewed as mere biological inputs. They represent active contributors to the transformation of agriculture from input-intensive models to systems grounded in biological complexity and resilience. If their development is guided by extensive science, supportive policy, and integrated system design, they may surpass conventional inputs. In doing so, they can become a foundational component of sustainable agricultural intensification and a key contributor to global food security.
The Author(s) 2025. Published by Higher Education Press. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0)
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