Sustainable Soil Disinfestation Approaches in Crop Production: From Chemical Dependency to Ecological Resilience

Abstract

Soil management is crucial for addressing soil-borne pathogens, weeds, and pests, ensuring sustainable crop productivity. Traditional chemical fumigants, such as methyl bromide, have been effective but pose serious environmental risks, including ozone depletion and reduced soil biodiversity. Consequently, attention has shifted toward more sustainable alternatives. Techniques like soil solarization, anaerobic soil disinfestation (ASD), biofumigation, and the use of biological control agents (BCAs) offer environmentally friendly options for managing soil-borne diseases. Steam and microwave disinfestation are also promising techniques; however, further development is required to improve their practical efficiency. Integrated management approaches, which combine multiple interventions, have proven particularly effective, offering flexibility and enhancing control through complementary techniques. Additionally, emerging technologies such as artificial intelligence and hyperspectral imaging provide new opportunities for real-time monitoring and decision-support to optimize the timing and targeting of pest management interventions. This review emphasizes the potential of sustainable soil pest control methods to reduce reliance on chemical fumigants, improve crop yield and quality, and support environmentally responsible farming practices. It also examines the challenges associated with scalability, cost, and variable effectiveness, while outlining the strengths, weaknesses, and mechanisms of each method. Further research on regional adaptation, technological integration, and long-term impacts is essential to fully optimize these innovative solutions for food security and sustainable agriculture.

1. Introduction

Soil management is a crucial practice in modern agriculture for controlling soil-borne pathogens that present significant risks to global food security and crop productivity. In particular, pathogens such as Fusarium spp., Pythium spp., Verticillium spp., and Rhizoctonia spp. are major contributors to significant crop losses worldwide. Soilborne diseases can be highly destructive, with several species capable of causing 50–75% yield losses in susceptible crops, representing one of the most severe constraints to agricultural productivity [1]. The Food and Agriculture Organization of the United Nations (FAO) reports that approximately USD 220 billion is spent annually worldwide on managing plant diseases [2], where soilborne plant pathogens—such as fungi, bacteria, viruses, and nematodes—pose particularly difficult management challenges. To address this problem, conventional soil treatment methods have been applied for years, primarily chemical-based approaches such as methyl bromide fumigation. Although effective in suppressing pathogens, such methods have been found to have significant negative environmental and health impacts. Methyl bromide, for example, is a potent ozone depleting substance, and its phase out under the “Montreal Protocol” highlights the urgent need for alternatives [3]. Additionally, chemical residues in soil can disrupt beneficial microbial communities, compromise soil health, and contaminate food, contributing to long-term agricultural sustainability concerns. In contrast, environmentally friendly soil disinfection approaches, which have evolved over the years as alternatives to chemical fumigants, have reported impressive results in mitigating environmental damage [4]. Sustainable soil management strategies include physical treatments such as solarization, soil heating with steam and microwave irradiation, or biological methods including biofumigation, anaerobic soil disinfestation, application of disease-suppressing compost, and use of biocontrol agents. Recent comparative research has indeed demonstrated that biological soil management—including anaerobic soil disinfestation (ASD) and organic amendments—not only reduces pathogen density such as Fusarium oxysporum but also strengthens the core microbiome and promotes a complex, resilient microbial network that confers long-lasting disease suppressiveness [5]. However, sustainable soil pest management remains an area of research that requires further exploration, especially to understand the long-term effects of these methods on soil health and microbial communities. For example, anaerobic soil disinfection is promising in pathogen suppression, but its effects on nutrient cycling and soil microbiome stability require further investigation [6]. Similarly, the effectiveness of biofumigation against emerging pathogens, such as those resistant to conventional treatments, remains uncertain [3]. Furthermore, the influence of these sustainable pest management practices on vegetable yield and quality also requires further investigation. Preliminary studies suggest that environmentally friendly methods can improve these traits by promoting healthier plant–soil interactions, but robust, large-scale evidence is still lacking [7]. Ultimately, since soil is a complex ecosystem that includes fungi, bacteria, insects, nematodes, and other microorganisms, understanding these interactions is essential to design effective soil and plant health management strategies, rather than targeting individual pathogen species [8]. Innovative approaches, including the integration of artificial intelligence (AI) with precision agriculture tools such as hyperspectral imaging, are among the emerging technologies in this field. Indeed, by providing real-time monitoring of soil health and early detection of pathogen outbreaks, they play a crucial role in optimizing the effectiveness of pest control treatments [9,10,11]. However, their practical implementation in commercial vegetable production remains a significant obstacle.

This review presents chemical, physical, and biological soil pest control methods, outlining their advantages, limitations, and recent innovations, with a focus on their effects on pathogen suppression and soil health. It also includes emerging tools, such as artificial intelligence-based diagnostics and advanced biological approaches, to identify current innovation paths in sustainable agriculture. Overall, it illustrates how these practices contribute to resilient, productive, and environmentally friendly cropping systems, improving not only yield but also the quality and sensory characteristics of vegetables.

The most relevant literature on the topic was selected using a structured narrative approach. References were identified primarily through targeted searches on platforms such as Google Scholar and Scopus, conducted iteratively within the manuscript. Search queries combined general and method-specific keywords, including “soil disinfestation,” “alternatives to soil fumigation,” “solarization,” “anaerobic soil disinfestation,” “biofumigation,” “soil steam disinfection,” “microwave soil treatment,” and “biological control agents,” often enriched with terms related to crops or pathogens. Studies were included based on their relevance to the review objectives, scientific relevance, and the utility of the proposed solutions. No a priori geographical restrictions were applied during the literature selection. Therefore, the geographic origin of the cited studies reflects the distribution of available research rather than an intentional regional focus.

2. Soil Disinfestation Methods

2.1. Chemical Methods

Chemical soil disinfestation (CSD) is a widely used agricultural practice in greenhouse vegetable production for its proven effectiveness against soil-borne pests, pathogens, and weeds. This control method involves the application of chemical fumigants, which, by releasing volatile compounds into the soil, disrupt the cellular and metabolic functions of pests. The main advantages of CSD are its broad-spectrum action, immediate pest suppression, and significant yield improvements. For example, fumigants such as methyl bromide (MB), dimethyl disulfide (DMDS) and metam sodium have demonstrated efficacy in controlling pathogens such as Fusarium oxysporum and nematodes such as Meloidogyne javanica, enabling high crop yields and supporting intensive agricultural production [12]. Additionally, the ability of fumigants to eliminate multiple threats in a single application simplifies pest management in resource-intensive greenhouse environments. However, despite these benefits, the environmental and economic sustainability of chemical fumigation remains a major concern. Among the most notable environmental concerns raised by the widespread use of methyl bromide is ozone depletion [13]. Similarly, modern fumigants such as DMDS and metam sodium, while less harmful to the atmosphere, still cause toxicity risks to humans and non-targeted organisms, requiring stringent application protocols [14]. Research has consistently shown that these treatments reduce microbial diversity and impede essential soil functions. Evidence from both field and microcosm studies consistently shows that fumigants negatively affect beneficial microbial communities, including nitrifiers and denitrifies, which are critical for nutrient cycling and soil ecosystem resilience [15]. Consequently, the long-term sustainability of fumigated soils may be compromised, particularly in systems that rely on continuous cropping cycles. Nevertheless, it has also been shown that the alteration of soil physicochemical properties caused by repeated fumigant use can sometimes have apparently positive implications. In some intensively managed systems, pathogen suppression through fumigation has coincided with short-term improvements in soil physicochemical properties, including reduced topsoil salinity associated with nitrate redistribution after dazomet application [16]. This benefit, however, as reported by Sennett et al. [17], is often offset by increased nitrate leaching and reductions in soil organic matter content. Indeed, fumigants often deplete soil organic matter and functional microbial groups, compromising the long-term ability of soil to recover and support healthy plant growth [18,19]. Such changes in soil carbon and nitrogen dynamics highlight the trade-offs inherent in chemical fumigation practices, where immediate benefits can come at the expense of long-term soil health. Lastly, despite its environmental impacts, chemical fumigation remains a practical option for managing soil-borne threats in greenhouse systems, where soil reuse is common. Sustainable practices, such as combining fumigation with organic amendments or adopting integrated pest management (IPM) strategies, can mitigate some of the above-mentioned drawbacks [20] (Figure 1).

2.2. Physical Methods

2.2.1. Soil Steam Disinfection

Soil steam disinfestation (SSD) is an effective and environmentally friendly method that uses water vapor to increase soil temperature, effectively eliminating pathogens such as Fusarium solani [21] and other harmful fungi [22], while also suppressing weeds and nematodes [23]. The process involves injecting hot steam into the soil through boilers and tubes, which can penetrate to varying depths. Unlike chemical fumigants, the SSD method leave no harmful residues because water is converted into steam, where it is applied to the soil at high temperatures (~70–90°C) [24,25], making it suitable for organic and sustainable farming practices. Bitarafan et al. [26] demonstrated that vacuum-assisted steaming achieved more than 90% reduction in seed germination of Avena fatua (L.), Echinochloa crus-galli (L.) P. Beauv., and Bromus sterilis (L.) at soil temperatures of 75–100 °C, regardless of soil type. These findings support soil steaming as a reliable, residue-free option for soil reuse and invasive species control; however, its performance remains strongly dependent on soil physical properties. Variations in particle size, pore structure, and moisture content critically influence heat transfer, temperature homogeneity, and overall energy efficiency, limiting the standardization of treatment protocols across contrasting soils [27,28]. In addition, the high energy demand required to achieve effective thermal inactivation constitutes a major barrier to adoption, as the combined costs of equipment and fuel can be prohibitive, particularly for small-scale farms. Economic analyses indicate that the feasibility of steam-based disinfestation is closely linked to economies of scale and supportive policy frameworks, while the integration of renewable energy sources—such as solar-assisted steam generation—offers a viable pathway to reduce operating costs and carbon emissions in regions with high solar availability [29,30]. Technologies such as band spraying, a precision application that targets specific regions of the soil, have also been developed to reduce energy consumption while maintaining pest suppression effectiveness [31]. Further innovation has focused on improving the energy efficiency of steam devices; Zhang et al. [32] optimized the design of fin-shaped heat exchangers within steam injectors to enhance thermal transfer and temperature homogeneity, achieving a 40% improvement in heating efficiency and reducing fuel consumption. Despite its successes, spraying can also have some disadvantages, such as its impact on soil properties. Although it effectively reduces pest populations, it can eliminates beneficial microorganisms, disrupting the ecological balance of the soil in the short term [21]. Soil microbiome recovery varies and may require additional interventions, such as the application of organic amendments or microbial inoculants, to restore soil health. Another concern is the risk of recontamination; once sterilized, soil becomes highly susceptible to recolonization by opportunistic pathogens or weeds, especially if post-treatment sanitation measures are not followed up carefully [22]. A study by Yang et al. [27] highlighted the importance of optimizing soil pore structure to improve heat and mass transfer during the process. Additionally, while steam treatment increased the release of soluble nutrients like K⁺, Mn²⁺, and NH₄⁺, it did not cause bacterial eradication or significant shifts in bacterial community structure; potential risks, such as the exploitation of soil resources and the possibility of manganese toxicity, should be carefully considered, especially in repeatedly steamed soils [33]. However, careful calibration of parameters, such as steam temperature, exposure time [23], and the addition of mitigants like calcium oxide [33], can address some of these risks. In conclusion, therefore, SSD is an effective and compatible alternative to chemical fumigation for soil pest management; however, the main disadvantages are high energy consumption and risks of recontamination. Integration with crop rotation, organic amendments and microbial inoculants, together with advances in energy-saving technology, can improve its sustainability.

2.2.2. Microwaves for Soil Disinfestation

Microwave soil heating is an innovative technique that uses microwave radiation to increase soil temperatures, targeting harmful soilborne microorganisms, pathogens, and pests. By penetrating the soil and vibrating water molecules, this method generates heat that disrupts biological processes in bacteria, fungi, and other organisms, rendering them non-viable. As a result, it offers an environmentally friendly alternative to chemical pest control approaches [34]. Experimental evidence indicates that, when energy input is appropriately calibrated, microwave treatment can achieve near-complete inhibition of weed seed germination, supporting its potential for targeted, localized weed management [35]. Beyond weed and pathogen suppression, microwave exposure has also been associated with positive crop responses, including enhanced vegetative propagation and improved early plant performance, likely linked to transient reductions in competing soil microorganisms and short-term modifications of the soil biological environment [36,37]. These responses are strongly mediated by treatment parameters and soil conditions. Modeling and experimental studies consistently show that irradiation time, soil depth, and moisture content govern heat distribution and pathogen inactivation efficiency, while excessive exposure risks nutrient degradation or unnecessary energy consumption [38,39]. A comparative dose–response study indicates that microwave efficiency is strongly influenced by soil type and moisture, making process optimization essential to balance effectiveness and energy demand [40]. Ruggeri and Garau [41] have developed precise heat transfer models, including nonlinear ones, that enable targeted applications while reducing energy consumption and the risk of overheating. These innovations make microwave soil treatment a promising tool for disease management in agriculture, ensuring controlled disinfection, increased safety, and less waste, which are essential for sustainable agricultural practices. Conflicting opinions regarding the ability of this method to discriminate between harmful and beneficial microorganisms raise doubts in the scientific community. Li et al. [42] observed that 2.45 GHz microwave treatment altered the bacterial community structure in Phaeozem soils of Northeast China, causing an initial reduction in microbial diversity, followed by a gradual recovery over time. These results are consistent with those of Khan et al. [43], who showed that while pre-sowing microwave treatments altered the soil microbial community, beneficial soil microbes showed a faster recovery. However, repeated use could have cumulative effects on soil microbial dynamics, with potential long-term consequences. In fact, according to Brodie et al. [36] and Khan et al. [44], although short-term effects may be limited, prolonged exposure to heat could degrade soil, requiring long recovery periods to re-establish fertility and microbial balance. Further research will therefore be needed to optimize the process and better understand its ecological impacts, and also effectively integrate it into broader pest management strategies. While microwave soil heating offers significant benefits, it also poses environmental and resource challenges that require attention. The technique demands substantial energy inputs, raising concerns about cost and scalability, particularly in regions characterized by high energy prices [43]. Moreover, soil moisture content is a critical factor, as dry soils hinder heat penetration, while excessively wet soils require higher energy to achieve effective heating [36,37]. To maximize the potential of microwave soil heating, future research must focus on optimizing energy efficiency, refining application methods, and mitigating risks associated with excessive heating. This includes developing calibrated exposure protocols to prevent damage to soil structure and biodiversity [38,39,43]. Efforts should also aim to integrate this technology into broader pest management systems, addressing sustainability and cost-effectiveness to ensure its viability for large-scale agricultural applications. Microwave soil heating, therefore, is a promising and environmentally friendly alternative to chemical pest control, offering benefits for pathogen suppression and crop production. However, challenges such as energy demand, potential impacts on soil biodiversity, and long-term fertility concerns must be addressed. Optimizing energy efficiency, refining application protocols, and integrating the technology into broader pest management strategies are essential steps to ensure its sustainability and scalability in agricultural practices.

2.2.3. Soil Solarization

Soil solarization is a hydrothermal pest control technique that uses solar energy to raise soil temperatures sufficiently to manage soil-borne pests, pathogens, and weeds. The technique involves covering moist soil with sheets of clear polyethylene or biodegradable plastic during periods of high solar intensity, particularly in hot climates. The heat trapped under plastic increases soil temperatures to levels that are lethal to various pests and pathogens, while also suppressing weed growth. Among sustainable agricultural practices, soil solarization has gained attention as a viable alternative to chemical fumigation, especially in arid and semi-arid regions. According to Jagtap et al. [45], soil temperatures under solarization can reach 45–60 °C, sufficient to reduce soil-borne pests. Key factors that influence the effectiveness of soil solarization include mulch type, soil moisture, application duration, and climate conditions. Moist soil, for example, improves thermal conductivity, making the process more efficient [46]. Transparent plastic films maximize heat penetration, whereas colored mulches such as black or silver can contribute to additional weed suppression through combined thermal and optical effects [47]. Longer solarization periods, moist soils, and high solar intensity maximize the effectiveness of the process, making it more suitable for regions with hot, sunny climates. Under arid and semi-arid conditions, solarization has also been shown to improve soil fertility while effectively suppressing soilborne pests, supporting its application in regions with limited water availability when appropriately managed [48]. Beyond pest control, solarization induces broader ecological effects by reducing parasitic nematode populations and restructuring soil bacterial communities toward disease-suppressive configurations, thereby contributing to both agronomic performance and soil health [49]. Recent work by Rippa et al. [50] introduced an innovative solarization approach using photo-selective films that allow targeted wavelengths to penetrate while minimizing water loss. Similarly, Vatchev [51] reported that combining solarization with organic matter incorporation (biosolarization) effectively controlled the crown and root rot disease complex in greenhouse vegetables. Additionally, soil solarization increases nutrient availability, particularly nitrogen and potassium, through accelerated decomposition of organic matter [52]. This increased nutrient availability can improve crop yields and reduce the need for synthetic fertilizers. Its reduced reliance on chemical fumigants lowers environmental and human health risks, while compatibility with biodegradable plastic films further strengthens its sustainability profile [11,53]. Nevertheless, the effectiveness of solarization remains strongly climate-dependent, as adequate pathogen suppression requires prolonged periods of high solar radiation and elevated soil temperatures, thereby constraining its applicability in cooler or less irradiated regions [45]. Furthermore, the process can be time-consuming, requiring weeks of application to achieve optimal results. For smallholder farmers, the cost of purchasing plastic mulch can be a financial challenge. In some cases, the heat generated may not completely eradicate heat-resistant pathogens or deeply buried weed seeds, necessitating additional control measures. Likewise, traditional polyethylene sheets, unless recycled or replaced with biodegradable alternatives, pose significant environmental concerns [53]. Contrasting effects have been observed for soil properties. While on the one hand, soil warming increases the decomposition of organic matter, and with it the availability of nutrients for plants, especially nitrogen and potassium [52], on the other hand this prolonged exposure to high temperatures can deplete organic carbon, negatively affecting soil health [54]. The main consequence of this is the damage of beneficial microbial communities, whose subsequent recovery depends on post-solarization soil management practices, as Shea et al. [49] observed. Furthermore, solarization can cause temporary changes in soil structure, including aggregation and porosity [54]. Future perspectives of this technique focus on optimizing its application in different agroclimatic conditions through innovative practices. For example, supplementing solarization with soil amendments such as biochar, organic fertilizers, or microbial inoculants could increase its effectiveness and mitigate its limitations. Öz [55] showed that the addition of biochar improved soil quality and crop yield under solarization. In summary, soil solarization is a powerful tool for sustainable pest and pathogen management. Its ability to control soil pests, improve nutrient availability, and reduce weed growth positions it as a viable alternative to chemical fumigation. However, its limitations, including climate dependency and temporary disruptions to soil health, need to be addressed through innovative research and integration with complementary practices. With advances in technology and materials, soil solarization has the potential to play a critical role in sustainable agriculture worldwide (Figure 2).

2.3. Biological Soil Disinfestation Methods

2.3.1. Suppressive Composts for Soilborne Diseases

Recent research highlights the significant role of compost and compost tea (CT) in improving soil health, suppressing soil-borne pathogens, and enhancing crop productivity, marking them as vital tools in sustainable agriculture. These amendments, created by soaking organic matter in water under specific conditions, interact through the release of bioactive compounds and enhancing microbial diversity and activity. Studies highlight their efficacy against significant pathogens such as Fusarium oxysporum, Rhizoctonia solani, and root-knot nematodes, among others [56,57,58]. Biocidal effects result from secondary metabolites, organic acids, and beneficial microbial consortia, which antagonize pathogens and induce plant resistance [59,60]. Furthermore, Bonanomi et al. [61] demonstrated that CT application in Mediterranean vegetable systems significantly enhanced soil enzymatic activity, microbial biomass, and nutrient availability, resulting in higher crop yield and improved product quality. The success of these amendments depends on multiple factors, including the source and type of organic material, preparation methods, application timing, and soil environmental conditions. Evidence indicates that aeration regimes and nutrient enrichment during preparation can markedly influence pathogen suppression and microbial diversity, while vermicompost-derived formulations consistently enhance soil organic matter content, enzymatic activity, and microbial balance, resulting in improved crop performance [60,62]. Beyond individual formulations, comparative analyses across 37 compost types have identified a conserved consortium of bacterial and fungal taxa—particularly Bacillus, Pseudomonas, and Streptomyces—that is consistently associated with disease-suppressive soils, suggesting the existence of functional microbial indicators that can guide more reliable compost selection and application strategies [63]. Despite their demonstrated potential, CT remains subject to important limitations related to variability in preparation and application. Differences in brewing parameters—such as aeration regime, extraction duration, and source material composition—can substantially alter the microbial activity and consistency of the final product, leading to unpredictable disease suppression outcomes [64]. Inadequate management or excessive application may further result in nutrient imbalances or the proliferation of undesirable microorganisms, posing risks to both plant performance and soil health [57]. In addition, expensive and labor-intensive preparation methods may limit large-scale adoption in some agricultural systems. The positive effects of these amendments on soil properties are well documented, demonstrating improvements in both physical and biological parameters. Indeed, CT applications are linked to increased soil fertility, organic matter levels, and microbial community structure [65]. Under challenging conditions such as saline–sodic soils, the combined application of CT with arbuscular mycorrhizal fungi has been shown to reinforce nutrient cycling, stimulate enzymatic activity, and suppress soilborne pathogens, resulting in improved crop productivity and soil resilience [66]. More broadly, the use of organic teas in disease management supports sustainable agricultural practices by reducing dependence on synthetic chemical inputs and contributing to the preservation of soil ecosystem integrity [67]. Overall, incorporation of CT and similar organic matter amendments presents an environmentally friendly and multifaceted approach to soil pest management and soil health management. Consistently positive results in studies underscore their potential as sustainable alternatives to traditional chemical treatments, offering long-term benefits for crop productivity and soil fertility. Though, addressing variability in preparation and application methods is critical to maximizing their effectiveness and wider adoption.

2.3.2. Biological Control Agents

Biological control agents (BCAs) provide a promising and sustainable alternative for soil disinfestation by targeting soilborne pathogens through mechanisms that reduce environmental impact while promoting plant health. These agents, which include a range of bacteria, fungi, and other microbes, employ diverse strategies such as direct antagonism, resource competition, and induced systemic resistance to manage soilborne diseases. Alqahtani, [68] reviewed the main groups of microbial biocontrol agents—including Trichoderma, Bacillus, and Pseudomonas spp.—summarizing their mechanisms of pathogen inhibition and their integration within sustainable pest-management frameworks. Among bacterial BCAs, Bacillus amyloliquefaciens and Bacillus subtilis are widely studied due to their broad-spectrum efficacy. These bacteria secrete antibiotics, enzymes, and volatile organic compounds (VOCs) that directly inhibit pathogens. Sabaté and Brandán [69] demonstrated how B. amyloliquefaciens improved rhizosphere microbial diversity while significantly reducing root rot severity in degraded soils. Similarly, Zaccardelli et al. [70] reported the successful utilization of composted aromatic plant waste to produce Bacillus strains, which not only controlled pathogens but also enhanced nutrient cycling and overall soil health. The application of fungi, particularly species of the genus Trichoderma, adds a further dimension to biological control: their species are effective through mycoparasitism, the secretion of hydrolytic enzymes, and competition for nutrients and space. Saldaña-Mendoza et al. [71] emphasized the dual benefits of Trichoderma spp. in controlling soilborne pathogens and enhancing crop resilience, including improved root architecture and drought tolerance. Similarly, Tyśkiewicz et al. [72] detailed the ability of Trichoderma to mitigate fungal infections, particularly those caused by aggressive pathogens like Fusarium spp., while simultaneously promoting plant growth via phytohormone production. Mycorrhizal fungi also play an integral role in biological control, particularly through the improvement of nutrient acquisition and modulation of plant immune responses. Aljawasim et al. [73] illustrated how arbuscular mycorrhizal fungi (Glomus spp.) significantly reduced disease severity caused by Rhizoctonia solani in cucumbers. These fungi also fostered better plant vigor and yield, highlighting their holistic impact on plant health. Boutaj et al. [74] further documented the protective effects of mycorrhizal fungi in reducing vascular wilt diseases, suggesting their potential as a sustainable solution for managing complex pathogen systems. In addition to mycorrhizal symbionts, several studies have highlighted the antagonistic potential of endophytic fungi against root-infecting fungal diseases. In this regard, Taha et al. [75] investigated naturally occurring endophytes from pepper (Capsicum L.) roots (Penicillium funiculosum, Aspergillus flavus, Myrothecium verrucaria), which markedly suppressed Fusarium and Rhizoctonia root rot in greenhouse trials. Soilborne pathogens like Sclerotinia sclerotiorum present significant challenges for agriculture, but several studies have explored the potential of BCAs to combat these threats. Coniothyrium minitans and Bacillus amyloliquefaciens are particularly effective against S. sclerotiorum. Current findings suggest that Coniothyrium minitans and Bacillus amyloliquefaciens reduce disease incidence and severity through complementary mechanisms, including direct mycoparasitism, hyphal degradation, and antibiotic production [76]. Genomic and transcriptomic analyses further reveal that C. minitans possesses specialized traits enabling disruption of fungal hyphae and inhibition of pathogen reproduction, supporting its targeted efficacy against S. sclerotiorum [77]. Moreover, Han et al. [78] further demonstrated that integrating BCAs with soil organic amendments enhanced pathogen suppression, improved soil structure, and supported a diverse soil microbiome. This synergistic approach underscores the potential of combining BCAs with other sustainable practices for more robust pathogen management. Rhizobacteria, especially plant growth-promoting rhizobacteria (PGPR), offer another avenue for sustainable soil disinfestation. These bacteria form beneficial associations with plant roots, suppressing pathogens while improving plant health. Abdelaziz et al. [79] identified various PGPR strains capable of reducing disease severity while promoting plant growth through mechanisms like nutrient solubilization and secretion of growth-promoting compounds. Das et al. [80] highlighted rhizobia’s antagonistic potential against fungal pathogens, attributing their success to secondary metabolites and competition for resources. These rhizobacteria not only mitigate pathogen activity but also enhance soil fertility and microbial diversity, leading to long-term agricultural benefits. The integration of BCAs into sustainable agricultural systems relies heavily on understanding their interactions with native soil microbiomes. Liu et al. [81] provided evidence that plants can actively recruit beneficial microbes under pathogen attack, enhancing their protective efficacy. Such interactions underline the dynamic role of the soil microbiome in shaping the success of biological control strategies. Mazzola and Freilich [82] stressed the importance of utilizing native microbiomes over synthetic microbial consortia, noting that indigenous microbes offer better resilience to environmental fluctuations and soil-specific challenges. Wolfgang et al. [83] suggested that VOCs produced by bacterial BCAs could serve as an innovative mechanism for controlling nematode-based diseases, providing a non-invasive and scalable solution for soil disinfestation. However, the successful implementation of BCAs faces several challenges. Environmental factors, such as soil pH, temperature, moisture, and organic matter, significantly influence their efficacy. Additionally, variability among microbial strains, inconsistent field performance, and potential non-target effects complicate their application. Ueki et al. [84] highlighted the role of anaerobic bacteria in biological soil disinfestation, noting their effectiveness in suppressing pathogens but warning about the temporary microbial imbalances that can occur. Niu et al. [85] underscored the need to explore interspecies interactions within multi-strain formulations to enhance consistency and effectiveness. By addressing these challenges, BCAs can become a cornerstone of sustainable soil health management in modern agriculture.

2.3.3. Biofumigation

Biofumigation is an environmentally friendly agricultural technique that utilizes the natural biocidal properties of certain plants, predominantly from the Brassicaceae family, to manage soilborne pathogens, pests, and weeds while promoting soil health. This practice leverages glucosinolates (GSLs), naturally occurring compounds in Brassica spp. plants such as mustard, radish, and rapeseed, which hydrolyze into bioactive products like isothiocyanates (ITCs) upon tissue breakdown. These ITCs act as natural fumigants, disrupting the cellular metabolism of harmful organisms and reducing their populations in the soil. According to Tagele et al. [86] and Mandal et al. [87], biofumigation not only suppresses pathogens and promotes beneficial soil microbes through the action of ITCs but also serves as a cornerstone of sustainable, reduced-chemical soil health management by enhancing nutrient cycling and overall microbial activity. Biofumigation can be implemented through multiple agronomic strategies, including the incorporation of green manure crops, application of biofumigant seed meals, and rotational use of Brassica species, with effectiveness strongly influenced by management choices and environmental context. Evidence shows that Brassica-derived amendments, such as Brassica carinata (A. Braun) seed meal, can provide effective suppression of soilborne pathogens, supporting their role as viable alternatives to synthetic fumigants [88]. Treatment success is closely linked to timing and preparation, as incorporation of macerated plant biomass at peak growth enhances the release of bioactive compounds, allowing biofumigation practices to be adapted to local climatic conditions and cropping systems [89]. Moreover, efficacy varies widely among Brassica species and formulations, depending on glucosinolate profiles, tissue type, soil characteristics, and resident microbial activity, which collectively regulate the hydrolysis of glucosinolates and subsequent isothiocyanate release [90]. Environmental conditions, particularly soil temperature and moisture, play a vital role in the hydrolysis of GSLs and the release of ITCs. Moreover, Walker et al. [91] emphasized that soil pH and microbial composition can also significantly impact ITC persistence and effectiveness. One of the most significant benefits of biofumigation is its ability to manage diverse soilborne pathogens, including Fusarium graminearum [92] and Pythium aphanidermatum [93], reducing crop losses in various agricultural systems. Additionally, biofumigation contributes to soil health by enriching organic matter, enhancing nutrient cycling, and fostering beneficial microbial activity, as observed by Li et al. [94]. The technique also aligns with global sustainability goals by reducing dependence on synthetic fumigants, which are often associated with environmental degradation and regulatory restrictions. Biofumigation’s integration into crop rotation and cover cropping systems can further enhance its efficacy and environmental benefits, providing farmers with a sustainable pest management option that also improves long-term soil health. However, despite its advantages, biofumigation has limitations that can affect its widespread adoption. The success of biofumigation can be inconsistent, as it is heavily influenced by external variables, such as environmental conditions, soil properties, and the quality of the biofumigant material [95]. Producing the high biomass necessary for effective biofumigation may also be challenging for small-scale or resource-limited farmers. Furthermore, biofumigants may temporarily suppress non-target soil organisms, including beneficial invertebrates like earthworms, as reported by Fouché et al. [96]. Another challenge is the risk of phytotoxicity, where residual ITCs in the soil can negatively affect subsequent crops if their levels remain excessively high. Impacts on soil properties are multifaceted, with biofumigation often improving nutrient availability and microbial diversity while occasionally causing temporary imbalances. For instance, Walker et al. [97] observed that long-term biofumigation practices enriched soil organic matter and altered microbial community dynamics, promoting beneficial populations over time. However, improper timing or excessive application of biofumigants can lead to temporary reductions in soil microbial diversity. Research by Tagele et al. [98] showed that optimized biofumigation strategies could improve crop yields without detriment to soil microbial health, underscoring the need for careful management. Looking to the future, biofumigation holds significant potential as a cornerstone of sustainable agriculture, particularly when integrated with other practices like biological control or precision agriculture. Advances in plant breeding could lead to the development of Brassica spp. varieties with enhanced GSL content tailored for specific pathogens or pests. Additionally, the combination of biofumigation with biopesticides or soil amendments may amplify its effects while addressing limitations like variability in efficacy. Ghosh et al. [99] suggested that such combinations could yield synergistic benefits, further enhancing crop protection and productivity. Furthermore, continued research into soil microbial interactions under biofumigation conditions could refine practices, ensuring their effectiveness while preserving soil ecological balance.

2.3.4. Anaerobic Soil Disinfestation

Anaerobic Soil Disinfestation (ASD) is an innovative and sustainable soil management technique that has garnered significant attention as a reduced-chemical alternative to conventional fumigation methods. ASD is particularly effective for controlling soilborne pathogens, pests, and weeds, relying on the creation of temporary anaerobic conditions in the soil to suppress harmful microorganisms and foster a healthier soil environment [100,101]. The process involves incorporating organic amendments such as crop residues, animal manure, or industrial by-products into the soil to serve as carbon sources, followed by saturating the soil with water to create waterlogged conditions, and finally covering it with an airtight plastic film to maintain anaerobic conditions. These conditions promote the activity of anaerobic microbes, which decompose organic material to produce volatile fatty acids, alcohols, and gases toxic to many pathogens and pests [84,102]. The success of ASD depends on several factors, including soil temperature, the type and quality of organic amendments, soil moisture, and the duration of treatment. Studies have shown that higher temperatures accelerate microbial activity and enhance the production of suppressive compounds, with temperatures above 25°C being particularly effective [102,103]. The choice of organic materials is also crucial, as it determines the carbon-to-nitrogen ratio and decomposition rate, directly influencing the production of pathogen-suppressive compounds [104,105]. Adequate soil saturation is essential for maintaining anaerobic conditions, while the duration of treatment typically ranges from three to six weeks to ensure optimal pathogen suppression. While several researchers have explored these variables, there is consensus that site-specific adaptations may be necessary to maximize efficacy in diverse environments [19,106]. The benefits of ASD are manifold and have been well-documented in the literature. One of its primary advantages is its ability to suppress a wide range of soilborne pathogens and pests, including Fusarium oxysporum, and reduce the viability of root-knot nematodes [100,105]. This is attributed to the production of pathogen-suppressive compounds under anaerobic conditions. Furthermore, ASD is highly effective in managing weed populations by inhibiting seed germination, thereby reducing competition for crops [107,108]. Another key benefit lies in its contribution to soil fertility, as the decomposition of organic amendments enriches the soil with nutrients such as nitrogen and phosphorus [109]. Studies have also highlighted the method’s environmental sustainability, as it avoids the use of chemical inputs that pose risks to human health and the environment [110]. Moreover, ASD applications span diverse systems, including open fields, greenhouses, and high-tunnel organic production, making it suitable for crops such as strawberries, lettuce, and solanaceous vegetables. Evidence from contrasting agro-climatic contexts indicates that ASD can substantially reduce weed pressure and soilborne diseases while remaining flexible across temperate and tropical environments, supporting its potential as a scalable and system-independent management strategy [103,111]. Post-ASD, beneficial microbes such as Trichoderma spp. and Bacillus spp. often dominate the microbial community, contributing to improved soil health and resilience against future pathogen outbreaks [112,113]. Despite its effectiveness, ASD presents important limitations, as some pathogens, including Fusarium spp., can tolerate anaerobic conditions or recolonize soils following treatment, highlighting the need for complementary strategies to achieve durable disease control [104,105]. Another limitation is the labor and material costs associated with the method, as it requires organic amendments and plastic films, which may be prohibitive for resource-constrained farmers [100]. Additionally, anaerobic decomposition can produce greenhouse gases such as methane (CH₄) and nitrous oxide (N₂O), raising concerns about its environmental sustainability [110]. The results of ASD can also vary depending on soil type, climate, and the specific pest or pathogen targeted, requiring precise tailoring of the method to specific conditions [111,114]. ASD significantly impacts soil properties, leading to both immediate and long-term changes. Anaerobic conditions foster the growth of specific microbial populations, which can shift the soil microbial community towards dominance by beneficial species [84,113]. He et al. [115] reported that ASD substantially improved microbial diversity and altered the abundance of beneficial bacteria and fungi in continuously cropped soils, mitigating replant disease symptoms. Moreover, the decomposition of organic matter increases nutrient availability, though excessive mineralization may lead to nutrient leaching if not properly managed [112]. Enhanced soil structure and aggregation have also been observed, improving water retention and aeration [101,111]. Collectively, available evidence indicates that ASD contributes not only to the suppression of soilborne pests and pathogens but also to improvements in soil quality and biological functioning. To enhance adoption and long-term efficacy, future research should prioritize strategies that address current environmental and economic constraints, including the development of biodegradable films to reduce plastic waste and the evaluation of diverse organic amendments—such as industrial by-products—to lower input costs while supporting circular economy approaches [109,112]. Combining ASD with other sustainable practices, such as solarization, may offer synergistic benefits in pest suppression while mitigating greenhouse gas emissions [108]. Long-term studies on the cumulative effects of ASD on soil health, carbon sequestration, and agricultural productivity are also needed to provide a comprehensive understanding of its potential benefits and limitations [102,103]. Furthermore, Song et al. [116] revealed that in situ crop residue retention, an ASD approach, enhanced multiple ecosystem functions such as nutrient cycling efficiency, carbon sequestration, and microbial stability, underlining the multifunctionality of biological disinfestation strategies in agroecosystems. Ultimately, ASD stands out as a promising approach in integrated pest management due to its ability to suppress pathogens while improving soil properties. It provides a sustainable, eco-friendly solution, particularly for organic and sustainable farming systems, making it a valuable tool in addressing the challenges of modern agriculture.

A comparative overview of chemical, physical, and biological soil disinfestation strategies is provided in

Table 1. Overview of chemical, physical, and biological soil disinfestation methods, highlighting efficacy, sustainability, and impacts on soil health.

Category	Method	Target Organisms	Main Advantages	Key Limitations	Impact on Soil Health	Sustainability Level
Chemical	Methyl bromide (MB)	Fungi, nematodes, weeds	Broad-spectrum, rapid and reliable control	Ozone depletion, toxicity, regulatory ban	Severe microbial depletion; slow recovery	Very low
	Dimethyl disulfide (DMDS)	Fungi, nematodes, weeds	Effective MB alternative; high efficacy	Human toxicity risk; strict handling	Temporary microbial disruption	Low
	Metam sodium/Dazomet	Fungi, nematodes, weeds	Cost-effective; widely used	Phytotoxicity risk; nutrient losses	Reduced microbial diversity; altered N cycling	Low–moderate
Physical	Steam disinfestation	Fungi, nematodes, weeds	Residue-free; effective and rapid	High energy demand; recontamination risk	Short-term microbial reduction; recoverable	Moderate
	Microwave heating	Fungi, bacteria, weeds	Precise heating; chemical-free	High energy costs; limited scalability	Temporary disturbance of microbial communities	Moderate
	Soil solarization	Fungi, nematodes, weeds	Low chemical input; simple technology	Climate-dependent; plastic use	Enhances nutrient availability; temporary microbial shifts	High (climate-dependent)
Biological	Suppressive composts/compost tea	Fungi, nematodes	Improves soil fertility and microbiome	Variable efficacy; preparation-dependent	Enhances microbial diversity and soil structure	High
	BCAs (e.g., Trichoderma, Bacillus)	Fungi, bacteria	Targeted control; plant growth promotion	Inconsistent field performance	Strengthens soil resilience and suppressiveness	High
	Biofumigation	Fungi, nematodes, weeds	Uses natural biocidal compounds	Biomass and timing constraints	Improves organic matter; transient imbalance	High
	Anaerobic soil disinfestation (ASD)	Fungi, nematodes, weeds	Broad suppression; improves fertility	Plastic use; GHG emissions	Promotes beneficial anaerobic microbiota	High–moderate

, summarizing their target organisms, agronomic benefits, limitations, and impacts on soil health and sustainability (Figure 3).

3. Integrated Pest Management for Soilborne Disease Control

Integrated Pest Management (IPM) for soilborne diseases has gained increasing attention as a sustainable and effective approach to agricultural productivity. Recent advances, as outlined by Devi et al. [117], emphasize that the integration of biological, physical, and cultural approaches within IPM frameworks offers a sustainable and multidisciplinary alternative to conventional chemical control. Bio-solarization, a combination of solarization and biological amendments, emerges as a promising technique. Elshahawy et al. [118] demonstrated the effectiveness of incorporating Trichoderma asperellum into solarized soils for controlling black root rot in strawberries, improving both pathogen suppression and crop yield. Correspondingly, Castello et al. [119] reported that solarization-based techniques, particularly when paired with organic amendments, significantly reduced Verticillium dahliae inoculum in tomatoes cultivated in greenhouses. These studies underscore bio-solarization’s potential to enhance soilborne pathogen control while restoring soil microbial diversity. Integration of anaerobic disinfestation with BCAs further demonstrates the potential of multi-pronged IPM approaches. Khadka and Miller [120] explored the combined use of ASD with Trichoderma spp., observing significant reductions in Rhizoctonia root rot. Shrestha et al. [121] similarly highlighted the potential of combining anaerobic techniques with microbial inoculants, emphasizing their complementary effects in pathogen suppression. Moreover, Studies by Ali et al. [122] and Huang et al. [123] indicate that reductive soil disinfestation (RSD), especially when combined with biochar and antagonistic microbial inoculants such as Trichoderma spp., effectively mitigates diseases like cucumber Fusarium wilt and Rhizoctonia damping-off. This integrated approach leverages the dual action of microbial antagonism and anaerobic conditions to target pathogens while fostering beneficial microbial communities. Conversely, some other results from Ali et al. [122] caution that improper implementation may increase greenhouse gas emissions, highlighting the need for environmentally conscious adaptations of this method. In this context, Shi et al. [124] demonstrated that combining Trichoderma spp. with low doses of dimethyl disulfide (DMDS) effectively controls Fusarium wilt in solanaceous crops, showing that a balanced bio–chemical approach within IPM can enhance disease suppression while preserving soil microbiota. Probiotic bacteria application combined with biofumigation using cover crops has also been identified as a sustainable strategy. Rahman et al. [22] showcased the effectiveness of mustard cover crops for releasing biocidal compounds that suppress pathogens while enhancing soil fertility. When used with probiotic bacteria, such as Bacillus strains, this approach offers the dual benefits of disease control and crop growth promotion. However, the success of biofumigation depends on the appropriate timing of crop incorporation and management of gas emissions. In parallel, Magallanes-Tapia et al. [125] showed that combining pre-plant biofumigation with post-plant Trichoderma and Bacillus inoculation effectively suppresses nematodes and enhances soil health within IPM systems. Steam disinfestation, complemented by biological reinforcements, provides another promising IPM method. Kim et al. [126] found that steam application, followed by Trichoderma inoculation, effectively eradicates soilborne pathogens while reintroducing beneficial microorganisms to the soil. Wu et al. [127] similarly reported improved soil health and cucumber production when beneficial microbes were applied post-fumigation. Despite its efficacy, steam sterilization can be energy-intensive, posing challenges for large-scale adoption. Liu et al. [128] expanded the scope of integrated strategies by testing ASD amended with yeast residues for weed control and yield enhancement in strawberries. In the context of greenhouse crop production, Gullino et al. [3] emphasized the importance of combining physical, biological, and cultural practices. The integration of fumigation alternatives, such as biofumigation, and biological agents like Trichoderma, offers scalable solutions for managing soilborne pathogens while reducing chemical dependency. These strategies are complemented by economic analyses like Xu et al. [29], which highlight the cost-effectiveness of adopting steam as a pre-plant–soil disinfestation method for strawberry cultivation in California, particularly when coupled with biocontrol agents to restore soil health. Collectively, these studies underscore the versatility of IPM in addressing soilborne diseases through an array of complementary techniques. Bio-solarization, RSD, biofumigation, steam disinfestation, and integrated biological controls highlight the efficacy of combining methods to enhance pathogen suppression, promote soil health, and improve crop productivity. While these approaches demonstrate significant promise, challenges such as energy costs, environmental trade-offs, and implementation complexity necessitate further refinement to optimize their application in diverse agricultural systems. Accordingly,

Table 2. Comparative sustainability metrics of soil disinfestation and soil health management techniques across agronomic systems.

Technique	Energy Use (MJ ha−1)	GHG Emissions (kg CO2-eq ha−1)	Cost (USD ha−1)	Plastic Waste (kg ha−1)	Notes on Data Robustness	Main Drivers of Variability	Key References
Chemical fumigation (e.g., MB alternatives, DMDS, metam sodium)	1000–3000	400–1200	2000–6000	200–500	Well-documented; includes fuel, product synthesis, and tarp use; strong baseline comparator	Active ingredient type and dose, tarp requirement and thickness, regulatory constraints, fuel use for application, regional labor and product costs	[14,17,18,25]
Soil solarization	100–400	30–120	300–1200	200–500	Energy low; plastic dominates environmental footprint; climate-dependent	Climate and solar radiation, duration of treatment, soil moisture, plastic film type and thickness, scale of application	[49,53,129]
Biosolarization (solarization + organic amendments)	200–600	80–250	600–1800	200–500	Slightly higher GHG due to biomass decomposition; better pathogen control	Organic amendment type and rate, decomposition dynamics, sealing efficiency, climate conditions, additional field operations	[49,109,119,130]
Anaerobic soil disinfestation (ASD)	300–900	150–600	800–3000	200–500	GHG strongly depends on amendment type and rate; good field evidence	Carbon source quality and amount, soil temperature, duration of anaerobic phase, post-treatment emissions (N2O, CH4), plastic sealing requirements	[19,101,109,110,131]
Soil steam disinfestation	8000–20,000	600–2000	3000–10,000	0–50	Energy-intensive; GHG depends on fuel/electricity source; high cost	Treatment depth, soil texture and moisture, fuel or electricity source, equipment efficiency, scale of operation	[25,27,28,29,132]
Microwave soil heating	5000–15,000	400–1500	2500–8000	0	Data mostly engineering-based; few full field LCAs	Power intensity and exposure time, soil moisture, treatment depth, electricity source, experimental vs. field-scale deployment	[34,36,43,44,133,134]
Biofumigation (Brassicaceae residues, seed meals)	200–800	80–300	300–1500	0–300	Energy and GHG often estimated from biomass and tillage; variable effectiveness	Biomass quantity and glucosinolate content, incorporation method, soil conditions, optional plastic sealing, variability in field operations	[86,88,95,109,130,135]
Suppressive composts/compost teas	50–300	20–150	200–1200	0	Metrics mostly input-based; no direct LCA; low-intensity practice	Compost source and maturity, application rate, preparation method, transport distance, on-farm vs. commercial inputs	[60,62,65,136]
BCAs	<50	<20	100–500	0	Field-scale energy and GHG rarely quantified; generally minimal inputs	Strain formulation and dose, application frequency, carrier materials, local soil–microbiome interactions, scale of production	[70,72,82,115]

Where n was not explicitly reported in the compiled extraction, we retained the study as highly relevant but flagged sample size as ‘not reported’; We prioritized field/greenhouse trials, long-term studies, and meta-analyses, and selected 3–4 anchor studies per method/paragraph.

provides a comparative overview of quantitative sustainability indicators across chemical, physical, and biological soil disinfestation strategies, highlighting trade-offs and sources of variability reported in the literature. Metrics are reported on an area basis (per hectare per treatment cycle) and include energy use (MJ ha⁻¹), greenhouse gas emissions (kg CO₂-eq ha⁻¹), cost (USD ha⁻¹), and plastic waste (kg ha⁻¹). Values are expressed as literature-derived ranges reflecting differences among studies in system boundaries, experimental scales (laboratory, pilot, or field), treatment depth and duration, climate, input type and rate, and energy source. Where values were not directly reported, ranges were derived from explicitly documented operational inputs using standard conversion factors and are indicated as indicative estimates. For suppressive composts and biological control agents, quantitative data on energy use and greenhouse gas emissions are limited in the literature and are therefore reported as low-input or not quantified categories based on documented management intensity. The final column summarizes the main drivers of variability for each technique to aid interpretation of the wide numerical ranges. Overall, values should be interpreted as indicative of relative magnitude and context-specific performance rather than fixed benchmarks (Figure 4).

4. Novel Approaches in Soilborne Disease Management

The convergence of hyperspectral imaging, machine learning, thermal imaging, and biocontrol methods represents a groundbreaking approach to soilborne disease management. Recent advancements in hyperspectral imaging (HSI), machine learning (ML), and precision agriculture are transforming detection and monitoring, supporting informed decision-making within sustainable disease management frameworks. High-resolution hyperspectral imaging has emerged as a pivotal technology, allowing for the identification of stress signals in crops long before visual symptoms appear. Results reported across diverse cropping systems indicate its effectiveness in capturing spectral signatures associated with soilborne disease development, supporting its use for timely and non-destructive monitoring of plant health [137,138]. In this context, Arroyo et al. [139] integrated biofumigation practices with phyto-spectral monitoring, demonstrating how precision remote sensing can inform the spatial and temporal planning of biofumigation practices, paving the way for site-specific, sustainable disease control. Coupling HSI data with machine learning algorithms, these studies achieved precise disease prediction, underscoring the potential for timely interventions and improved risk assessment in crop protection strategies. The integration of thermal imaging with hyperspectral sensing further enhances early disease detection by providing complementary information on plant physiological status and stress responses. Combined use of active and passive infrared data with spectral analysis has been shown to improve the identification of early-stage soilborne infections through robust, non-invasive monitoring approaches [9,10,11]. More recently, the fusion of three-dimensional, multispectral, and thermal imaging with machine-learning algorithms has enabled high-accuracy diagnosis of soilborne pathogen infections under controlled and experimental conditions, illustrating the potential of AI-driven frameworks to advance precision disease monitoring [140]. Machine learning has played a crucial role in translating complex hyperspectral data into actionable insights for decision-support and early warning within disease management systems. Applications based on canopy-level hyperspectral data demonstrate that pattern-recognition algorithms can support precision monitoring and inform biologically based disease control strategies, particularly in intensive horticultural systems such as baby leaf vegetables [141,142]. These efforts align with innovations like the AI-assisted push-broom hyperspectral system described by Neri et al. [143], which enables real-time disease diagnostics in precision agriculture contexts. In parallel, coupling biological control agents with advanced sensing technologies has emerged as a promising pathway for sustainable crop protection, as hyperspectral vegetation indices can be used to monitor biocontrol activity and associated plant responses [144]. Similarly, Reis Pereira et al. [145] examined disease diagnosis methods using hyperspectral sensing and found that non-parametric approaches such as Gaussian Process Classification could significantly improve detection accuracy, further validating the synergy of advanced diagnostics with biological interventions. Precision agriculture systems that incorporate these technologies are advancing sustainable crop management by optimizing resource use and improving disease suppression strategies. Proximal sensing technologies have been shown to enhance the efficiency of crop input application while reducing environmental impacts, reinforcing their value within integrated disease management frameworks [146]. Nevertheless, the large-scale adoption of these innovations remains constrained by high investment costs, technical complexity, and operational challenges, particularly in greenhouse and open-field systems [147]. Additionally, the lack of standardized protocols for integrating hyperspectral imaging and machine-learning tools across diverse cropping systems limits reproducibility and transferability, underscoring the need for harmonized methodologies to ensure consistent and reliable performance [148]. Ultimately, the convergence of hyperspectral imaging, machine learning, thermal imaging, and biocontrol methods represents a groundbreaking approach to soilborne disease management. By facilitating early detection, precise diagnosis, and sustainable intervention, these technologies offer significant advantages in supporting treatment evaluation, optimization, and adaptive decision-making, compared with traditional methods. However, addressing scalability, cost, and integration challenges remains vital to realizing the full potential of these advancements in precision agriculture.

5. Effect of Soil Disinfestation Treatments on Crop Yields

Soil disinfestation treatments significantly affect the productivity of fresh cut vegetables and other crops. Soil solarization has shown promise in improving yields by creating favorable conditions for plant growth. Indeed, as shown in the study by Öz [55], solarization resulted in a significant improvement in mineral uptake and, consequently, increased yield of lettuce (Lactuca sativa L.). This method promotes the release of nutrients like nitrogen and phosphorus, which are essential for optimal plant growth and development. Additionally, protected cultivation systems have also benefited, as shown by Sabatino et al. [149], where solarization combined with calcium cyanamide enhanced strawberry yields and plant vigor due to improved nitrogen management and reduced nutrient loss through volatilization or leaching. Recent findings by López-Moreno et al. [150] further confirmed that both biosolarization and chemical disinfection significantly enhanced asparagus yield and spear quality, demonstrating the practical benefits of integrated disinfestation strategies in high-value vegetable crops. As for ASD, it has gained ground due to its dual effect of pathogen suppression and enhancement of beneficial microbial populations. For example, Guo et al. [151] demonstrated that ASD effectively controlled nematodes and weeds in tomato production, achieving yields comparable to chemical fumigation. Furthermore, Rahman [22] found that ASD combined with mustard biofumigation increased strawberry yield in organic systems. Indeed, biofumigation also shows promise in increasing yields while reducing chemical inputs. On the other hand, biofumigation techniques using Brassica spp. cover crops, as illustrated by Waisen et al. [152] in cucurbit systems, increase yield while simultaneously improving soil health. Therefore, when comparing sustainable pest control methods such as solarization, ASD, and biofumigation with traditional chemical fumigation, a clear trend emerges: sustainable practices maintain or improve crop productivity while preserving soil health. Indeed, chemical fumigation, although effective against pathogens, often disrupts microbial communities, as reported by Cheng et al. [153]. This study also reports that post-fumigation microbial inoculations restore yield levels but at the same time require intervention to reestablish microbial balance. In contrast, sustainable approaches such as ASD and biofumigation not only control soil-borne diseases but also improve long-term soil fertility. Meng et al. [154] found that biofumigation reduced pathogen populations while maintaining soil microbial diversity, thus being more effective than chemical treatments. In lettuce production, Zou et al. [155] found that biosolarization with organic amendments such as green tea and fish waste improved yields compared to untreated soils, illustrating the potential for integrating sustainability into crop management. Overall, sustainable methods strike a balance between pathogen control and ecological stability, unlike chemical alternatives that often require remediation to offset negative soil impacts. Case studies from different regions underscore the versatility of soil disinfestation techniques across diverse crops and climates. In Egypt, Abd-El-Kareem et al. [156] combined bio-solarization with Trichoderma asperellum to suppress black root rot in strawberries, achieving increased yields and disease control. In Ethiopia, Gebreegziher et al. [48] showed that a combination of solarization and manure significantly increased tomato yields while suppressing Orobanche infestation. Comparatively, in Hawaii, Waisen et al. [152] employed biofumigation with brassicaceous crops to improve cucumber yields while restoring soil health, illustrating the applicability of these techniques in tropical climates. In arid regions, Öz [55] showed that novel polyethylene mulch for solarization in lettuce production increased yields, emphasizing innovations in solarization methods. Similarly, in semiarid conditions, Sánchez-Navarro et al. [157] documented the efficiency of solarization in improving yields of intensive horticultural crops while maintaining soil quality. These case studies reveal the adaptability of soil disinfestation methods in managing specific regional challenges. For instance, ASD and biofumigation are effective in high-pathogen-pressure regions, while solarization proves beneficial in warmer climates. The integration of biological controls, such as T. asperellum or organic amendments, further amplifies the success of these methods across crops and geographies. Sustainable disinfestation techniques not only enhance yields but also contribute to long-term soil health, making them preferable alternatives to conventional chemical methods. By continuing to explore their combined effects, researchers can develop comprehensive strategies tailored to diverse agricultural systems.

A comparative synthesis of yield-related outcomes and disease control efficacy is provided in

Table 3. Evidence table summarizing agronomic efficacy of sustainable soil disinfestation and biological soil management strategies.

Method Paragraph	Key Study	Crop/System (geo)	Disinfestation/Amendment Strategy	Main Agronomic Outcome	Effect Size (vs. Control/Comparator)	Sample Size/Design
Steam disinfestation	[21]	Controlled greenhouse soil (USA)	Steam disinfestation	Suppression of Fusarium solani	Reduced to below detection immediately after steaming	Replicated microcosms (n not reported)
	[23]	Soil (S. Korea)	High-temperature steam (optimized)	Nematode control	>95% mortality at optimized conditions	Box–Behnken; 15 runs
	[31]	Leafy greens and carrot (USA–CA)	Band steam disinfestation	Weed and disease control	80–99% weed control in steamed bands	Field trials; replicated plots (n not reported)
Microwave disinfestation	[35]	Portulaca oleracea seeds (Italy)	Microwave irradiation	Seed germination inhibition	Up to 100% inhibition (dose-dependent)	Lab bioassays; replicated (n not reported)
	[36]	Strawberry mother plants (Australia)	Microwave soil heating	Crop performance	+20–30% runners; improved progeny performance	Field; replicated plots (n not reported)
	[38]	Soil (China)	Short-duration microwave heating	Lethal soil heating	Soil >60 °C within minutes	Lab + pilot experiments (n not reported)
Solarization	[45]	Field soil (India)	Plastic-film solarization	Soil heating and moisture conservation	Soil temperature +8–15 °C	Field; replicated plots (n not reported)
	[49]	Soil (USA–CA)	Solarization/biosolarization	Nematode suppression	>70% reduction in parasitic nematodes	Field; replicated plots (n not reported)
Solarization + inputs	[149]	Strawberry protected system (Italy)	Solarization + CaCN2	Yield and quality enhancement	Early yield +105%; total yield +53%	Greenhouse; replicated factorial
	[55]	Lettuce (Turkey)	Solarization + biochar	Yield improvement	~+38% with biochar-enhanced solarization	Greenhouse; replicated (n not reported)
Biofumigation	[90]	Eggplant (China)	Brassica tissue biofumigation	Disease (Verticillium dahliae) and yield	Disease ↓; yield ↑ (season-dependent)	Field experiment (n not reported)
	[92]	Wheat–maize rotation (UK)	Brassica green manures	Pathogen (Fusarium graminearum) suppression	Significant inoculum reduction	Field trials (n not reported)
	[88]	Soil (Italy)	Brassica carinata seed meal	Disease suppression	Disease pressure significantly reduced	Pot + field (n not reported)
BSD/compost tea	[58]	Seedlings (Egypt)	Compost tea	Damping-off (Rhizoctonia solani) control	≈50–70% damping-off reduction	Greenhouse trials (n not reported)
	[94]	Strawberry (China)	Compost tea (ISR induction)	Disease severity (Verticillium dahlia)	Disease severity significantly reduced (ISR-type response)	Greenhouse pot exp. (n not reported)
	[62]	Onion (Egypt)	Compost + compost tea	Yield and quality	Yield and bulb quality significantly improved	Field; replicated plots (n not reported)
Microbial BCAs	[158]	Cucumber (Iraq)	AMF (Glomus spp.)	Damping-off (R. solani) suppression	>50% disease reduction	Controlled study (n not reported)
	[159]	Soybean (USA–IN)	Coniothyrium minitans + Bacillus	White mold (Sclerotinia) control	Disease incidence reduced	Field study (n not reported)
	[72]	Multiple crops (global)	Application of Trichoderma spp. as microbial biocontrol agents	Suppression of soil-borne fungal pathogens and stimulation of plant growth	Consistent disease suppression and growth promotion reported across crops and systems	Narrative review of experimental, greenhouse, and field studies
ASD	[114]	Horticultural crops (global)	Anaerobic soil disinfestation	Yield response	Mean yield ~+30% vs. untreated	Meta-analysis; 123 studies
	[104]	Strawberry (Spain)	ASD (Industrial organic wastes)	Weed and disease control (Fusarium wilt)	Disease reduction and crop protection	Greenhouse/field trials
	[111]	Baby leaf lettuce (USA)	ASD	Weed and disease control	Yield maintained or increased	High-tunnel field trials (n not reported)
Integrated approaches	[118]	Strawberry (Egypt)	Solarization + Trichoderma	Black root rot control	Disease severity reduced vs. solarization alone	Field + greenhouse (n not reported)
	[122]	Cucumber (China)	RSD + biochar + BCAs	Fusarium wilt control	Fusarium wilt suppression; yield ↑	Significant disease reduction; yield increase

Upward arrows (↑) indicate an increase or positive effect relative to the untreated control or baseline condition, whereas downward arrows (↓) denote a decrease or reduction.

, while

Table 4. Evidence table summarizing environmental and soil-biological impacts of sustainable soil disinfestation strategies.

Method Paragraph	Key Study	Geographical Area	Disinfestation/Amendment Strategy	Environmental/Soil Endpoint(s)	Effect Size/Magnitude	Sample Size/Design
Steam	[33]	Italy	Steam disinfestation	Soil chemistry + microbiology	Temporary ↑ NH4+ and ↑ microbial biomass C after steaming	Greenhouse soil; replicated (n not reported)
	[27]	China	Steam disinfestation	Energy demand	Fine soils increased energy use ~20–30%	Lab + modeling
	[32]	China	Engineered steam systems	Engineering efficiency	Heat-transfer efficiency +18–25%	Computational + prototype
Microwave	[43]	Australia	Microwave soil heating	Bacterial diversity resilience	Strong initial reduction followed by community reassembly	Field soil cores; replicated (n not reported)
	[42]	NE China	Microwave disinfestation	Physicochemical + bacteria	Temporary bacterial shifts; partial recovery	Field samples; replicated (n not reported)
	[134]	China	Solar-assisted microwave	Sustainability/energy	Solar-assisted system reduced grid energy demand	Pilot-scale testing
Solarization/biosolarization	[53]	Italy	Solarization (biodegradable films)	Mulch sustainability	Biodegradable films: comparable efficacy, improved sustainability	Field experiment
	[49]	USA–CA	Biosolarization	Bacterial community	Diversity shifted; recovery observed	Field experiment
	[50]	Italy	Innovative solarization	Fungal biodiversity	Beneficial biodiversity partially preserved	Field trials
Biofumigation	[97]	Australia	Long-term biofumigation	Long-term soil health	10 years altered soil characteristics and microbiota	Long-term field study
	[94]	China	Biofumigation vs. fumigation	Biofumigation vs. chemical fumigation	Greater microbial diversity under biofumigation	Field + lab analyses
	[96]	South Africa	Biofumigants	Ecotoxicology	No severe earthworm ecotoxic effects at field rates	Soil ecotox assays
ASD/RSD	[110]	China	ASD (OM-dependent)	N2O + N leaching	56–91% of seasonal N2O emitted during ASD	Field trials
	[116]	China	Crop-residue BSD	Multifunctionality	BSD with residue retention improved multifunctionality over 4 years	Long-term field study
	[115]	China (Guizhou)	RSD	Karst soils	Improved microbial + physicochemical indicators post-RSD	Field trials
Compost/compost tea	[63]	Switzerland/Europe	Compost diversity	Suppressive taxa discovery	37 composts linked to suppressiveness signatures	Large compost survey (n = 37)
Post-fumigation “bio-activation”	[153]	China	Microbial re-inoculation	Microbiome restoration	Beneficial microbes restored suppressiveness; pathogen abundance reduced	Greenhouse + field

Upward arrows (↑) indicate an increase or positive effect relative to the untreated control or baseline condition.

summarizes the main environmental and soil biological effects associated with the same disinfestation strategies.

6. Effect of Soil Disinfestation Treatments on Crop Quality

The nutritional quality of fresh cut vegetables is the main determinant of their marketability, especially for high-value products; this is especially true for fresh cut products. Since soil disinfestation methods can influence soil health, nutrient availability, and plant physiological responses, they can in turn influence the nutritional profile of plants. Among the treatments described, soil solarization has been the most studied in relation to its impact on crop quality. Some studies, in fact, indicate that this treatment can increase the levels of antioxidants, vitamins, and other bioactive compounds, which are essential for consumer health. For example, Mauromicale et al. [160] observed that tomatoes grown in solarized soil had higher levels of vitamins and antioxidants, attributing these improvements to the reduction in pathogen stress and improved soil health. Similarly, Castronuovo et al. [161] reported that organic pumpkin crops grown in solarized soil showed significantly increased antioxidant activity, including elevated levels of carotenoids and phenolic compounds. Furthermore, Sabatino et al. [149] found that strawberries grown in solarized soil, especially when combined with CaCN2, showed improved postharvest quality, including firmer texture, better color retention, and increased nutritional value (ascorbic acid, anthocyanins, polyphenols). These improvements were linked to reduced pathogen pressure, resulting in healthier plant tissues and better fruit quality. Indeed, Rippa et al. [50] reported that innovative solarization systems not only suppressed soilborne pathogens but also enhanced soil biodiversity and improved the nutritional quality of produce, providing a tangible link between physical disinfestation and product quality. Likewise, Solaiman et al. [162] demonstrated that biologically based treatments can stimulate the synthesis of defense-related phytohormones in cucumber, enhancing plant resistance and indirectly contributing to improved quality attributes and stress tolerance. Therefore, while research on solarization and its direct impact on the quality and sensory attributes of vegetables has already begun, for other sustainable methods such as biofumigation and biological control there are still no studies going in this direction. This limitation represents a critical gap, as different approaches may interact differently with soil microbiota and plant physiology, potentially leading to different post-harvest outcomes. Future studies should prioritize understanding how diverse sustainable practices influence vegetable quality, including their nutritional, sensory, and storage attributes. Additionally, exploring consumer acceptance of produce grown under these methods, particularly in relation to organic labeling and certification, could inform strategies to promote sustainable agriculture. By addressing these gaps, the agricultural sector can better leverage sustainable soil disinfestation practices to meet market demands and environmental goals.

7. Conclusions and Future Perspectives

Several authoritative reviews have addressed soil disinfestation and soil-borne disease management, focusing primarily on pathogen suppression efficacy, regulatory constraints, or single methodological categories. Previous reviews cited in this manuscript have extensively examined soil disinfestation strategies and soil-borne disease management, either through comprehensive overviews or through method- and risk-focused analyses. Nevertheless, yield effects are often treated qualitatively, quality attributes receive limited attention, and emerging monitoring technologies are generally discussed outside an integrated soil management framework. In contrast, this review offers a comprehensive and integrative synthesis that explicitly links soil management methods with both yield and quality outcomes, including nutritional, functional, and postharvest attributes, across a wide range of vegetable cropping systems. Furthermore, this manuscript uniquely incorporates novel approaches for soil-borne disease detection, such as hyperspectral imaging, thermal sensing, and AI-based diagnostics, and discusses their role in assessing treatment efficacy and supporting adaptive decision-making. By jointly addressing soil management strategies, agronomic performance, product quality, and emerging precision agriculture tools within a single framework, this review goes beyond descriptive methodological comparisons and contributes to a more holistic perspective on sustainable soil health management. Despite these advances, important knowledge gaps remain. The long-term effects of sustainable soil disinfestation methods on soil microbiome stability, nutrient cycling, and functional resilience are still insufficiently understood, particularly for ASD and solarization, while evidence on their effectiveness against emerging soilborne pathogens and on consistent yield and quality responses across vegetable species and agro-climatic conditions remains fragmented. To address these limitations, future research should prioritize the following: (i) long-term assessment of soil biological and functional resilience; (ii) region-specific optimization of physical and biological techniques; (iii) integration of BCAs and organic amendments to improve consistency and durability of disease suppression; and (iv) coupling soil disinfestation with digital and precision tools, including proximal sensing and AI-based diagnostics. Based on these priorities, testable hypotheses for the next five years include the ability of repeated ASD or biosolarization cycles to establish stable disease-suppressive microbiomes, the occurrence of synergistic effects only under optimized carbon inputs and soil thermal–hydrological conditions, and the potential of microbial reinoculation and sensing-guided interventions to stabilize crop yield and quality. Addressing these directions will support the transition from input-intensive practices toward ecologically resilient, data-driven soil health management systems.