Cultural and agronomic practices are foundational to integrate fungal disease management, which aims to reduce inoculum levels and create environmental conditions that are unfavourable to pathogen development. These include crop rotation with non-host species, fallow periods, sanitation, and residue management, which have been shown to suppress soil-borne pathogens, such as F. oxysporum and V. dahliae (Scott et al., 2014; Kowalska, 2021). Soil management techniques, such as improving drainage, reducing compaction, and adjusting pH, can limit disease-conducive conditions, while tillage practices can influence microbial communities, with no-till systems supporting higher microbial resilience (Noel et al., 2022). Optimizing plant spacing, canopy structure, and airflow reduces humidity and leaf wetness, suppressing foliar diseases (Douma and Noordhoek, 2025). Using disease-free seed material, enforcing quarantine, and applying non-chemical treatments can help prevent the introduction of pathogens (Mancini and Romanazzi, 2014). Thermal soil treatments, such as solarization and steam, combined with organic amendments, enhance suppressive soil microbial communities (Rippa et al., 2025). The use of compost and organic soil amendments can also promote microbial communities that are antagonistic to pathogens. These practices contribute to the development of disease-suppressive soils, where beneficial microorganisms inhibit pathogen activity and enhance rhizosphere resilience (Tziros et al., 2024; Rippa et al., 2025). Finally, practices such as intercropping, crop diversification, and cover cropping can reduce host continuity and promote beneficial microbes, leading to improved disease resistance and system resilience (Yu et al., 2022; Shrestha et al., 2025).

From a One Health perspective, these cultural and agronomic practices extend benefits beyond plant health by influencing ecosystem processes, human exposure, and overall agroecosystem resilience. By enhancing soil microbial diversity and nutrient cycling, promoting disease-suppressive soils, and reducing dependence on chemical fungicides, they minimize environmental contamination and occupational exposure risks for farm workers (Tziros et al., 2024; Douma and Noordhoek, 2025; Rippa et al., 2025). The use of disease-free planting material and non-chemical interventions further contributes to safer food systems and reduced human and animal health risks (Mancini and Romanazzi, 2014). Integrating these approaches fosters resilient agroecosystems that align plant disease management with broader One Health objectives, linking plant, environmental, and human well-being.

Many fungal pathogens persist in plant debris or soil between cropping seasons, making inoculum reduction a key strategy in disease management. Crop rotation with non-host or poor-host species, the implementation of fallow periods, deep ploughing, and the removal or incorporation of infected residues are proven methods for decreasing disease pressure. These approaches are particularly effective against soil-borne pathogens such as F. oxysporum and V. dahliae (Fradin and Thomma, 2006; Scott et al., 2014; Kowalska, 2021). For example, V. dahliae, the causal agent of Verticillium wilt, poses a significant threat to crops such as tomato, potato, and cotton. The pathogen produces long-lived microsclerotia capable of surviving in soil for several years, thereby maintaining inoculum levels between cropping cycles. Rotating susceptible crops with non-host species, such as cereals (e.g., wheat or barley), for several seasons has been shown to substantially reduce the soil inoculum potential. Similarly, deep ploughing can help decrease disease incidence by burying infested residues and microsclerotia deeper into the soil profile, where environmental conditions are less conducive to survival (Kowalska, 2021). In the case of F. oxysporum f. sp. lycopersici, the causal agent of Fusarium wilt in tomato, the removal and destruction of infected plant material after harvest or the implementation of a fallow period have been demonstrated to effectively reduce inoculum levels and subsequent disease severity (Chitwood-Brown et al., 2021). In addition, using clean propagation material and adhering to strict sanitation practices helps prevent the introduction and buildup of fungal inoculum.

From a One Health perspective, inoculum-reduction strategies extend benefits beyond crop protection by influencing ecosystem health, human exposure, and agroecosystem resilience. Crop rotation, fallow periods, residue management, and deep ploughing not only suppress soil-borne pathogens but also enhance soil microbial diversity and nutrient cycling, supporting disease-suppressive soils (Scott et al., 2014; Kowalska, 2021). By reducing the need for chemical fungicides, these practices lower environmental contamination and decrease occupational exposure risks for farm workers, as well as potential residues in food and water systems (Fradin and Thomma, 2006). The use of disease-free propagation material and strict sanitation prevents pathogen introduction, contributing to safer food production and reduced human and animal health risks (Mancini and Romanazzi, 2014; Chitwood-Brown et al., 2021). Collectively, these interventions create more resilient agroecosystems, linking crop-level disease management decisions to broader ecosystem processes and One Health outcomes. Integrating such practices highlights the cross-domain benefits of cultural and agronomic strategies, aligning sustainable disease control with plant, environmental, and public health objectives.

Soil structure, health, and moisture management play critical roles in fungal pathogen dynamics. Practices that improve drainage, prevent compaction, and enhance soil tilth can reduce pathogen proliferation. Adjusting soil pH and increasing organic matter content can also make the environment less conducive to fungal disease proliferation. Notably, a study comparing no-till and conventional systems found that no-till practices improved microbial resilience to fungicide applications, indicating the potential of certain tillage systems to support disease-suppressive microbial communities (Noel et al., 2022). From a One Health perspective, these soil management practices extend benefits beyond plant health by influencing ecosystem functions, human exposure, and agroecosystem resilience. Well-structured and biologically active soils support diverse microbial communities that enhance nutrient cycling, suppress pathogens, and reduce the need for chemical fungicides, thereby lowering environmental contamination and occupational exposure risks. By preventing the accumulation of pathogen inoculum and promoting ecological stability, these interventions contribute to broader agroecosystem resilience and link local disease management decisions to cross-domain One Health outcomes, benefiting plants, people, and the environment.

Plant density and canopy structure markedly influence microclimatic conditions such as humidity and leaf wetness, which are critical for the development of many foliar fungal pathogens. Agronomic practices include proper plant spacing, pruning, trellising, and thinning that improve airflow and reduce humidity, thereby suppressing disease development without chemical input. These strategies are especially important in high-value fruit and vine crops where canopy microclimate plays a major role in pathogen dynamics (Douma and Noordhoek, 2025). From a One Health perspective, optimizing plant density and canopy structure provides benefits that extend beyond plant disease suppression. By reducing leaf wetness and humidity, these practices limit foliar pathogen development while minimizing the need for chemical fungicides, thereby lowering environmental contamination and potential human exposure. Improved airflow and canopy management also support beneficial microbial communities on leaf surfaces and in the rhizosphere, contributing to ecosystem health and resilience. Integrating these canopy-focused practices within a One Health framework demonstrates interconnected benefits for plant, environmental, and human health outcomes, while enhancing crop quality and yield stability.

Preventing the introduction of fungal pathogens through contaminated planting material is a critical preventive strategy. Seed- and propagule-borne fungi can cause systemic infections and rapid disease spread if not managed at the source. The use of disease-free material, non-chemical seed treatments, nursery sanitation, and quarantine enforcement is effective in minimizing this risk (Mancini and Romanazzi, 2014; Hamelin et al., 2021). This is particularly vital in crops relying upon vegetative propagation, where pathogens can persist asymptomatically. From a One Health perspective, using disease-free seed and propagules provides benefits that extend beyond plant protection. Preventing the introduction of fungal pathogens reduces the need for chemical interventions, thereby minimizing environmental contamination and limiting human and animal exposure. Nursery sanitation, quarantine enforcement, and non-chemical treatments support healthy microbial communities in soils and propagation systems, enhancing ecosystem resilience. By controlling pathogens at the source, these measures also contribute to safer food production and lower risks of pathogen spread across agricultural landscapes. Integrating clean planting material within a One Health framework highlights the interconnected benefits for plant, environmental, and human health outcomes.

Diversifying cropping systems through intercropping, rotation, and cover cropping interrupts pathogen life cycles by reducing continuous host availability. These practices also enhance soil microbial diversity, which supports disease suppression through mechanisms like resource competition, antagonism and stimulation of plant immunity. For example, leguminous cover crops have been shown to improve soil fungal community composition by increasing beneficial fungi and reducing pathogen populations (Boudreau, 2013; Yu et al., 2022; Shrestha et al., 2025). Overall, these strategies build ecological stability and align with long-term goals of sustainable disease management.

Cultural practices offer several important strengths in plant disease management. They are generally low-cost, widely accessible to farmers, and form a core component of integrated pest management (IPM) systems (Pretty and Bharucha, 2015; Wang et al., 2021). Practices such as crop rotation, sanitation and optimal planting arrangements can substantially reduce disease risk and inoculum levels, making them a sustainable first line of defence. Yet, these approaches also have evident limitations. Their effectiveness is often partial and slower acting compared to chemical controls, and they typically require system-level changes and consistent implementation of good agronomic practices to be effective (Lichtfouse et al., 2009). In high disease pressure scenarios, cultural methods alone may not provide sufficient control and are best used in combination with other strategies. Nevertheless, they serve as an essential foundation for layering on additional non-chemical tools, contributing to more resilient and environmentally sound crop protection systems.

From a One Health perspective, crop diversification, intercropping, and cover cropping provide benefits that extend beyond direct disease suppression. By enhancing soil microbial diversity and promoting beneficial fungi, these practices improve ecosystem functions such as nutrient cycling and disease-suppressive soil formation (Boudreau, 2013; Yu et al., 2022; Shrestha et al., 2025). Reducing continuous host availability and pathogen pressure decreases reliance on chemical fungicides, lowering environmental contamination and minimizing human and animal exposure to harmful residues. These practices also contribute to agroecosystem resilience, supporting long-term productivity, soil health, and adaptive capacity under changing climatic conditions. When integrated with sanitation, optimal planting arrangements, and other cultural methods, host management strategies foster multi-layered disease control that aligns plant protection with broader health and sustainability outcomes. Framing these interventions within a One Health model explicitly links agricultural management choices to cross-domain benefits for plants, people, and the environment.

Genetic host resistance remains a cornerstone of sustainable disease management, providing a first line of defence against fungal pathogens (Dangl et al., 2013). Both qualitative (major gene) and quantitative (polygenic) traits can substantially reduce disease burden, yet resistance is often overcome by rapidly evolving pathogens, particularly in monocultures or when deployed without complementary strategies. Integrating host resistance with cultural, biological, and agronomic interventions reduces selection pressure on pathogens and prolongs resistance durability, while simultaneously lowering the need for chemical fungicides. This integration contributes to a One Health framework by protecting soil and water quality, reducing human and animal exposure to harmful chemicals, and supporting resilient agroecosystems that maintain productivity and ecosystem services (Turrà et al., 2014; Köhl et al., 2019).

Induced resistance and defence priming offer additional layers of protection. This involves sensitizing the plant’s immune system through prior exposure to specific stimuli, such as microbial signals, plant extracts, or signalling molecules like salicylic acid, jasmonic acid, and their analogues. These signals prime the plant to mount a more rapid and stronger defence upon challenged by a pathogen. Mechanistically, induced resistance involves the activation of key defence pathways, including the accumulation of pathogenesis-related (PR) proteins, reactive oxygen species (ROS), phytoalexin production, cell wall reinforcement (e.g., callose deposition), and systemic responses, such as systemic acquired resistance (SAR) and induced systemic resistance (ISR) (van Verk et al., 2009; Pieterse et al., 2012). These mechanisms can markedly reduce disease severity even when there is no direct antagonism by the pathogen (Pieterse et al., 2014).

From a One Health perspective, induced resistance and defence priming not only enhance plant immunity but also influence broader ecosystem and human health outcomes. By reducing disease severity without relying on chemical fungicides, these strategies minimize environmental contamination and occupational exposure risks for farm workers, while lowering residues in food and water systems (Walters et al., 2013; Köhl et al., 2019). The activation of plant defence pathways can also affect soil and rhizosphere microbial communities, promoting beneficial microbes that contribute to nutrient cycling and disease-suppressive soils (Korenblum et al., 2022). Furthermore, resilient plants with primed defences may maintain productivity under pathogen pressure, supporting stable food supplies and ecosystem services. Integrating induced resistance with complementary cultural, biological, and genetic strategies thus exemplifies a cross-domain One Health approach, linking plant health, environmental integrity, and human well-being (van Verk et al., 2009; Pieterse et al., 2014).

In addition to genetic host resistance and inducing defence priming, elicitors and defence-activating compounds such as β-aminobutyric acid (BABA), chitosan, and various plant-derived molecules can be applied as foliar sprays or seed treatments to trigger plant defences artificially. These inputs bolster the plant’s immunity rather than targeting the pathogen itself and, therefore, are less likely to contribute to resistance development (Walters et al., 2013). The schematic representation presented in Figure 1 depicts various compounds that trigger elicitors and defence-activating compounds in plants. These strategies come with both strengths and limitations. On the positive side, defence-based methods are less likely to drive pathogen resistance, are compatible with other interventions, and can be applied prophylactically. On the negative side, their efficacy can vary with crop species, environmental conditions, and the specific pathogen that is involved. In some cases, they may only offer partial suppression rather than full control, and the cost or regulatory approval of certain elicitors may limit their widespread use (Fenster and Eckert, 2021).

In practice, the most effective disease suppression often results from combining genetic resistance (both constitutive and inducible) with microbial biocontrol agents and cultural practices. This layered approach reduces dependence upon any single method and contributes to more resilient, sustainable crop protection systems. From a One Health perspective, elicitors and defence-activating compounds represent plant-centred interventions that enhance host immunity while minimizing direct ecological and human exposure to antimicrobial agents. Compounds such as β-aminobutyric acid and chitosan activate endogenous defence pathways, reducing disease pressure without exerting strong selective pressure on pathogens and thereby lowering risks of resistance development (Walters et al., 2013). Because these strategies do not rely on direct toxicity, they can reduce chemical inputs and associated environmental contamination, with potential benefits for non-target organisms and occupational exposure of farm workers. However, their context-dependent efficacy and partial disease suppression necessitate integration with genetic resistance, microbial biocontrol and cultural practices to ensure consistent field performance (Fenster and Eckert, 2021). When deployed within integrated systems, defence-activating compounds contribute to resilient crop protection frameworks that align plant immunity, ecosystem integrity and human health objectives under a One Health model. The next section of this review will explore microbial and plant product-based interventions, which constitute most non-chemical strategies.

Nanotechnology has shown significant potential using biologically synthesized nanoparticles (NPs), nano-carriers, and nano-formulations of anti-fungal compounds. These systems enhance the targeted delivery, stability, and controlled release of active ingredients, allowing for lower application rates and reduced environmental impacts. A recent review highlights the efficacy of metallic nanoparticles (e.g., silver and copper), graphene-based nanomaterials, and nanocomposites against major fungal pathogens such as F. oxysporum and Botrytis cinerea (Balusamy et al., 2023). These nanoparticles disrupt the fungal cell membranes, generate reactive oxygen species (ROS), and facilitate deeper penetration of active agents into the pathogen’s tissues. Nano-formulations are also being designed to encapsulate beneficial microbes or RNA molecules, enhancing both their efficacy and environmental persistence (Khundi et al., 2025). Though nanotechnology offers powerful tools for plant disease management, but its environmental risks must be carefully considered within a One Health framework. Metallic nanoparticles such as silver and copper can accumulate in soil and water, potentially disrupting beneficial microbial communities that underpin soil health and ecosystem stability (Maurer-Jones et al., 2013). Their ability to generate reactive oxygen species (ROS), while effective against pathogens, may also exert toxicity on non-target organisms, including soil invertebrates, aquatic species, and plant-associated microbiota (Khodakovskaya et al., 2009). Concerns have also been raised about the long-term persistence, bioaccumulation, and trophic transfer of nanoparticles in agroecosystems, which could indirectly affect animal and human health (Lead et al., 2018). Assessing nanoparticle fate and ecological effects is therefore critical to ensuring that nanotechnology supports, rather than undermines, One Health goals for safe, sustainable plant disease management.

RNA interference (RNAi) is an advanced molecular technology that has gained significant attention as a promising strategy for controlling fungal plant pathogens. This naturally occurring gene-silencing mechanism is activated by the presence of double-stranded RNA (dsRNA), which triggers the degradation of complementary messenger RNA (mRNA), thereby inhibiting the expression of specific target genes. First discovered in the free-living nematode Caenorhabditis elegans (Fire et al., 1998), RNAi has since been adapted in plant pathology to silence genes crucial for the growth, virulence, or survival of phytopathogenic fungi (Rosa et al., 2018).

Fungal pathogens are responsible for substantial crop losses globally, affecting key agricultural commodities such as wheat, maize, rice, and fruits. Conventional control methods, including fungicide application and breeding for resistant cultivars, are increasingly undermined by environmental concerns, fungicide resistance, and regulatory challenges. RNAi provides a highly specific and environmentally sustainable alternative by targeting only essential fungal genes, reducing off-target effects on non-pathogenic organisms (Figure 2) (Mann et al., 2023).

A notable approach in RNAi-based pathogen control is host-induced gene silencing (HIGS), where plants are genetically engineered to produce dsRNA that targets key fungal genes. Upon infection, the fungus takes up these dsRNAs, initiating RNAi and suppressing pathogenicity. This process has been successfully demonstrated in controlling Fusarium graminearum (anamorph of Gibberella zeae [Schwein.] Petch.; Nectriaceae), which is the causative agent of Fusarium head blight, by silencing genes such as cytochrome P450s (Koch et al., 2013).

An alternative, non-transgenic approach is spray-induced gene silencing (SIGS), which involves the external application of synthetic dsRNA to plant surfaces. This method avoids genetic modification and enables temporary, environmentally safe gene silencing. SIGS has shown its effectiveness against fungal pathogens such as B. cinerea and the ascomycete pathogen Sclerotinia sclerotiorum, making it compatible with integrated pest management systems (Smagghe, 2025).

Despite its potential, RNAi-based control faces hurdles, including dsRNA stability under field conditions, uptake efficiency across fungal species, and the robustness of fungal RNAi machinery. Innovations such as nanoparticle carriers and bio-formulated sprays are under investigation to overcome these limitations (Mann et al., 2023). Furthermore, emerging studies demonstrate that targeting virulence-related genes like MET6 and MsrA can impair fungal growth and pathogenicity (Hassouni et al., 1999; Saint-Macary et al., 2015; Molina-Santiago and Vela-Corcía, 2025). Additionally, beneficial biocontrol agents are being engineered to produce RNA molecules that silence fungal genes or which boost their own antagonistic capabilities (Liu et al., 2024).

Implementing RNAi technologies at small and large scales presents both opportunities and challenges that must be evaluated within a One Health framework. At the small-scale level, SIGS offers a non-transgenic and accessible option for growers, yet adoption may be constrained by high dsRNA synthesis costs, rapid environmental degradation of dsRNA by UV radiation and nucleases, and the need for repeated applications (Dalakouras et al., 2020; Tian et al., 2023; Luo et al., 2024). In large-scale agriculture, successful deployment requires cost-effective production systems such as microbial biofactories or chloroplast-based dsRNA expression along with regulatory harmonization and scalable delivery technologies, which remain major bottlenecks (Augustyniak et al., 2018; Dubrovina and Kiselev, 2019). Environmental concerns include dsRNA persistence, impacts on soil and phyllosphere microbiomes, and unintentional off-target gene silencing in non-target fungi or beneficial species, raising One Health considerations regarding ecosystem balance, food safety, and long-term biodiversity impacts (Parker et al., 2019; Dietz-Pfeilstetter et al., 2021). Moreover, off-target effects remain a significant concern, particularly in complex agroecosystems where partial sequence homology may affect beneficial fungi, insects, or symbionts (Roberts et al., 2015; Castellanos et al., 2022). Addressing these barriers will require improved dsRNA design algorithms, comprehensive ecological risk assessments, and environmentally safe delivery systems such as biodegradable nanoparticle formulations that minimize exposure beyond the target organism and help in advancing One Health framework.

Microbiome engineering and the use of synthetic microbial consortia represent innovative and rapidly advancing strategies in the biological control of fungal plant pathogens. These approaches aim to enhance the resilience of the rhizosphere (i.e., the region of the soil immediately surrounding plant roots), by either transplanting disease-suppressive soil microbiomes or assembling defined communities of beneficial microbes with complementary functions (Berg et al., 2016).

Unlike the application of single microbial strains, synthetic consortia can provide more robust and consistent suppression of soil-borne pathogens, particularly under variable environmental conditions. These engineered communities are designed to exploit synergistic interactions among microbes, such as resource sharing, competition with pathogens, or activation of host defence pathways, thereby reducing the likelihood of pathogenic fungal colonization and disease development.

The strategic design and deployment of these microbial consortia are increasingly guided by advances in meta-omic technologies, including metagenomics, metatranscriptomics, and metabolomics, which provide insights into microbial community structure and function (Zhang et al., 2019). Additional tools, such as machine learning and network modelling, are being employed to predict microbial interactions and identify keystone taxa that are critical for disease suppression (Fitzpatrick et al., 2020; Leggieri et al., 2021). These developments are accelerating the rational design of microbial inoculants that can be tailored to specific crops, soil types, or pathogens. When integrated with sustainable agronomic practices such as crop rotation, organic amendments, and reduced chemical inputs, microbiome-based solutions have the potential to offer long-term and environmentally friendly alternatives to chemical fungicides.

Microbiome engineering raises biosafety concerns related to the unintended spread, persistence, or ecological displacement of introduced microbes or synthetic consortia beyond their target environments. Engineered communities may also disrupt native microbial networks in unpredictable ways, potentially influencing nutrient cycling, non-target organisms, or pathogen evolution. Addressing these risks requires rigorous ecological risk assessment, long-term monitoring frameworks, and regulatory guidelines that reflect community-level and ecosystem-wide dynamics. At the same time, microbiome engineering and synthetic microbial consortia advance a One Health approach by enhancing rhizosphere resilience and reducing reliance on chemical fungicides, thereby lowering risks to human, animal, and environmental health. By harnessing synergistic microbial interactions and tailoring communities to specific crops and soils, these strategies offer sustainable and ecosystem-friendly solutions for durable fungal disease management.

In parallel with biological developments, artificial intelligence (AI) and precision sensing technologies are improving the timing, placement and efficiency of disease control interventions. AI algorithms using hyper-spectral imaging and remote sensing can detect early disease symptoms and trigger localized treatments with biocontrol agents or RNAi formulations, thereby minimizing resource waste and maximizing protection (Wen et al., 2023).

Despite their promise, these technologies face key limitations. Many remain at the proof-of-concept phase or are restricted to the pilot scale. Challenges include high production costs, complex formulations, regulatory uncertainty (especially for gene silencing and nanomaterials), and variable field efficacy under different agro-climatic conditions. Furthermore, public acceptance and ecological safety, particularly around gene editing and nanotechnology, require transparent risk assessment and regulation.

Key research and policy challenges in advancing novel non-chemical approaches for fungal disease management include the need to better understand the environmental fate and ecotoxicity of nano-materials, particularly their long-term impacts on soil health, non-target organisms, and ecological balance (Schlich et al., 2017; Lead et al., 2018). Also, evaluating off-target effects of RNA interference (RNAi) and genetically engineered microbes is critical to ensure biosafety, especially in complex field environments where unintended interactions may occur (Karaoğlan et al., 2024; Germing et al., 2025). Another pressing challenge is the development of robust and adaptive regulatory frameworks that can keep pace with rapidly evolving biotechnologies, while maintaining public trust and environmental safeguards. Finally, there remains a significant gap between laboratory innovations and practical, field-scale implementation; bridging this requires large-scale demonstration trials, context-specific adaptation, and comprehensive cost-benefit analyses to assess viability and scalability across different agroecosystems. In conclusion, while these advanced tools are not yet replacements for existing practices, they represent a transformative shift toward smart, integrated, and resilient plant disease management systems.

Advanced plant-health technologies such as genome-edited crops, RNAi biopesticides, engineered microbial inoculants, and digital surveillance platforms offer significant promise for sustainable agriculture. However, their integration into agroecosystems highlights persistent regulatory, ethical, and biosafety gaps with implications for One Health, encompassing plant, human, animal, and environmental well-being (Table 3).